From 0f8fea3e4c6e73d624de8b9cde3e0a8375f382aa Mon Sep 17 00:00:00 2001 From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com> Date: Wed, 5 Jun 2024 18:00:06 -0700 Subject: [PATCH] experiments --- notebooks/mixed_set_summarization.ipynb | 2328 +++++++++-------------- 1 file changed, 874 insertions(+), 1454 deletions(-) diff --git a/notebooks/mixed_set_summarization.ipynb b/notebooks/mixed_set_summarization.ipynb index 1c6950ca7..7489f4638 100644 --- a/notebooks/mixed_set_summarization.ipynb +++ b/notebooks/mixed_set_summarization.ipynb @@ -2090,6 +2090,8 @@ "outputs": [], "source": [ "\n", +INSERT KEY + "\n", "client = OpenAI(\n", " # This is the default and can be omitted\n", " api_key=os.environ.get(\"OPENAI_API_KEY\"),\n", @@ -2985,7 +2987,7 @@ }, { "cell_type": "code", - "execution_count": 188, + "execution_count": 194, "id": "2d327ca8-8204-43cd-8b01-476ef4a0f14b", "metadata": {}, "outputs": [], @@ -3011,18 +3013,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -3054,7 +3056,7 @@ }, { "cell_type": "code", - "execution_count": 189, + "execution_count": 195, "id": "423d5291-2789-4abd-964f-d4bc5cf79565", "metadata": {}, "outputs": [ @@ -3083,18 +3085,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Engineered:Bioreactor\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -3145,7 +3147,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 0:\n", - "ChatCompletion(id='chatcmpl-9WpBxrQXKaMmlg7GOgtEqkEtnldxM', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='Sure. Below is the detailed relationships between observed features and environmental properties of the Engineered:Bioreactor ecosystem, represented in the desired JSON format:\\n\\n```json\\n{\\n \"Engineered:Bioreactor\": {\\n \"1\": {\\n \"feature_id\": \"GO:0018551 * IPR005126\",\\n \"feature_label\": \"dissimilatory sulfite reductase activity * NapC/NirT cytochrome c, N-terminal\",\\n \"bio_property\": \"sulfate reduction * anaerobic respiration\",\\n \"env_property\": \"anaerobic * high sulfate\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Dissimilatory sulfite reductase is essential for the reduction of sulfates in anaerobic conditions where high sulfate concentration is prevalent.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR004763 * IPR016300\",\\n \"feature_label\": \"Cation efflux system CzcA/CusA/SilA/NccA/HelA/CnrA * Arsenical pump ATPase, ArsA/GET3\",\\n \"bio_property\": \"heavy metal resistance * detoxification\",\\n \"env_property\": \"high metal concentration * toxicity\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Both features are involved in the efflux and resistance mechanisms against toxic heavy metals, indicating an environment with high metal concentrations.\"\\n },\\n \"3\": {\\n \"feature_id\": \"GO:0031460\",\\n \"feature_label\": \"glycine betaine transport\",\\n \"bio_property\": \"osmoprotection * stress response\",\\n \"env_property\": \"marine * high salinity\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Glycine betaine is a known osmoprotectant in high osmolarity environments such as those with high salinity.\"\\n },\\n \"4\": {\\n \"feature_id\": \"GO:0008743 * IPR014234\",\\n \"feature_label\": \"L-threonine 3-dehydrogenase activity * N-acetylmuramoyl-L-alanine amidase CwlD\",\\n \"bio_property\": \"enzyme activity * cell wall metabolism\",\\n \"env_property\": \"nutrient flux * cell wall turnover\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"L-threonine 3-dehydrogenase is involved in amino acid metabolism and the CwlD amidase in bacterial cell wall turnover, both of which relate to dynamic nutrient flux and cell wall recycling in the ecosystem.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR011868 * sk__Bacteria;k__;p__Candidatus_Gottesmanbacteria\",\\n \"feature_label\": \"Molybdate ABC transporter, ATP-binding protein * Candidatus Gottesmanbacteria\",\\n \"bio_property\": \"molybdate transport * specialized metabolism\",\\n \"env_property\": \"trace element concentration * microbial diversity\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"The presence of a molybdate transporter suggests a necessity for trace element acquisition, while Candidatus Gottesmanbacteria indicates specialized microbial taxa adapted to unique biochemical conditions.\"\\n }\\n }\\n}\\n```\\n\\n### Key Points in Relationships\\n- **High sulfate and anaerobic conditions** likely contribute to the presence of dissimilatory sulfite reductase and cytochrome systems supporting sulfate reduction processes.\\n- **High metal concentrations** necessitate the bioavailability and active transport of cations, leading to the presence of ATPase/plasma membrane cation efflux proteins.\\n- **High salinity environments** explain the necessity for osmoprotectants like glycine betaine transport.\\n- **Nutrient flux and cell wall turnover** processes are indicated by metabolism-related enzymes, showing dynamic bioreactor conditions.\\n- **Trace elements and microbial diversity** contribute to supporting specialized bacterial populations and their transport systems.\\n\\nBy focusing on these different features and environmental properties, we can effectively characterize the biogeochemical and ecological functionalities of the Engineered:Bioreactor ecosystem. The confidence levels are based on established associations between these features and their typical environments, ensuring the relevancy and reliability of the reported findings.', role='assistant', function_call=None, tool_calls=None))], created=1717610305, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=871, prompt_tokens=987, total_tokens=1858))\n", + "ChatCompletion(id='chatcmpl-9Wuaj3xs72dHOGuZhHdvNJ1UtgHdB', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Engineered:Bioreactor\": {\\n \"1\": {\\n \"feature_id\": \"GO:0018551 * IPR005126\",\\n \"feature_label\": \"dissimilatory sulfite reductase activity * NapC/NirT cytochrome c, N-terminal\",\\n \"bio_property\": \"anaerobic respiration * sulfur metabolism\",\\n \"env_property\": \"anoxic * sulfur-rich\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Dissimilatory sulfite reductase and associated cytochrome c are indicative of microbial sulfur cycling, which occurs primarily in anoxic and sulfur-rich conditions typical of engineered bioreactors.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0031460 * IPR004763\",\\n \"feature_label\": \"glycine betaine transport * Cation efflux system CzcA/CusA/SilA/NccA/HelA/CnrA\",\\n \"bio_property\": \"osmoprotection * ion transport\",\\n \"env_property\": \"osmotic stress * metal-rich\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Glycine betaine transport and cation efflux systems are crucial in environments experiencing osmotic stress and the presence of heavy metals, both of which are often encountered in engineered bioreactors.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR007117 * IPR011868\",\\n \"feature_label\": \"Expansin, cellulose-binding-like domain * Molybdate ABC transporter, ATP-binding protein\",\\n \"bio_property\": \"cell wall modification * molybdenum transport\",\\n \"env_property\": \"organic-rich * high molybdate availability\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"The presence of expansin for cell wall modification and molybdate transport proteins suggests an environment rich in organic materials and available molybdate, such as one found in engineered bioreactors.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR016300 * IPR019949\",\\n \"feature_label\": \"Arsenical pump ATPase, ArsA/GET3 * Luciferase family oxidoreductase, group 1\",\\n \"bio_property\": \"arsenic resistance * oxidative stress response\",\\n \"env_property\": \"toxic metal contamination * high oxidative stress\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Arsenical pump ATPase and luciferase family oxidoreductases denote resistance to toxic metals and oxidative stress management, relevant to bioreactor conditions that handle waste with heavy metal contaminants.\"\\n },\\n \"5\": {\\n \"feature_id\": \"GO:0008743 * IPR001360\",\\n \"feature_label\": \"L-threonine 3-dehydrogenase activity * Glycoside hydrolase family 1\",\\n \"bio_property\": \"amino acid metabolism * carbohydrate degradation\",\\n \"env_property\": \"nutrient cycling * high organic load\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"L-threonine 3-dehydrogenase and glycoside hydrolases are involved in the breakdown of amino acids and carbohydrates, respectively, indicating active nutrient cycling in environments with a high organic load, typical in engineered bioreactors.\"\\n },\\n \"6\": {\\n \"feature_id\": \"IPR014242 * IPR002723\",\\n \"feature_label\": \"Spore cortex biosynthesis protein, YabQ * N(4)-bis(aminopropyl)spermidine synthase, C-terminal\",\\n \"bio_property\": \"sporulation * polyamine biosynthesis\",\\n \"env_property\": \"nutrient-limited * stress conditions\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Proteins involved in spore formation and polyamine biosynthesis correlate with nutrient limitation and high-stress conditions, commonly present in engineered bioreactors designed to manage waste and recycling processes.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631061, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=833, prompt_tokens=1003, total_tokens=1836))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -3168,18 +3170,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Engineered:Bioremediation:Terephthalate:Wastewater\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -3253,7 +3255,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 1:\n", - "ChatCompletion(id='chatcmpl-9WpCFMhpuKtKZHLngr3XKbRtghfsX', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Engineered:Bioremediation:Terephthalate:Wastewater\": {\\n \"1\": {\\n \"feature_id\": \"GO:0004114 * IPR004501\",\\n \"feature_label\": \"3\\',5\\'-cyclic-nucleotide phosphodiesterase activity * Phosphotransferase system, EIIC component, type 3\",\\n \"bio_property\": \"signal transduction * sugar transport\",\\n \"env_property\": \"high organic load * nutrient dense\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Systems involved in signal transduction and sugar transport are crucial for microbial responses to high organic load environments.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0008901 * IPR010960\",\\n \"feature_label\": \"ferredoxin hydrogenase activity * Flavocytochrome c\",\\n \"bio_property\": \"electron transport chain * anaerobic respiration\",\\n \"env_property\": \"oxygen-limited * high organic load\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Ferredoxin hydrogenase and Flavocytochrome c are indicative of anaerobic conditions often found in high organic load environments, enhancing the electron transport chain.\"\\n },\\n \"3\": {\\n \"feature_id\": \"GO:0019512 * IPR004300\",\\n \"feature_label\": \"lactose catabolic process via tagatose-6-phosphate * Glycoside hydrolase family 57, N-terminal domain\",\\n \"bio_property\": \"lactose metabolism * carbohydrate degradation\",\\n \"env_property\": \"high organic load * carbohydrate-rich conditions\",\\n \"confidence\": \"high\",\\n \"explanation\": \"These features are involved in carbohydrate metabolism, crucial for environments rich in organic carbon sources such as those present in terephthalate wastewater.\"\\n },\\n \"4\": {\\n \"feature_id\": \"GO:0004037 * IPR017813\",\\n \"feature_label\": \"allantoicase activity * Mycothiol acetyltransferase\",\\n \"bio_property\": \"amino acid metabolism * detoxification\",\\n \"env_property\": \"nutrient dense * potentially toxin-rich\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Enzymes involved in amino acid metabolism and detoxification are likely to be relevant in environments that are nutrient-dense and may contain toxic compounds.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR014580 * IPR014984\",\\n \"feature_label\": \"Uncharacterised conserved protein UCP033199 * HopJ type III effector protein\",\\n \"bio_property\": \"unknown function * pathogenicity\",\\n \"env_property\": \"diverse microbial community * complex interactions\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Presence of pathogenicity-related proteins indicates the environment might support a complex microbial community, including potential microbial interactions.\"\\n },\\n \"6\": {\\n \"feature_id\": \"IPR000957 * GO:0043462\",\\n \"feature_label\": \"Sulphate/thiosulphate-binding, conserved site * regulation of ATP-dependent activity\",\\n \"bio_property\": \"sulphur metabolism * energy regulation\",\\n \"env_property\": \"sulphate-rich * variable energy availability\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Features relating to sulphur metabolism and energy regulation suggest adaptation to environments that have high levels of sulphate and variable energy sources.\"\\n },\\n \"7\": {\\n \"feature_id\": \"sk__Bacteria;k__;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides * sk__Bacteria;k__;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella\",\\n \"feature_label\": \"Bacteroides * Collinsella\",\\n \"bio_property\": \"complex carbohydrate breakdown * secondary metabolism\",\\n \"env_property\": \"high fiber * complex organic matter\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Bacteroides and Collinsella are known for their roles in breaking down complex carbohydrates, indicating adaptation to high fiber and complex organic matter environments.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717610323, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_aa87380ac5', usage=CompletionUsage(completion_tokens=903, prompt_tokens=1372, total_tokens=2275))\n", + "ChatCompletion(id='chatcmpl-9Wub2Hzpbvv0dIPDq8eiPDw7XI78W', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Engineered:Bioremediation:Terephthalate:Wastewater\": {\\n \"1\": {\\n \"feature_id\": \"GO:0008743 * IPR001360 * GO:0019512\",\\n \"feature_label\": \"L-threonine 3-dehydrogenase activity * Glycoside hydrolase family 1 * lactose catabolic process via tagatose-6-phosphate\",\\n \"bio_property\": \"amino acid metabolism * carbohydrate metabolism * glycoside hydrolase function\",\\n \"env_property\": \"organic carbon-rich * nutrient recycling * pollutant-degrading\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The presence of enzymes involved in the metabolism of amino acids and carbohydrates, such as L-threonine 3-dehydrogenase and glycoside hydrolases, indicates active nutrient recycling processes. In an environment rich with organic carbon, such as terephthalate wastewater, these enzymes contribute significantly to breaking down complex organic pollutants.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0008901 * IPR009677 * IPR012441\",\\n \"feature_label\": \"ferredoxin hydrogenase activity * Protein of unknown function DUF1266 * Protein of unknown function DUF1643\",\\n \"bio_property\": \"electron transport * molecular function\",\\n \"env_property\": \"anaerobic conditions * redox potential variations\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Ferredoxin hydrogenase activity plays a crucial role in electron transport under anaerobic conditions. Alongside proteins of unknown functions (DUF1266 and DUF1643), this suggests adaptation to varying redox conditions within the wastewater environment, facilitating the breakdown of pollutants without oxygen.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR000036 * IPR006391\",\\n \"feature_label\": \"Peptidase A26, omptin * P-type ATPase, B chain, subfamily IA\",\\n \"bio_property\": \"protein degradation * ion transport\",\\n \"env_property\": \"high metal ion concentration\",\\n \"confidence\": \"high\",\\n \"explanation\": \"P-type ATPases are involved in ion transport and homeostasis. The presence of peptidase A26, which catalyzes protein degradation, suggests adaptation to an environment with high metal ion concentrations where maintaining ion balance is crucial.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR004840 * GO:0043462\",\\n \"feature_label\": \"Amino acid permease, conserved site * regulation of ATP-dependent activity\",\\n \"bio_property\": \"amino acid transport * enzymatic regulation\",\\n \"env_property\": \"nutrient absorption challenges\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"The amino acid permease site indicates efficient nutrient uptake mechanisms, crucial for survival in a bioremediation environment where resources may be unevenly distributed. Coupled with regulatory activity, this suggests an adaptable organism capable of optimizing metabolic functions in response to environmental nutrient availability.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR010106 * IPR017813\",\\n \"feature_label\": \"Recombination-promoting nuclease RpnA * Mycothiol acetyltransferase\",\\n \"bio_property\": \"DNA repair * antioxidative stress response\",\\n \"env_property\": \"chemical stress * oxidative stress\",\\n \"confidence\": \"high\",\\n \"explanation\": \"These proteins are involved in cellular defense mechanisms against chemical and oxidative stress, common in polluted environments like terephthalate wastewater. In particular, mycothiol acetyltransferase plays a role in maintaining redox balance, crucial for microbial survival and pollutant degradation.\"\\n },\\n \"6\": {\\n \"feature_id\": \"1PR016300 * GO:0019068\",\\n \"feature_label\": \"Arsenical pump ATPase, ArsA/GET3 * virion assembly\",\\n \"bio_property\": \"heavy metal detoxification * viral replication\",\\n \"env_property\": \"toxic compounds * microbial interaction\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Arsenical pump ATPase reflects adaptation to toxic environments with heavy metals, common in industrial wastewater. Virion assembly indicates viral influences in microbial communities within the ecosystem, potentially affecting microbial dynamics and biodegradation processes.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631080, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=918, prompt_tokens=1379, total_tokens=2297))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -3276,18 +3278,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Engineered:Built environment\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -3320,7 +3322,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 2:\n", - "ChatCompletion(id='chatcmpl-9WpCakIiAtsE2C5vBO1fmhB3em8WK', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Engineered:Built environment\": {\\n \"1\": {\\n \"feature_id\": \"IPR009413\",\\n \"feature_label\": \"Hemolysin, aegerolysin type\",\\n \"bio_property\": \"cell lysis * pathogenicity\",\\n \"env_property\": \"humid * high dust load\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Hemolysins like aegerolysin type are often associated with environments rich in organic material, where they can easily access hemolytic substrates. In the built environment, these conditions are typically found in dusty, humid areas which provide the needed substrates and conditions for microbial growth.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR010960\",\\n \"feature_label\": \"Flavocytochrome c\",\\n \"bio_property\": \"electron transport * oxidative stress response\",\\n \"env_property\": \"industrial * pollutant-rich\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Flavocytochromes are involved in electron transport chains and are crucial for oxidative stress response. In built environments, particularly in industrial settings with pollutants, organisms with such features may prevail due to their enhanced ability to manage oxidative stress caused by pollutants.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR021822\",\\n \"feature_label\": \"Protein of unknown function DUF3405\",\\n \"bio_property\": \"potential regulatory function * protein-protein interaction\",\\n \"env_property\": \"varies\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Though the exact function is unknown, proteins with DUF3405 domains may be involved in regulatory processes and protein-protein interactions. These properties tend to be universal and can adapt to a variety of environmental conditions.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR022190\",\\n \"feature_label\": \"Protein of unknown function DUF3716\",\\n \"bio_property\": \"potential stress response * structural component\",\\n \"env_property\": \"high foot traffic * biofilm formation\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Proteins with DUF3716 might play roles in structural integrity or stress response within microbial communities. In high-traffic areas where human interaction is frequent, biofilm formation is a common adaptive response, suggesting DUF3716 proteins may contribute to biofilm resilience.\"\\n },\\n \"5\": {\\n \"feature_id\": \"sk__Eukaryota;k__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Aspergillaceae\",\\n \"feature_label\": \"Eurotiales (fungal order including Aspergillus)\",\\n \"bio_property\": \"decomposition * secondary metabolite production\",\\n \"env_property\": \"indoor air * material degradation\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Members of the Aspergillaceae family, such as Aspergillus, are known for their ability to decompose organic matter and produce numerous secondary metabolites. These fungi commonly thrive in indoor environments where they can contribute to material degradation.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717610344, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=656, prompt_tokens=680, total_tokens=1336))\n", + "ChatCompletion(id='chatcmpl-9WubGiWiILilBI20kkcNpYb9i2rIL', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Engineered:Built\": {\\n \"1\": {\\n \"feature_id\": \"IPR009413 * sk__Eukaryota;k__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Aspergillaceae\",\\n \"feature_label\": \"Hemolysin, aegerolysin type * Fungi (Aspergillaceae)\",\\n \"bio_property\": \"hemolysis * virulence factor\",\\n \"env_property\": \"high human presence * possible contamination with organic material\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Hemolysins are virulence factors in pathogenic fungi; their presence in built environments suggests potential contamination or human infection risk.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR010960\",\\n \"feature_label\": \"Flavocytochrome c\",\\n \"bio_property\": \"electron transport * oxidative metabolism\",\\n \"env_property\": \"nutrient cycling * redox potential\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Flavocytochrome c is involved in electron transport and plays a role in oxidative metabolism, indicating active biochemical processes including nutrient cycling in the environment.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR021822 * IPR022190\",\\n \"feature_label\": \"Protein of unknown function DUF3405 * Protein of unknown function DUF3716\",\\n \"bio_property\": \"unknown protein * possible role in stress response or environmental adaptation\",\\n \"env_property\": \"variable environmental conditions * potential for diverse microbial adaptation\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Proteins of unknown function may imply unexplained or poorly understood adaptive mechanisms to variable conditions, common in built environments with fluctuating parameters.\"\\n },\\n \"4\": {\\n \"feature_id\": \"sk__Eukaryota;k__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Aspergillaceae\",\\n \"feature_label\": \"Aspergillaceae (Fungi)\",\\n \"bio_property\": \"decomposition * biofilm formation * allergen production\",\\n \"env_property\": \"indoor air quality * humidity * presence of organic material\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Aspergillaceae is known for their role in decomposition and biofilm formation, which impacts indoor air quality and sustainability in built environments.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631094, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=527, prompt_tokens=697, total_tokens=1224))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -3343,18 +3345,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Engineered:Food production\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -3392,7 +3394,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 3:\n", - "ChatCompletion(id='chatcmpl-9WpCl3UH1RLTgU0bBz3Q4Qmr4shXR', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='Here\\'s the requested analysis based on the provided features and environmental context:\\n\\n```json\\n{\\n \"Engineered:Food production\": {\\n \"1\": {\\n \"feature_id\": \"IPR007210 * GO:0031460\",\\n \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\\n \"bio_property\": \"osmoprotection * stress response\",\\n \"env_property\": \"marine * high salinity\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Glycine betaine is a known osmoprotectant in high osmolarity environments.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0004638 * IPR022380\",\\n \"feature_label\": \"phosphoribosylaminoimidazole carboxylase activity * Glutamyl-Q tRNA(Asp) synthetase\",\\n \"bio_property\": \"nucleotide biosynthesis * translation accuracy\",\\n \"env_property\": \"nutrient-rich * chemically regulated\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Phosphoribosylaminoimidazole carboxylase is crucial for purine biosynthesis, which is essential in nutrient-rich environments where rapid cell division occurs. Glutamyl-Q tRNA(Asp) synthetase maintains fidelity in protein synthesis under such conditions.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR002914 * IPR000477\",\\n \"feature_label\": \"Pollen allergen Poa p IX/Phl p VI * Reverse transcriptase domain\",\\n \"bio_property\": \"immune response * retrotransposition\",\\n \"env_property\": \"biologically diverse * viral presence\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Allergens like Poa p IX can elicit immune responses, indicating a complex biological system. Reverse transcriptase suggests viral elements often found in such environments.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR002631 * IPR004264\",\\n \"feature_label\": \"Plasmid replication protein * Transposase, Tnp1/En/Spm-like\",\\n \"bio_property\": \"genetic mobility * DNA replication\",\\n \"env_property\": \"antibiotic-rich * high genetic variability\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Plasmid replication proteins and transposases facilitate genetic exchange and mobility. Such features are typical in environments where antibiotic resistance and genetic adaptability are crucial.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR004501 * IPR024309\",\\n \"feature_label\": \"Phosphotransferase system, EIIC component, type 3 * Nuclear Testis protein, N-terminal\",\\n \"bio_property\": \"sugar transport * transcription regulation\",\\n \"env_property\": \"nutrient fluctuation * regulatory complexity\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Phosphotransferase systems are involved in sugar uptake, critical in fluctuating nutrient environments. Nuclear testis proteins often regulate gene expression, crucial in environments requiring intricate cellular coordination.\"\\n },\\n \"6\": {\\n \"feature_id\": \"GO:0004984 * IPR018216\",\\n \"feature_label\": \"olfactory receptor activity * Cathelicidin, conserved site\",\\n \"bio_property\": \"sensory perception * antimicrobial activity\",\\n \"env_property\": \"microbial interaction * complex signaling\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Olfactory receptors and antimicrobial peptides like cathelicidins indicate complex microbial interactions and signaling typical in highly regulated, biologically active environments.\"\\n }\\n }\\n}\\n```\\n\\n### Key Points:\\n1. **Feature Groupings**: Grouped features by combining where they complement each other biologically, as this often reflects shared environmental adaptations or requirements.\\n2. **Environmental Context**: Focused on properties like nutrient availability, salinity, biological diversity, and genetic variability which are crucial in engineered food production environments.\\n3. **Confidence Levels**: Assigned based on the strength of known biological-environmental relationships and consistency with the environment\\'s expectations.', role='assistant', function_call=None, tool_calls=None))], created=1717610355, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=873, prompt_tokens=743, total_tokens=1616))\n", + "ChatCompletion(id='chatcmpl-9WubSiIJsP8rWTuqMU5VbO1bSSXMh', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Environmental:Engineered:Food production\": {\\n \"1\": {\\n \"feature_id\": \"GO:0004638 * IPR022380\",\\n \"feature_label\": \"phosphoribosylaminoimidazole carboxylase activity * Glutamyl-Q tRNA(Asp) synthetase\",\\n \"bio_property\": \"nucleotide biosynthesis * protein synthesis\",\\n \"env_property\": \"nutrient-rich * controlled conditions\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Phosphoribosylaminoimidazole carboxylase activity is involved in nucleotide biosynthesis pathways, which are critical in nutrient-rich environments typical of food production systems. The Glutamyl-Q tRNA(Asp) synthetase is essential for protein translation, supporting efficient growth in controlled nutrient environments.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR000477 * IPR004264 * IPR004501\",\\n \"feature_label\": \"Reverse transcriptase domain * Transposase, Tnp1/En/Spm-like * Phosphotransferase system, EIIC component, type 3\",\\n \"bio_property\": \"genetic element mobility * carbohydrate transport\",\\n \"env_property\": \"genetically engineered * carbohydrate-rich\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Reverse transcriptase and transposase are indicative of genome mobility mechanisms, commonly observed in genetically engineered organisms. The Phosphotransferase system (PTS) component is involved in carbohydrate transport systems, which are prevalent in carbohydrate-rich environments of food production.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR018216 * IPR002914\",\\n \"feature_label\": \"Cathelicidin, conserved site * Pollen allergen Poa p IX/Phl p VI\",\\n \"bio_property\": \"antimicrobial peptide * allergen\",\\n \"env_property\": \"controlled microbial populations * presence of plants\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Cathelicidins are antimicrobial peptides that play a role in controlling microbial populations, a necessary function in managing food production environments. The presence of pollen allergens suggests a coexistence with plant materials within the food production ecosystem.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631106, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=479, prompt_tokens=760, total_tokens=1239))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -3415,18 +3417,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Engineered:Food production:Dairy products\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -3483,7 +3485,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 4:\n", - "ChatCompletion(id='chatcmpl-9WpD2IqcFxGb41Go1QYtXMqJUWOfC', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='Here is a JSON output structure based on the relationships between microbial metagenomic features and environmental properties of the Engineered:Food production:Dairy products ecosystem. The JSON will prioritize reporting relationships involving groups of multiple features:\\n\\n```json\\n{\\n \"Engineered:Food production:Dairy products\": {\\n \"1\": {\\n \"feature_id\": \"GO:0001510 * GO:0017148 * IPR006848\",\\n \"feature_label\": \"RNA methylation * negative regulation of translation * Transcription regulator, putative, lactococcus phage-type\",\\n \"bio_property\": \"gene expression regulation * transcriptional control\",\\n \"env_property\": \"nutrient-rich * temperature-controlled\",\\n \"confidence\": \"high\",\\n \"explanation\": \"In dairy product ecosystems, regulating gene expression and transcription is crucial for the adaptation to nutrient-rich, temperature-controlled environments often found in fermentation processes.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0008740 * IPR011735 * IPR028955\",\\n \"feature_label\": \"L-rhamnose isomerase activity * WlaTC/HtrL glycosyltransferase * Immunity protein 57\",\\n \"bio_property\": \"carbohydrate metabolism * immune response\",\\n \"env_property\": \"sugar-rich * varied microbial interactions\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Carbohydrate metabolism and immune response are important in dairy production where sugar content is high, and there are complex microbial interactions, including preservation against pathogens.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR001360 * IPR023870\",\\n \"feature_label\": \"Glycoside hydrolase family 1 * Poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA\",\\n \"bio_property\": \"polysaccharide breakdown * biofilm formation\",\\n \"env_property\": \"lactose presence * biofilm-prone surfaces\",\\n \"confidence\": \"high\",\\n \"explanation\": \"In dairy products, glycoside hydrolases facilitate the breakdown of lactose while biofilm formation is significant for microbial stability and interaction on dairy processing surfaces.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR004501 * IPR008300\",\\n \"feature_label\": \"Phosphotransferase system, EIIC component, type 3 * Phosphate propanoyltransferase\",\\n \"bio_property\": \"phosphate and sugar transport * phosphorylation\",\\n \"env_property\": \"nutrient uptake * fermentation by-products\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Phosphate and sugar transport systems are essential for microbial growth and energy utilization in the fermentation processes of dairy product production, leading to significant nutrient uptake and by-products.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR010133 * IPR007464 * IPR017559\",\\n \"feature_label\": \"Bacteriocin-type signal sequence * Bacteriocin, class IId * Alkyl hydroperoxide reductase subunit C\",\\n \"bio_property\": \"antibacterial activity * oxidative stress response\",\\n \"env_property\": \"microbial competition * aeration\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Antibacterial activity and oxidative stress response play crucial roles in dairy ecosystems where microbial competition and varying aeration conditions influence microbial community dynamics.\"\\n }\\n }\\n}\\n```\\n\\nEach entry in the JSON provides detailed and high-confidence relationships between the specific features and environmental properties relevant to the dairy product production ecosystem. The key biological properties such as gene regulation, carbohydrate metabolism, and antibacterial activity are tied with environmental properties like nutrient-rich conditions, sugar presence, and microbial competition in fermentation settings. This nuanced understanding supports the production processes by highlighting the microbial functionalities and their environmental dependencies.', role='assistant', function_call=None, tool_calls=None))], created=1717610372, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=797, prompt_tokens=1026, total_tokens=1823))\n", + "ChatCompletion(id='chatcmpl-9WubdzTP3QvcLeFxhDCIf4Ks5BrPI', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Engineered:Food production:Dairy products\": {\\n \"1\": {\\n \"feature_id\": \"GO:0008740 * IPR003491 * GO:0017148\",\\n \"feature_label\": \"L-rhamnose isomerase activity * Replication initiation factor * Negative regulation of translation\",\\n \"bio_property\": \"sugar metabolism * DNA replication * gene expression regulation\",\\n \"env_property\": \"nutrient-rich * temperature-controlled * high microbial activity\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Dairy production environments are nutrient-rich and foster diverse microbial activity. L-rhamnose isomerase facilitates sugar metabolism from plant-based ingredients. Replication initiation factors are crucial for microbial proliferation. Negative regulation of translation hints at complex gene expression regulation due to the diverse microbiota.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR001360 * IPR011735 * GO:0004638\",\\n \"feature_label\": \"Glycoside hydrolase family 1 * WlaTC/HtrL glycosyltransferase * phosphoribosylaminoimidazole carboxylase activity\",\\n \"bio_property\": \"polysaccharide degradation * cell wall synthesis * nucleotide biosynthesis\",\\n \"env_property\": \"rich in polysaccharides * stable pH * anaerobic niches\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Dairy environments are rich in lactose and other polysaccharides, necessitating glycoside hydrolase activity. WlaTC/HtrL glycosyltransferase is involved in cell wall formation, crucial in dense microbial environments. Phosphoribosylaminoimidazole carboxylase activity is part of purine biosynthesis, supporting rapid microbial growth.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR007464 * IPR010133 * IPR017559\",\\n \"feature_label\": \"Bacteriocin, class IId * Bacteriocin-type signal sequence * Alkyl hydroperoxide reductase subunit C\",\\n \"bio_property\": \"antimicrobial peptide production * stress response * oxidative stress defense\",\\n \"env_property\": \"competitive microbial interactions * oxidative stress conditions * community-specific signaling\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Bacteriocins are antimicrobial peptides produced by bacteria to inhibit competitors, relevant in densely populated dairy microbial communities. Alkyl hydroperoxide reductase alleviates oxidative stress, enhancing survival in the competitive, high-interaction environment.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR007210 * IPR028955\",\\n \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * Immunity protein 57\",\\n \"bio_property\": \"osmoprotection * microbial defense\",\\n \"env_property\": \"variable osmolarity * potential for bacteriophage presence\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Glycine betaine transport systems provide osmoprotection in environments with varying osmolarity, which can occur with ingredient changes. Immunity proteins suggest defense mechanisms against bacteriophages, common in diverse microbial ecosystems such as dairy.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR004501 * IPR003491 * IPR010960\",\\n \"feature_label\": \"Phosphotransferase system, EIIC component, type 3 * Replication initiation factor * Flavocytochrome c\",\\n \"bio_property\": \"sugar transport * DNA replication * electron transport\",\\n \"env_property\": \"nutrient-rich * redox-active\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The phosphotransferase system is crucial for sugar uptake in nutrient-rich dairy environments. Replication initiation factors support active microbial growth. Flavocytochrome c is involved in electron transport, significant for redox processes critical in microbial metabolism in dairy production.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631117, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=837, prompt_tokens=1040, total_tokens=1877))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -3506,18 +3508,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Engineered:Food production:Fermented beverages\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -3578,7 +3580,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 5:\n", - "ChatCompletion(id='chatcmpl-9WpDKsxRtdIkIKJAOqF88SUxwH5nq', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Engineered:Food production:Fermented beverages\": {\\n \"1\": {\\n \"feature_id\": \"GO:0004122 * IPR004642\",\\n \"feature_label\": \"Cystathionine beta-synthase activity * Serine dehydratase, alpha subunit\",\\n \"bio_property\": \"amino acid metabolism * sulfur compound biosynthesis\",\\n \"env_property\": \"nutrient-rich * acidic conditions\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Fermented beverages often contain sulfur-containing amino acids, and enzymes involved in their metabolism are active in nutrient-rich environments with varying pH levels, including acidic conditions.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0042176 * IPR000938\",\\n \"feature_label\": \"Regulation of protein catabolic process * CAP Gly-rich domain\",\\n \"bio_property\": \"protein degradation * stress response\",\\n \"env_property\": \"dynamic conditions * varying pH\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"The regulation of protein catabolic processes is crucial in environments with dynamic conditions such as those found during fermentation where there are fluctuations in pH and other stress factors.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR004868 * GO:0031460\",\\n \"feature_label\": \"DNA-directed DNA polymerase, family B, mitochondria/virus * Glycine betaine transport\",\\n \"bio_property\": \"DNA replication * osmoprotection\",\\n \"env_property\": \"high temperature * high salinity\",\\n \"confidence\": \"high\",\\n \"explanation\": \"DNA-directed polymerase activities are important in high-temperature environments where specialized replication mechanisms are needed. Glycine betaine transport is crucial for osmoprotection in high-salinity conditions, often encountered together in fermentation setups.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR006541 * IPR019895\",\\n \"feature_label\": \"Bacteriocin-associated integral membrane protein * Putative bacteriocin export ABC transporter, lactococcin 972 group\",\\n \"bio_property\": \"bacteriocin production * antimicrobial activity\",\\n \"env_property\": \"competitive microbial community * nutrient-rich\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Bacteriocins play a key role in microbial competition and self-preservation within nutrient-rich communities typical of fermented environments, helping dominant strains outcompete others.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR004501 * IPR007165\",\\n \"feature_label\": \"Phosphotransferase system, EIIC component, type 3 * Mycobacterial 4 TMS phage holin, superfamily IV\",\\n \"bio_property\": \"sugar transport * phage attack resistance\",\\n \"env_property\": \"carbon-rich * high microbial density\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Phosphotransferase systems are involved in sugar uptake within carbon-rich environments. Holins provide resistance to phage attacks, which can be frequent in high-density microbial communities such as those in fermentation.\"\\n },\\n \"6\": {\\n \"feature_id\": \"IPR014242 * IPR024405\",\\n \"feature_label\": \"Spore cortex biosynthesis protein, YabQ * Prophage protein BhlA/UviB\",\\n \"bio_property\": \"sporulation * prophage immunity\",\\n \"env_property\": \"fluctuating nutrients * potential phage presence\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Sporulation is a survival strategy in fluctuating nutrient environments. Prophage immunity elements help protect against phage infections that could arise during fermentation disruptions.\"\\n }\\n }\\n}\\n```\\n\\nThis JSON output is structured to provide clear and concise relationships between observed metagenomic features and environmental properties in the context of the Engineered:Food production:Fermented beverages ecosystem. Each entry contains detailed explanations to justify the association.', role='assistant', function_call=None, tool_calls=None))], created=1717610390, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=834, prompt_tokens=1128, total_tokens=1962))\n", + "ChatCompletion(id='chatcmpl-9WubsQklOlI2cmR7FtbcoNRloB48m', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Engineered:Food production:Fermented beverages\": {\\n \"1\": {\\n \"feature_id\": \"GO:0004114 * IPR004501 * IPR007354\",\\n \"feature_label\": \"3\\',5\\'-cyclic-nucleotide phosphodiesterase activity * Phosphotransferase system, EIIC component, type 3 * Bisanhydrobacterioruberin hydratase CruF-like\",\\n \"bio_property\": \"signal transduction * carbohydrate uptake * carotenoid biosynthesis\",\\n \"env_property\": \"nutrient-rich * low pH * anaerobic\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The combination of these features suggests a complex system of signaling, carbohydrate uptake, and carotenoid biosynthesis highly adapted to the nutrient-rich, low pH, and anaerobic conditions commonly found in fermented beverage production.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0004122 * IPR004642\",\\n \"feature_label\": \"cystathionine beta-synthase activity * Serine dehydratase, alpha subunit\",\\n \"bio_property\": \"amino acid metabolism * sulfur amino acid biosynthesis\",\\n \"env_property\": \"nutrient-rich * stable temperature\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"The presence of cystathionine beta-synthase and serine dehydratase indicates active amino acid metabolism and sulfur amino acid biosynthesis, processes vital in nutrient-rich and stable temperature conditions typical of fermentation environments.\"\\n },\\n \"3\": {\\n \"feature_id\": \"GO:0005871 * IPR004868\",\\n \"feature_label\": \"kinesin complex * DNA-directed DNA polymerase, family B, mitochondria/virus\",\\n \"bio_property\": \"intracellular transport * DNA replication\",\\n \"env_property\": \"controlled temperature * anaerobic\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Kinesin complexes and mitochondrial/viral DNA polymerases are essential for intracellular transport and replication processes, crucial in the controlled temperature and anaerobic conditions of fermented beverage ecosystems.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR006541 * IPR007165 * IPR019895\",\\n \"feature_label\": \"Bacteriocin-associated integral membrane protein * Mycobacterial 4 TMS phage holin, superfamily IV * Putative bacteriocin export ABC transporter, lactococcin 972 group\",\\n \"bio_property\": \"antimicrobial activity * cell lysis * transporter activity\",\\n \"env_property\": \"high microbial diversity * anaerobic\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Features related to bacteriocin production, phage holins, and bacteriocin transporters are indicative of mechanisms to control microbial diversity and ensure survival in anaerobic conditions found in fermented habitats.\"\\n },\\n \"5\": {\\n \"feature_id\": \"GO:0042176 * IPR002631\",\\n \"feature_label\": \"regulation of protein catabolic process * Plasmid replication protein\",\\n \"bio_property\": \"proteolysis regulation * plasmid maintenance\",\\n \"env_property\": \"nutrient-rich * variable pH\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Regulation of protein catabolic processes and plasmid replication proteins are critical in maintaining plasmid integrity and protein turnover, which are vital in nutrient-rich and varying pH conditions seen in fermented beverages.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631132, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=739, prompt_tokens=1141, total_tokens=1880))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -3601,18 +3603,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Engineered:Solid waste:Composting\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -3657,7 +3659,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 6:\n", - "ChatCompletion(id='chatcmpl-9WpDYn3PgWfCFX4nauKfhnVKbVdxR', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Engineered:Solid waste:Composting\": {\\n \"1\": {\\n \"feature_id\": \"GO:0004122 * IPR002723\",\\n \"feature_label\": \"cystathionine beta-synthase activity * N(4)-bis(aminopropyl)spermidine synthase, C-terminal\",\\n \"bio_property\": \"sulfur metabolism * polyamine biosynthesis\",\\n \"env_property\": \"nutrient recycling * high organic matter\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Cystathionine beta-synthase is involved in sulfur amino acid metabolism, critical for nutrient recycling in compost. Polyamines play roles in cellular growth and death, prevalent in high organic matter conditions.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0016999 * IPR008557\",\\n \"feature_label\": \"antibiotic metabolic process * Alkaline phosphatase PhoX\",\\n \"bio_property\": \"antibiotic biosynthesis * phosphorus metabolism\",\\n \"env_property\": \"antibiotic presence * fluctuating pH\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The antibiotic metabolic process is important for microbial competition in composting environments. Alkaline phosphatase is crucial in phosphorus cycling, especially in environments with variable pH.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR014242 * IPR014931 * IPR014580\",\\n \"feature_label\": \"Spore cortex biosynthesis protein, YabQ * Protein of unknown function DUF1805 * Uncharacterised conserved protein UCP033199\",\\n \"bio_property\": \"spore formation * stress response proteins\",\\n \"env_property\": \"high temperature * variable moisture levels\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Spore formation is a key survival strategy in composting environments due to the fluctuating and often extreme conditions such as high temperature and variable moisture levels.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR022343 * IPR022380\",\\n \"feature_label\": \"GCR1-cAMP receptor * Glutamyl-Q tRNA(Asp) synthetase\",\\n \"bio_property\": \"signal transduction * tRNA modification\",\\n \"env_property\": \"variable substrate availability\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Signal transduction mechanisms and tRNA modifications are essential in adapting to nutrient availability fluctuations typical in composting environments.\"\\n },\\n \"5\": {\\n \"feature_id\": \"sk__Bacteria;k__;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides\",\\n \"feature_label\": \"Bacteroides\",\\n \"bio_property\": \"degradation of complex organic material\",\\n \"env_property\": \"high organic material load\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Bacteroides are well-known for their ability to degrade complex polysaccharides and proteins, which is essential in the composting process of solid waste with high organic content.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717610404, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=667, prompt_tokens=889, total_tokens=1556))\n", + "ChatCompletion(id='chatcmpl-9Wuc6JgRJK7sBcWIMIinTRL7iTHdX', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Engineered:Solid waste:Composting\": {\\n \"1\": {\\n \"feature_id\": \"GO:0016999 * IPR002723\",\\n \"feature_label\": \"antibiotic metabolic process * N(4)-bis(aminopropyl)spermidine synthase, C-terminal\",\\n \"bio_property\": \"antibiotic production * polyamine biosynthesis\",\\n \"env_property\": \"organic-rich * dynamic temperature\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The antibiotic metabolic process is significant in composting as antibiotics can suppress harmful microbial species. N(4)-bis(aminopropyl)spermidine synthase is involved in polyamine synthesis, crucial for microbial cell growth under organic-rich conditions and dynamic temperatures.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0004638 * IPR004501\",\\n \"feature_label\": \"phosphoribosylaminoimidazole carboxylase activity * Phosphotransferase system, EIIC component, type 3\",\\n \"bio_property\": \"purine biosynthesis * carbohydrate metabolism\",\\n \"env_property\": \"nutrient-rich * fluctuating pH\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Phosphoribosylaminoimidazole carboxylase is crucial for purine biosynthesis, supporting rapid microbial growth in nutrient-rich conditions. The phosphotransferase system aids in carbohydrate metabolism, essential for energy extraction in environments with fluctuating pH.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR008016 * IPR014242 * IPR014580\",\\n \"feature_label\": \"Portal protein Gp10 * Spore cortex biosynthesis protein, YabQ * Uncharacterised conserved protein UCP033199\",\\n \"bio_property\": \"phage infection * spore formation * unknown\",\\n \"env_property\": \"diverse microbial population * high organic content\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Portal protein Gp10 links to viral infections prevalent in diverse microbial populations. The Spore cortex biosynthesis protein, YabQ, is vital for spore formation, crucial for microbial survival in high organic content environments. The function of UCP033199 is unknown but may have a role in adaptation.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR014931 * IPR019060 * IPR022343\",\\n \"feature_label\": \"Protein of unknown function DUF1805 * Domain of unknown function DUF2382 * GCR1-cAMP receptor\",\\n \"bio_property\": \"unknown * unknown * signal transduction\",\\n \"env_property\": \"variable nutrient availability * anaerobic pockets\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Although DUF1805 and DUF2382 proteins have unknown functions, their presence in diverse environments suggests roles in adaptation to variable nutrient availability. The GCR1-cAMP receptor is involved in signal transduction, enabling microbial communication in anaerobic pockets.\"\\n },\\n \"5\": {\\n \"feature_id\": \"GO:0004122 * IPR022380\",\\n \"feature_label\": \"cystathionine beta-synthase activity * Glutamyl-Q tRNA(Asp) synthetase\",\\n \"bio_property\": \"amino acid metabolism * protein synthesis\",\\n \"env_property\": \"high nitrogen content * thermophilic conditions\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Cystathionine beta-synthase activity is crucial for sulfur amino acid metabolism, significant in high nitrogen content environments. Glutamyl-Q tRNA(Asp) synthetase is vital for protein synthesis, supporting microbial activity in thermophilic conditions typical of composting.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631146, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=799, prompt_tokens=903, total_tokens=1702))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -3680,18 +3682,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Engineered:Wastewater\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -3748,7 +3750,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 7:\n", - "ChatCompletion(id='chatcmpl-9WpDmqLMy9Q0w4KmTCHh8Tw6tXBRs', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Engineered:Wastewater\": {\\n \"1\": {\\n \"feature_id\": \"GO:0018551 * IPR007343\",\\n \"feature_label\": \"dissimilatory sulfite reductase activity * zinc metallopeptidase putative\",\\n \"bio_property\": \"sulfate reduction * cellular metal ion homeostasis\",\\n \"env_property\": \"anaerobic * high metal ion content\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Dissimilatory sulfite reductase is crucial for sulfate reduction in anaerobic environments. Zinc metallopeptidases often play a role in managing metal ion concentrations in cells.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0008901 * IPR001360\",\\n \"feature_label\": \"ferredoxin hydrogenase activity * Glycoside hydrolase family 1\",\\n \"bio_property\": \"energy production * carbohydrate metabolism\",\\n \"env_property\": \"nutrient-rich * presence of organic material\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Ferredoxin hydrogenases are involved in energy production, while glycoside hydrolases assist in breaking down complex carbohydrates, both essential in nutrient-rich environments rich in organic material.\"\\n },\\n \"3\": {\\n \"feature_id\": \"GO:0019068 * IPR005021\",\\n \"feature_label\": \"virion assembly * Terminase large subunit-like\",\\n \"bio_property\": \"viral replication * DNA packaging\",\\n \"env_property\": \"microbial diverse * high microbial load\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Virion assembly and the terminase large subunit are vital components in the life cycle of viruses, suggesting a significant presence of viral populations in a highly diverse microbial environment.\"\\n },\\n \"4\": {\\n \"feature_id\": \"GO:0019512 * IPR006879\",\\n \"feature_label\": \"lactose catabolic process via tagatose-6-phosphate * Carbohydrate deacetylase YdjC-like\",\\n \"bio_property\": \"lactose metabolism * polysaccharide degradation\",\\n \"env_property\": \"high organic carbon * diverse substrate availability\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Lactose catabolism and carbohydrate deacetylation are crucial for breaking down complex sugars and polysaccharides, indicating a high availability of diverse organic substrates in the environment.\"\\n },\\n \"5\": {\\n \"feature_id\": \"GO:0015858 * IPR014984\",\\n \"feature_label\": \"nucleoside transport * HopJ type III effector protein\",\\n \"bio_property\": \"nucleotide transport * host-pathogen interaction\",\\n \"env_property\": \"high microbial competition * pathogen presence\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Nucleoside transport and type III effector proteins are associated with high microbial competition and interactions, typical in environments with pathogenic and resistant microbial strains.\"\\n },\\n \"6\": {\\n \"feature_id\": \"IPR022458 * IPR035576\",\\n \"feature_label\": \"Conjugative coupling factor TraG/TraD * Type VI secretion system TssC\",\\n \"bio_property\": \"horizontal gene transfer * competitive advantage\",\\n \"env_property\": \"high microbial diversity * presence of pathogenic bacteria\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Conjugative coupling factors and Type VI secretion systems facilitate gene transfer and microbial warfare, indicating a highly diverse microbial ecosystem with competitive and pathogenic interactions.\"\\n },\\n \"7\": {\\n \"feature_id\": \"GO:0080009 * IPR032191\",\\n \"feature_label\": \"mRNA methylation * CCR4-NOT transcription complex subunit 1, CAF1-binding domain\",\\n \"bio_property\": \"gene regulation * mRNA stability\",\\n \"env_property\": \"high microbial activity * rapid environmental change\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"mRNA methylation and CCR4-NOT complex involvement are crucial for gene regulation and adaptation, which are essential in dynamic environments with rapid changes.\"\\n },\\n \"8\": {\\n \"feature_id\": \"IPR000494 * IPR021725\",\\n \"feature_label\": \"Receptor L-domain * Pathogenicity locus\",\\n \"bio_property\": \"signal transduction * virulence\",\\n \"env_property\": \"pathogen-prevalent * high selective pressure\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Receptor L-domain and pathogenicity loci are critical for signal transduction and virulence in bacterial pathogens, indicative of environments with high selective pressure and prevalent pathogens.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717610418, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=985, prompt_tokens=1028, total_tokens=2013))\n", + "ChatCompletion(id='chatcmpl-9WucT7bg25JQ3F9DlZ07Ef3I4CJt2', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Engineered:Wastewater\": {\\n \"1\": {\\n \"feature_id\": \"GO:0018551 * IPR001613\",\\n \"feature_label\": \"dissimilatory sulfite reductase activity * Flavin amine oxidase\",\\n \"bio_property\": \"sulfate reduction * amine catabolism\",\\n \"env_property\": \"anaerobic conditions * presence of organic amines\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Dissimilatory sulfite reductase is crucial in anaerobic conditions for reducing sulfate to sulfide, common in wastewater environments. The presence of flavin amine oxidase indicates catabolism of organic amines which are typically found in wastewater.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0003968 * GO:0080009 * IPR028962\",\\n \"feature_label\": \"RNA-dependent RNA polymerase activity * mRNA methylation * Immunity protein 10\",\\n \"bio_property\": \"viral replication * gene expression regulation * bacterial immunity\",\\n \"env_property\": \"high viral load * presence of phages\",\\n \"confidence\": \"high\",\\n \"explanation\": \"RNA-dependent RNA polymerase indicates viral replication, mRNA methylation suggests viral or host gene expression regulation, and immunity protein points to bacterial immune response to phages, all indicative of environments with high viral presence as seen in wastewater.\"\\n },\\n \"3\": {\\n \"feature_id\": \"GO:0008901 * IPR035576\",\\n \"feature_label\": \"ferredoxin hydrogenase activity * Type VI secretion system TssC\",\\n \"bio_property\": \"hydrogen production * bacterial competition\",\\n \"env_property\": \"anaerobic conditions * microbial competition\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Ferredoxin hydrogenase is involved in anaerobic hydrogen production, and Type VI secretion system TssC is associated with bacterial competition. Both processes are pertinent to the dynamic microbial communities in wastewater.\"\\n },\\n \"4\": {\\n \"feature_id\": \"GO:0019068 * IPR021725\",\\n \"feature_label\": \"virion assembly * Pathogenicity locus\",\\n \"bio_property\": \"viral assembly * pathogenicity\",\\n \"env_property\": \"high microbial diversity * presence of pathogens\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Virion assembly is related to viral activity and pathogenicity loci indicate the presence of pathogenic bacteria. Wastewater is known for its diverse microbial population including pathogens.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR001360 * GO:0019512\",\\n \"feature_label\": \"Glycoside hydrolase family 1 * lactose catabolic process via tagatose-6-phosphate\",\\n \"bio_property\": \"carbohydrate metabolism * lactose catabolism\",\\n \"env_property\": \"nutrient-rich * presence of organic compounds\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Glycoside hydrolase family 1 enzymes are involved in breaking down complex carbohydrates, and lactose catabolism processes indicate the presence of lactose and other organic compounds, typical in nutrient-rich wastewater.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631169, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=673, prompt_tokens=1045, total_tokens=1718))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -3771,18 +3773,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Engineered:Wastewater:Activated Sludge\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -3833,7 +3835,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 8:\n", - "ChatCompletion(id='chatcmpl-9WpE6PlMcviSIce3pxKRx9BeO1D3p', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Engineered:Wastewater:Activated Sludge\": {\\n \"1\": {\\n \"feature_id\": \"GO:0015444 * IPR010706\",\\n \"feature_label\": \"P-type magnesium transporter activity * Fatty acid cis-trans isomerase\",\\n \"bio_property\": \"magnesium transport * fatty acid isomerization\",\\n \"env_property\": \"metal ion rich * nutrient dense\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The activity of a magnesium transporter can be vital for microorganisms in environments rich in metal ions, while fatty acid isomerization is significant for adapting membrane fluidity in nutrient-dense conditions.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0018551 * IPR004462\",\\n \"feature_label\": \"dissimilatory sulfite reductase activity * Desulfoferrodoxin, N-terminal domain\",\\n \"bio_property\": \"sulfur metabolism * iron-sulfur cluster binding\",\\n \"env_property\": \"sulfurous * anaerobic\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Dissimilatory sulfite reductase is crucial for sulfur reduction in sulfur-rich environments, and desulfoferrodoxin is involved in iron-sulfur metabolism, often occurring under anaerobic conditions.\"\\n },\\n \"3\": {\\n \"feature_id\": \"GO:0008901 * IPR019235\",\\n \"feature_label\": \"ferredoxin hydrogenase activity * Protein of unknown function DUF2178, transmembrane\",\\n \"bio_property\": \"hydrogen metabolism * transmembrane transport\",\\n \"env_property\": \"redox active * variable osmolarity\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Ferredoxin hydrogenases play a role in electron transfer and hydrogen metabolism, while the transmembrane protein might facilitate ion or molecule transport in redox-active and fluctuating osmolarity environments.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR001360 * IPR007117\",\\n \"feature_label\": \"Glycoside hydrolase family 1 * Expansin, cellulose-binding-like domain\",\\n \"bio_property\": \"carbohydrate degradation * plant cell wall modification\",\\n \"env_property\": \"organic matter rich * structured\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Glycoside hydrolases and expansins are involved in breaking down complex carbohydrates and modifying plant cell walls, respectively, indicating a role in environments abundant with organic matter and structured matrices.\"\\n },\\n \"5\": {\\n \"feature_id\": \"GO:0019068 * IPR008016\",\\n \"feature_label\": \"virion assembly * Portal protein Gp10\",\\n \"bio_property\": \"viral replication * structural viral component\",\\n \"env_property\": \"biologically diverse * microbial dense\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Virion assembly and portal proteins are essential for the formation of viral particles, reflecting a high diversity of biological entities and a dense microbial population susceptible to viral infection.\"\\n },\\n \"6\": {\\n \"feature_id\": \"IPR035576 * IPR033762\",\\n \"feature_label\": \"Type VI secretion system TssC * MCM OB domain\",\\n \"bio_property\": \"protein secretion * DNA replication licensing\",\\n \"env_property\": \"competitive * high cell density\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The Type VI secretion system and MCM OB domain indicate mechanisms for competitive interactions and efficient DNA replication, essential in environments with high cellular density and competitive inter-microbial interactions.\"\\n },\\n \"7\": {\\n \"feature_id\": \"GO:0006928 * IPR032830\",\\n \"feature_label\": \"obsolete movement of cell or subcellular component * Helicase XPB/Ssl2, N-terminal domain\",\\n \"bio_property\": \"DNA repair * cellular motility\",\\n \"env_property\": \"stressful * fluctuating chemical conditions\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"The obsolete movement of cellular components and helicase activity are pivotal for DNA repair and motility under stress conditions, which are typical of environments with fluctuating chemical characteristics.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717610438, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=890, prompt_tokens=926, total_tokens=1816))\n", + "ChatCompletion(id='chatcmpl-9Wuccd4CttcfFBjRcDZdab6OwaJvH', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Engineered:Wastewater:Activated Sludge\": {\\n \"1\": {\\n \"feature_id\": \"GO:0015444 * GO:0008901\",\\n \"feature_label\": \"P-type magnesium transporter activity * ferredoxin hydrogenase activity\",\\n \"bio_property\": \"metal ion transport * hydrogen metabolism\",\\n \"env_property\": \"metal-rich * anaerobic\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Activated sludge systems often contain high levels of various metals, and P-type magnesium transporters are important for managing magnesium ion concentrations. Ferredoxin hydrogenase activity is crucial in anaerobic conditions often found in wastewater treatment where hydrogen is involved in redox reactions.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0018551 * IPR004462\",\\n \"feature_label\": \"dissimilatory sulfite reductase activity * Desulfoferrodoxin, N-terminal domain\",\\n \"bio_property\": \"sulfur metabolism * redox reactions\",\\n \"env_property\": \"sulfate-rich * anaerobic\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Dissimilatory sulfite reductase and the desulfoferrodoxin domain are involved in the reduction of sulfite to sulfide, a key process in anaerobic environments such as those found in activated sludge, which are commonly sulfate-rich.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR001360 * IPR010706\",\\n \"feature_label\": \"Glycoside hydrolase family 1 * Fatty acid cis-trans isomerase\",\\n \"bio_property\": \"polysaccharide degradation * fatty acid metabolism\",\\n \"env_property\": \"organic-rich * diverse carbon substrates\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Activated sludge contains diverse organic matter. Glycoside hydrolases break down complex carbohydrates while fatty acid cis-trans isomerases modify fatty acids, both of which are important for metabolizing the varied carbon sources present.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR035576 * IPR032830\",\\n \"feature_label\": \"Type VI secretion system TssC * Helicase XPB/Ssl2, N-terminal domain\",\\n \"bio_property\": \"bacterial competition * DNA repair\",\\n \"env_property\": \"microbial diversity * high competition\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The Type VI secretion system is used by bacteria to compete with others in densely populated environments. Helicase domains are involved in DNA repair mechanisms, which are crucial in high-stress, competitive environments like those found in activated sludge.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR008707 * GO:0019068\",\\n \"feature_label\": \"PilC beta-propeller domain * virion assembly\",\\n \"bio_property\": \"cell adhesion * viral life cycle\",\\n \"env_property\": \"high microbial interaction * viral presence\",\\n \"confidence\": \"high\",\\n \"explanation\": \"PilC domains facilitate bacterial adhesion to surfaces and other cells, while virion assembly is indicative of viral activity. Both are integral in environments with high microbial interactions and viral presence, such as activated sludge.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631178, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=685, prompt_tokens=939, total_tokens=1624))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -3856,18 +3858,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Engineered:Wastewater:Water and sludge\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -3918,7 +3920,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 9:\n", - "ChatCompletion(id='chatcmpl-9WpEOcTXXAlM6mLKuDxwh0LPzY6kx', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='Below is the requested JSON output structure, reflecting the relationships between microbial metagenomic features and environmental properties in the Engineered:Wastewater:Water and sludge ecosystem.\\n\\n```json\\n{\\n \"Engineered:Wastewater:Water and sludge\": {\\n \"1\": {\\n \"feature_id\": \"GO:0019512 * GO:0033920 * IPR010945\",\\n \"feature_label\": \"lactose catabolic process via tagatose-6-phosphate * 6-phospho-beta-galactosidase activity * Malate dehydrogenase, type 2\",\\n \"bio_property\": \"lactose metabolism * carbohydrate degradation * energy production\",\\n \"env_property\": \"high organic load * rich in nutrients\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The presence of lactose catabolic pathways and relevant enzymes indicates an adaption to environments rich in organic matter and nutrients typically found in wastewater.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0045151 * IPR011868\",\\n \"feature_label\": \"acetoin biosynthetic process * Molybdate ABC transporter, ATP-binding protein\",\\n \"bio_property\": \"secondary metabolite production * trace element transport\",\\n \"env_property\": \"variable redox conditions * metal-rich\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Acetoin production and molybdate transport are adaptive traits relevant to variable redox conditions and the presence of trace metals often found in wastewater environments.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR017821 * IPR018470 * IPR017559\",\\n \"feature_label\": \"Succinate CoA transferase * Periplasmic metal-binding protein Tp34-type * Alkyl hydroperoxide reductase subunit C\",\\n \"bio_property\": \"energy production * metal binding and transport * oxidative stress response\",\\n \"env_property\": \"anaerobic zones * presence of heavy metals * oxidative stress conditions\",\\n \"confidence\": \"high\",\\n \"explanation\": \"These proteins are indicative of microbial metabolic versatility in adapting to anaerobic conditions, binding and managing heavy metals, and responding to oxidative stress in wastewater environments.\"\\n },\\n \"4\": {\\n \"feature_id\": \"GO:0019068 * IPR010517 * IPR010789\",\\n \"feature_label\": \"virion assembly * Phage tail tube protein, Siphoviridae * Terminase small subunit, Skunalikevirus-type\",\\n \"bio_property\": \"viral replication and assembly\",\\n \"env_property\": \"microbial infections * high microbial diversity\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The presence of phage-related proteins and virion assembly processes suggest active viral replication, contributing to microbial control dynamics and diversity in the wastewater environment.\"\\n },\\n \"5\": {\\n \"feature_id\": \"GO:0004521 * GO:0017148\",\\n \"feature_label\": \"RNA endonuclease activity * negative regulation of translation\",\\n \"bio_property\": \"RNA processing * gene expression regulation\",\\n \"env_property\": \"stress conditions * nutrient competition\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Regulation of RNA and translation suggests adaptive mechanisms to environmental stress and nutrient competition, frequent conditions in wastewater ecosystems.\"\\n },\\n \"6\": {\\n \"feature_id\": \"IPR014984 * IPR011119\",\\n \"feature_label\": \"HopJ type III effector protein * Uncharacterised domain, helicase/relaxase, putative\",\\n \"bio_property\": \"host interaction * DNA modification\",\\n \"env_property\": \"high microbial interaction * presence of host organisms\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"These proteins are typically associated with microbial interactions and possibly pathogenic relationships, suggesting a complex microbial ecosystem with host interactions in wastewater.\"\\n },\\n \"7\": {\\n \"feature_id\": \"- sk__Bacteria;k__;p__Verrucomicrobia;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia\",\\n \"feature_label\": \"Verrucomicrobiae; Akkermansia\",\\n \"bio_property\": \"gut symbiotic relationships * mucus degradation\",\\n \"env_property\": \"organic matter decomposition * anaerobic conditions\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"The presence of Akkermansia, typically associated with mucus degradation, indicates their role in organic matter decomposition under anaerobic conditions prevalent in sludge.\"\\n }\\n }\\n}\\n```\\n\\nThis structured approach reflects the connections between the metagenomic features and the environmental properties of the specific engineered wastewater ecosystem. Each set of features highlights specific biological activities relevant to adapting to the varied and complex wastewater environment.', role='assistant', function_call=None, tool_calls=None))], created=1717610456, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=1006, prompt_tokens=976, total_tokens=1982))\n", + "ChatCompletion(id='chatcmpl-9WucmQuGnbGVBuWB5nMhIlzwfbMof', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Engineered:Wastewater:Water and sludge\": {\\n \"1\": {\\n \"feature_id\": \"GO:0019512 * GO:0033920\",\\n \"feature_label\": \"lactose catabolic process via tagatose-6-phosphate * 6-phospho-beta-galactosidase activity\",\\n \"bio_property\": \"carbohydrate metabolism\",\\n \"env_property\": \"high organic matter * nutrient-rich\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Lactose catabolism and beta-galactosidase activity indicate the utilization of organic compounds prevalent in wastewater environments.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR017821 * IPR011868\",\\n \"feature_label\": \"Succinate CoA transferase * Molybdate ABC transporter, ATP-binding protein\",\\n \"bio_property\": \"energy metabolism * nutrient transport\",\\n \"env_property\": \"anaerobic conditions * high metal content\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Succinate CoA transferase is involved in anaerobic energy production, and molybdate transporters assist in handling metal ions commonly found in wastewater.\"\\n },\\n \"3\": {\\n \"feature_id\": \"GO:0045151 * IPR017559\",\\n \"feature_label\": \"acetoin biosynthetic process * Alkyl hydroperoxide reductase subunit C\",\\n \"bio_property\": \"stress response * antioxidant activity\",\\n \"env_property\": \"variable oxygen levels * oxidative stress\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Acetoin biosynthesis and alkyl hydroperoxide reductase are responses to oxidative stress, a common condition in wastewater treatment processes due to fluctuating oxygen levels.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR003491 * IPR010789 * IPR010517\",\\n \"feature_label\": \"Replication initiation factor * Terminase small subunit, Skunalikevirus-type * Phage tail tube protein, Siphoviridae\",\\n \"bio_property\": \"viral replication * phage assembly\",\\n \"env_property\": \"high microbial diversity * high phage activity\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Replication initiation factors and phage-related proteins are indicative of high microbial and phage activities, reflecting the microbial richness in wastewater.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR008707 * IPR014984\",\\n \"feature_label\": \"PilC beta-propeller domain * HopJ type III effector protein\",\\n \"bio_property\": \"cell adhesion * pathogenicity\",\\n \"env_property\": \"high microbial interaction * pathogen presence\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Proteins involved in cell adhesion and pathogenicity suggest interactions among microbes and potential pathogen prevalence in wastewater.\"\\n },\\n \"6\": {\\n \"feature_id\": \"GO:0019068 * IPR010789\",\\n \"feature_label\": \"virion assembly * Terminase small subunit, Skunalikevirus-type\",\\n \"bio_property\": \"viral assembly\",\\n \"env_property\": \"high microbial diversity * high phage activity\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The presence of proteins related to virion assembly is indicative of a dynamic virome in wastewater environments.\"\\n },\\n \"7\": {\\n \"feature_id\": \"IPR010945 * IPR017821\",\\n \"feature_label\": \"Malate dehydrogenase, type 2 * Succinate CoA transferase\",\\n \"bio_property\": \"energy metabolism\",\\n \"env_property\": \"anaerobic conditions\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Key enzymes of the TCA cycle and related anaerobic pathways are crucial under low oxygen conditions typical of sludge environments.\"\\n },\\n \"8\": {\\n \"feature_id\": \"GO:0004521 * IPR011119\",\\n \"feature_label\": \"RNA endonuclease activity * Uncharacterised domain, helicase/relaxase, putative\",\\n \"bio_property\": \"RNA processing * genetic regulation\",\\n \"env_property\": \"dynamic nutrient changes\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"RNA endonucleases and helicase-related domains play roles in genetic regulation, significant in environments with dynamic nutrient fluctuations.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631188, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=925, prompt_tokens=989, total_tokens=1914))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -3941,18 +3943,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Environmental:Aquatic:Estuary\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -3988,7 +3990,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 10:\n", - "ChatCompletion(id='chatcmpl-9WpEfSIrVI9i7kFoB2dO5Lnre6fKE', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Environmental:Aquatic:Estuary\": {\\n \"1\": {\\n \"feature_id\": \"IPR011802\",\\n \"feature_label\": \"Adenylylsulphate reductase, beta subunit\",\\n \"bio_property\": \"sulfate reduction pathway * energy metabolism\",\\n \"env_property\": \"sulfate-rich * anaerobic conditions\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Adenylylsulphate reductase is integral to the sulfate reduction pathway, which is crucial in sulfate-rich, anaerobic estuary environments.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR011946\",\\n \"feature_label\": \"Integrase, integron-type\",\\n \"bio_property\": \"genetic recombination * horizontal gene transfer\",\\n \"env_property\": \"high microbial density * variable environmental conditions\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Integron-type integrases facilitate genetic recombination and horizontal gene transfer, often observed in environments with high microbial interaction and variable conditions.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR014984\",\\n \"feature_label\": \"HopJ type III effector protein\",\\n \"bio_property\": \"pathogenesis * host-pathogen interaction\",\\n \"env_property\": \"biotic interactions * nutrient flux\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"The HopJ type III effector protein is involved in bacterial pathogenesis, indicating an environment with significant biotic interactions and nutrient flux.\"\\n },\\n \"4\": {\\n \"feature_id\": \"GO:0046797\",\\n \"feature_label\": \"viral procapsid maturation\",\\n \"bio_property\": \"virus assembly * viral replication\",\\n \"env_property\": \"high viral abundance * nutrient cycling\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Procapsid maturation is a pivotal step in viral replication, reflecting high viral activity and turnover within nutrient cycles in estuaries.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR028282\",\\n \"feature_label\": \"WASH complex subunit 7, central domain\",\\n \"bio_property\": \"actin cytoskeleton organization * endosomal trafficking\",\\n \"env_property\": \"dynamic sediment composition * pollutant presence\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"WASH complex is involved in actin cytoskeleton remodeling and might relate to the dynamic sediment and pollutant interactions prevalent in estuarine environments.\"\\n },\\n \"6\": {\\n \"feature_id\": \"sk__Bacteria;k__;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Candidatus_Pelagibacter;s__Candidatus_Pelagibacter_ubique\",\\n \"feature_label\": \"Pelagibacter ubique\",\\n \"bio_property\": \"oligotrophy * marine microbial loop\",\\n \"env_property\": \"nutrient-poor * oligotrophic conditions\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Pelagibacter ubique is a model organism for oligotrophy, thriving in nutrient-poor, oligotrophic conditions often found in clear estuarine waters.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717610473, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=692, prompt_tokens=753, total_tokens=1445))\n", + "ChatCompletion(id='chatcmpl-9Wud2ltQWIlye6WY4fNWNdH94AhIF', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Environmental:Aquatic:Estuary\": {\\n \"1\": {\\n \"feature_id\": \"IPR011802 * IPR011946\",\\n \"feature_label\": \"Adenylylsulphate reductase, beta subunit * Integrase, integron-type\",\\n \"bio_property\": \"sulfur metabolism * genetic recombination\",\\n \"env_property\": \"nutrient-rich * variable salinity\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Adenylylsulphate reductase is critical in sulfur metabolism, a common process in nutrient-rich environments like estuaries. Integron-type integrases facilitate genetic exchange, which can offer adaptive advantages in the highly variable salinity and nutrient conditions of estuaries.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0046797 * IPR014984\",\\n \"feature_label\": \"viral procapsid maturation * HopJ type III effector protein\",\\n \"bio_property\": \"viral life cycle * host-pathogen interaction\",\\n \"env_property\": \"high viral activity * microbial interactions\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"The occurrence of viral procapsid maturation suggests high viral activity, a common aspect in estuary ecosystems due to their dynamic microbial communities. The HopJ type III effector protein indicates active host-pathogen interactions, which align with the high biodiversity and microbial interactions prevalent in estuaries.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR028282 * sk__Bacteria;k__;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Candidatus_Pelagibacter;s__Candidatus_Pelagibacter_ubique\",\\n \"feature_label\": \"WASH complex subunit 7, central domain * Candidatus Pelagibacter ubique\",\\n \"bio_property\": \"cytoskeletal organization * abundant marine bacteria\",\\n \"env_property\": \"low nutrient availability\",\\n \"confidence\": \"high\",\\n \"explanation\": \"WASH complex subunit 7 is involved in cytoskeletal organization, important for maintaining cellular structure in complex environments. Candidatus Pelagibacter ubique is one of the most abundant marine bacteria, well-adapted to low nutrient conditions, which can also be found in estuarine environments.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631204, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=511, prompt_tokens=768, total_tokens=1279))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -4011,18 +4013,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Environmental:Aquatic:Estuary:Sediment\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -4055,7 +4057,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 11:\n", - "ChatCompletion(id='chatcmpl-9WpEyts3FIOMYpxx757quw8qBBMjG', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Environmental:Aquatic:Estuary:Sediment\": {\\n \"1\": {\\n \"feature_id\": \"GO:0005471\",\\n \"feature_label\": \"ATP:ADP antiporter activity\",\\n \"bio_property\": \"cellular energy transport * metabolic regulation\",\\n \"env_property\": \"dynamic environment * variable nutrient availability\",\\n \"confidence\": \"high\",\\n \"explanation\": \"ATP:ADP antiporters are crucial for maintaining energy homeostasis in environments with fluctuating nutrient levels.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR007343\",\\n \"feature_label\": \"Uncharacterised protein family, zinc metallopeptidase putative\",\\n \"bio_property\": \"proteolysis * metal ion binding\",\\n \"env_property\": \"metal-rich sediments\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Zinc metallopeptidases participate in protein degradation and are typically found in metal-rich environments where metal ions serve as cofactors.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR010518\",\\n \"feature_label\": \"Flagellar regulatory FleQ\",\\n \"bio_property\": \"motility regulation * signal transduction\",\\n \"env_property\": \"turbid water * variable oxygen levels\",\\n \"confidence\": \"high\",\\n \"explanation\": \"FleQ regulates flagellar synthesis, which is essential for motility in turbid, oxygen-variable estuary sediments.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR014984\",\\n \"feature_label\": \"HopJ type III effector protein\",\\n \"bio_property\": \"pathogenesis * host interaction\",\\n \"env_property\": \"biotic interactions * high microbial diversity\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Type III effector proteins, such as HopJ, are commonly associated with microbial pathogenesis and interactions within highly diverse microbial communities.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR021249\",\\n \"feature_label\": \"Protein of unknown function DUF2788\",\\n \"bio_property\": \"unknown function\",\\n \"env_property\": \"unknown\",\\n \"confidence\": \"unknown\",\\n \"explanation\": \"The protein function is currently unknown, preventing reliable association with specific environmental properties.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717610492, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=490, prompt_tokens=679, total_tokens=1169))\n", + "ChatCompletion(id='chatcmpl-9WudBV4Nu5SCYyvELPtbVCgDQToTg', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Environmental:Aquatic:Estuary:Sediment\": {\\n \"1\": {\\n \"feature_id\": \"GO:0005471 * IPR007343\",\\n \"feature_label\": \"ATP:ADP antiporter activity * Uncharacterised protein family, zinc metallopeptidase putative\",\\n \"bio_property\": \"energy metabolism * enzymatic activity * metal ion binding\",\\n \"env_property\": \"estuarine * nutrient cycling\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The ATP:ADP antiporter is integral to energy metabolism, which is crucial in nutrient-rich estuarine environments. The presence of zinc metallopeptidase indicates enzymatic activity essential for nutrient degradation and metal ion binding, common in sediment ecosystems.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR010518 * IPR014984 * IPR021249\",\\n \"feature_label\": \"Flagellar regulatory FleQ * HopJ type III effector protein * Protein of unknown function DUF2788\",\\n \"bio_property\": \"motility regulation * pathogenesis * protein interaction\",\\n \"env_property\": \"sediment * microbial community interaction\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"The Flagellar regulatory FleQ is involved in motility, essential for bacteria navigating sedimentary environments. HopJ type III effector proteins often play roles in pathogenesis and interactions within microbial communities, while the DUF2788 protein likely contributes to yet unidentified microbial functions within the sediment.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR007343 * IPR021249\",\\n \"feature_label\": \"Uncharacterised protein family, zinc metallopeptidase putative * Protein of unknown function DUF2788\",\\n \"bio_property\": \"enzymatic activity * metal ion binding * unknown function\",\\n \"env_property\": \"estuarine * metal-rich\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Zinc metallopeptidases play crucial roles in enzymatic activity, which is key in the nutrient-rich and often metal-rich environments found in estuarine sediments. Protein of unknown function DUF2788 suggests additional, unidentified roles that contribute to the complexity of this ecosystem.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631213, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=478, prompt_tokens=691, total_tokens=1169))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -4078,18 +4080,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Environmental:Aquatic:Freshwater:Lake\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -4119,7 +4121,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 12:\n", - "ChatCompletion(id='chatcmpl-9WpF9DNrYyeboTRcdS4GlpgMd2TeH', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Environmental:Aquatic:Freshwater:Lake\": {\\n \"1\": {\\n \"feature_id\": \"IPR026395\",\\n \"feature_label\": \"CshA domain\",\\n \"bio_property\": \"cold shock response * RNA chaperone activity\",\\n \"env_property\": \"low temperature\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The CshA domain is associated with cold shock proteins which help organisms survive and function under low-temperature conditions by preventing the formation of secondary RNA structures.\"\\n },\\n \"2\": {\\n \"feature_id\": \"sk__Bacteria;k__;p__Actinobacteria;c__Actinobacteria;o__Micrococcales;f__Microbacteriaceae;g__Candidatus_Limnoluna\",\\n \"feature_label\": \"Actinobacteria in genus Candidatus Limnoluna\",\\n \"bio_property\": \"organic matter degradation * nutrient cycling\",\\n \"env_property\": \"nutrient-rich\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Actinobacteria, particularly those in the genus Candidatus Limnoluna, are known for their role in breaking down complex organic molecules and cycling nutrients in freshwater ecosystems, indicating the presence of nutrient-rich conditions.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717610503, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=273, prompt_tokens=657, total_tokens=930))\n", + "ChatCompletion(id='chatcmpl-9WudICZRw8b02Wn6ZGixALifV2jYV', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Environmental:Aquatic:Freshwater:Lake\": {\\n \"1\": {\\n \"feature_id\": \"IPR026395 * sk__Bacteria;k__;p__Actinobacteria;c__Actinobacteria;o__Micrococcales;f__Microbacteriaceae;g__Candidatus_Limnoluna\",\\n \"feature_label\": \"CshA domain * Candidatus_Limnoluna\",\\n \"bio_property\": \"RNA helicase activity * cold shock response\",\\n \"env_property\": \"low temperature * freshwater\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The CshA domain is associated with cold shock proteins which are crucial for cold shock response. Actinobacteria, specifically Candidatus_Limnoluna, are often found in freshwater environments where temperature can vary significantly.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631220, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=185, prompt_tokens=670, total_tokens=855))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -4142,18 +4144,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Environmental:Aquatic:Freshwater:Lotic:Sediment\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -4184,7 +4186,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 13:\n", - "ChatCompletion(id='chatcmpl-9WpFEmxkoj4U9QfIXL7O5cjB7KsF9', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='Sure, given the specified features and their descriptions, here is an analysis of their relationships with the environmental properties of the Environmental:Aquatic:Freshwater:Lotic:Sediment ecosystem.\\n\\n**Feature Analysis and Relationships:**\\n\\n1. **Feature Identifier(s):** IPR004813\\n - **Feature Description(s):** Oligopeptide transporter, OPT superfamily\\n - **Bio_property:** Nutrient uptake * Peptide transport\\n - **Env_property:** Nutrient cycling * Organic matter decomposition\\n - **Confidence Level:** High\\n - **Brief Explanation:** The oligopeptide transporter (OPT) superfamily plays a crucial role in the absorption and transport of small peptides, which are significant for nutrient cycling and the decomposition of organic matter in sediment environments. These functions are essential for sustaining the microbial community and overall ecosystem health.\\n\\n2. **Feature Identifier(s):** IPR012657\\n - **Feature Description(s):** 23S rRNA-intervening sequence protein\\n - **Bio_property:** Ribosome function * Protein synthesis\\n - **Env_property:** High microbial activity * Rich in microbial biomass\\n - **Confidence Level:** Medium\\n - **Brief Explanation:** The presence of 23S rRNA-intervening sequence proteins indicates active ribosomal function and protein synthesis, which are indicative of high microbial activity and biomass in sedimentary environments. This relationship suggests a rich and diverse microbial community that can adapt to various environmental conditions.\\n\\n3. **Feature Identifier(s):** IPR022380\\n - **Feature Description(s):** Glutamyl-Q tRNA(Asp) synthetase\\n - **Bio_property:** Protein translation fidelity * Specialized aminoacyl-tRNA synthesis\\n - **Env_property:** Low nutrient availability * Stress adaptation\\n - **Confidence Level:** High\\n - **Brief Explanation:** Glutamyl-Q tRNA(Asp) synthetase is crucial for maintaining protein translation fidelity under various stress conditions, frequently observed in environments with low nutrient availability. This feature reflects the ability of microbial communities to adapt to and thrive in challenging environments by ensuring accurate protein synthesis under stress.\\n\\n```json\\n{\\n \"Environmental:Aquatic:Freshwater:Lotic:Sediment\": {\\n \"1\": {\\n \"feature_id\": \"IPR004813\",\\n \"feature_label\": \"Oligopeptide transporter, OPT superfamily\",\\n \"bio_property\": \"Nutrient uptake * Peptide transport\",\\n \"env_property\": \"Nutrient cycling * Organic matter decomposition\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The OPT superfamily plays a key role in nutrient uptake and peptide transport, crucial for nutrient cycling and organic matter decomposition in sediment.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR012657\",\\n \"feature_label\": \"23S rRNA-intervening sequence protein\",\\n \"bio_property\": \"Ribosome function * Protein synthesis\",\\n \"env_property\": \"High microbial activity * Rich in microbial biomass\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"The presence of 23S rRNA-intervening sequence proteins suggests high ribosomal function and protein synthesis, indicative of high microbial activity and biomass.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR022380\",\\n \"feature_label\": \"Glutamyl-Q tRNA(Asp) synthetase\",\\n \"bio_property\": \"Protein translation fidelity * Specialized aminoacyl-tRNA synthesis\",\\n \"env_property\": \"Low nutrient availability * Stress adaptation\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Glutamyl-Q tRNA(Asp) synthetase is essential for maintaining protein translation fidelity, reflecting microbial adaptation to low nutrient availability and stress.\"\\n }\\n }\\n}\\n```\\n\\nThis JSON output provides an organized and detailed analysis of each feature, explaining the relationship between microbial metagenomic features and the environmental properties of the lotic sediment ecosystem, with high and medium confidence levels.', role='assistant', function_call=None, tool_calls=None))], created=1717610508, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=823, prompt_tokens=665, total_tokens=1488))\n", + "ChatCompletion(id='chatcmpl-9WudLLWTX53JiT8ljNJCOyJZO3jxs', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Environmental:Aquatic:Freshwater:Lotic:Sediment\": {\\n \"1\": {\\n \"feature_id\": \"IPR004813 * IPR022380\",\\n \"feature_label\": \"Oligopeptide transporter, OPT superfamily * Glutamyl-Q tRNA(Asp) synthetase\",\\n \"bio_property\": \"nutrient transport * protein synthesis\",\\n \"env_property\": \"nutrient variable * fluctuating nutrient levels\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Oligopeptide transporters are critical in the uptake of peptides from the environment, essential in nutrient-variable conditions such as those found in lotic freshwater sediments. The presence of Glutamyl-Q tRNA(Asp) synthetase supports active protein synthesis, necessary for metabolic adaptation to fluctuating nutrient levels.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR012657\",\\n \"feature_label\": \"23S rRNA-intervening sequence protein\",\\n \"bio_property\": \"ribosomal function * gene regulation\",\\n \"env_property\": \"high microbial activity * sediment-associated microbial community\",\\n \"confidence\": \"high\",\\n \"explanation\": \"23S rRNA-intervening sequence proteins are involved in maintaining and modifying ribosomal function, which is crucial for high levels of microbial activity observed in sediment environments. These proteins reflect an adaptation to densely populated microbial communities within sediment layers.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631223, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=305, prompt_tokens=675, total_tokens=980))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -4207,18 +4209,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Environmental:Aquatic:Lentic:Brackish\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -4259,7 +4261,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 14:\n", - "ChatCompletion(id='chatcmpl-9WpFULhW0tJpBEufCM5wFNX4SxAPw', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Environmental:Aquatic:Lentic:Brackish\": {\\n \"1\": {\\n \"feature_id\": \"IPR007210 * GO:0031460\",\\n \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\\n \"bio_property\": \"osmoprotection * stress response\",\\n \"env_property\": \"marine * high salinity\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Glycine betaine is a known osmoprotectant in high osmolarity environments.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0043093 * IPR011735\",\\n \"feature_label\": \"FtsZ-dependent cytokinesis * WlaTC/HtrL glycosyltransferase\",\\n \"bio_property\": \"cell division * cell wall synthesis\",\\n \"env_property\": \"versatile nutrient sources * variable carbon availability\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"WlaTC/HtrL glycosyltransferase is involved in cell wall synthesis, which is crucial for cell division especially in variable carbon availability conditions.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR009677 * IPR020484 * IPR021239 * IPR025123\",\\n \"feature_label\": \"Protein of unknown function DUF1266 * Protein of unknown function DUF5503 * Protein of unknown function DUF2625 * Domain of unknown function DUF4049\",\\n \"bio_property\": \"unknown * potentially regulatory or structural proteins\",\\n \"env_property\": \"dynamic environmental conditions\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Domains of unknown function often indicate adaptive proteins, which can play a crucial role in responding to dynamic environmental conditions.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR028955 * IPR031834\",\\n \"feature_label\": \"Immunity protein 57 * Antitoxin RnlB/LsoB\",\\n \"bio_property\": \"bacterial immunity * toxin neutralization\",\\n \"env_property\": \"microbial competition * high bacterial diversity\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Immunity proteins and antitoxins are critical for survival in environments with high microbial competition, preventing self-toxicity and neutralizing toxins from other bacteria.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR000036\",\\n \"feature_label\": \"Peptidase A26, omptin\",\\n \"bio_property\": \"protein degradation * virulence\",\\n \"env_property\": \"high bacterial load\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Omptins are known for their role in protein degradation and virulence, which can be advantageous in environments with high bacterial loads and competition.\"\\n },\\n \"6\": {\\n \"feature_id\": \"IPR005126\",\\n \"feature_label\": \"NapC/NirT cytochrome c, N-terminal\",\\n \"bio_property\": \"electron transport * nitrate reduction\",\\n \"env_property\": \"variable redox conditions * rich organic matter\",\\n \"confidence\": \"high\",\\n \"explanation\": \"NapC/NirT cytochrome c are involved in electron transport and nitrate reduction, which are essential processes in environments with variable redox conditions and rich organic matter.\"\\n },\\n \"7\": {\\n \"feature_id\": \"IPR023870\",\\n \"feature_label\": \"Poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA\",\\n \"bio_property\": \"biofilm formation * cell adhesion\",\\n \"env_property\": \"sediment stability * nutrient trapping\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Biofilm formation and cell adhesion facilitated by PgaA can contribute to sediment stability and efficient nutrient trapping in brackish environments.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717610524, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=825, prompt_tokens=804, total_tokens=1629))\n", + "ChatCompletion(id='chatcmpl-9WudQPk1PYhAx6nLTTuY3v229VPs7', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Environmental:Aquatic:Lentic:Brackish\": {\\n \"1\": {\\n \"feature_id\": \"GO:0017148 * GO:0043093\",\\n \"feature_label\": \"negative regulation of translation * FtsZ-dependent cytokinesis\",\\n \"bio_property\": \"cell cycle control * protein synthesis regulation * cell division\",\\n \"env_property\": \"fluctuating nutrient levels\",\\n \"confidence\": \"high\",\\n \"explanation\": \"In brackish waters with fluctuating nutrient levels, there might be a need for stringent cell cycle control and protein synthesis regulation to optimize resource usage and division timing.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR000036 * IPR025123\",\\n \"feature_label\": \"Peptidase A26, omptin * Domain of unknown function DUF4049\",\\n \"bio_property\": \"protein degradation * stress response\",\\n \"env_property\": \"variable salinity\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Omptin peptidases are known to be involved in stress responses, which would be crucial in brackish environments with fluctuating salinity. Domain DUF4049 might also be implicated in stress-related functions.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR005126 * IPR011735\",\\n \"feature_label\": \"NapC/NirT cytochrome c, N-terminal * WlaTC/HtrL glycosyltransferase\",\\n \"bio_property\": \"electron transport * glycosylation processes\",\\n \"env_property\": \"low oxygen levels\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"NapC/NirT cytochrome c proteins are essential for electron transport in low oxygen conditions, common in lentic brackish environments. Glycosyltransferases like WlaTC/HtrL could play roles in modifying proteins for optimal function under these conditions.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR023870 * IPR028955\",\\n \"feature_label\": \"Poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA * Immunity protein 57\",\\n \"bio_property\": \"biofilm formation * antimicrobial resistance\",\\n \"env_property\": \"microbial community interactions\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Biofilms provide structural integrity and protection in brackish environments, supporting diverse microbial communities. Immunity proteins contribute to the defense against competing organisms or phages.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR031834\",\\n \"feature_label\": \"Antitoxin RnlB/LsoB\",\\n \"bio_property\": \"toxin-antitoxin systems\",\\n \"env_property\": \"variable pH\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Toxin-antitoxin systems help bacteria survive harsh conditions, such as variable pH levels found in brackish waters, by regulating cell death and survival.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631228, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=642, prompt_tokens=816, total_tokens=1458))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -4282,18 +4284,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Environmental:Aquatic:Marine\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -4358,7 +4360,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 15:\n", - "ChatCompletion(id='chatcmpl-9WpFjAHdGKk6GrKu2juEM8dYhyB9m', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Environmental:Aquatic:Marine\": {\\n \"1\": {\\n \"feature_id\": \"GO:0031460 * IPR007210\",\\n \"feature_label\": \"glycine betaine transport * Glycine betaine/proline betaine transport system ATP-binding protein ProV-like\",\\n \"bio_property\": \"osmoprotection * stress response\",\\n \"env_property\": \"marine * high salinity\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Glycine betaine is a known osmoprotectant used by organisms to maintain osmotic balance in high salinity environments typically encountered in marine settings.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0004037 * GO:0008743 * IPR010036\",\\n \"feature_label\": \"allantoicase activity * L-threonine 3-dehydrogenase activity * Magnesium-dependent phosphatase-1, eukaryotic/archaeal type\",\\n \"bio_property\": \"nitrogen metabolism * amino acid metabolism\",\\n \"env_property\": \"marine * nitrogen cycling\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Allantoicase and L-threonine 3-dehydrogenase are enzymes involved in nitrogen metabolism and amino acid pathways which are crucial for nutrient cycling in marine environments. The magnesium-dependent phosphatase-1 is also involved in these metabolic processes.\"\\n },\\n \"3\": {\\n \"feature_id\": \"GO:0018551 * IPR011802 * IPR007037\",\\n \"feature_label\": \"dissimilatory sulfite reductase activity * Adenylylsulphate reductase, beta subunit * Siderophore-interacting protein, C-terminal domain\",\\n \"bio_property\": \"sulfur metabolism * iron acquisition\",\\n \"env_property\": \"marine * sulfate-rich * iron-limited\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Dissimilatory sulfite reductase and adenylylsulphate reductase are key enzymes in sulfur metabolism, transforming sulfate to sulfide in sulfate-rich marine environments. Siderophore-interacting proteins are involved in iron acquisition, critical in iron-limited marine settings.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR016300 * IPR011868\",\\n \"feature_label\": \"Arsenical pump ATPase, ArsA/GET3 * Molybdate ABC transporter, ATP-binding protein\",\\n \"bio_property\": \"heavy metal resistance * detoxification\",\\n \"env_property\": \"marine * heavy metal presence * pollutant presence\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The arsenical pump ATPase and molybdate ABC transporter are linked to heavy metal resistance and detoxification, processes essential in marine ecosystems where pollutants and heavy metals are often present.\"\\n },\\n \"5\": {\\n \"feature_id\": \"GO:0004638 * IPR006322\",\\n \"feature_label\": \"phosphoribosylaminoimidazole carboxylase activity * Glutathione reductase, eukaryote/bacterial\",\\n \"bio_property\": \"purine biosynthesis * oxidative stress response\",\\n \"env_property\": \"marine * oxidative environments\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Phosphoribosylaminoimidazole carboxylase is part of purine biosynthesis, which is fundamental for cellular functions. Glutathione reductase plays a crucial role in maintaining redox balance, which is vital in marine environments with varying oxidative stresses.\"\\n }\\n }\\n}\\n```\\n', role='assistant', function_call=None, tool_calls=None))], created=1717610539, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=757, prompt_tokens=1212, total_tokens=1969))\n", + "ChatCompletion(id='chatcmpl-9WudZ59vVsOevHTyF7JaYVqEWaJz4', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='Given the observed features in the Environmental:Aquatic:Marine ecosystem, let us identify and explain relationships between these features and the environmental properties of the marine ecosystem.\\n\\n```json\\n{\\n \"Environmental:Marine\": {\\n \"1\": {\\n \"feature_id\": \"GO:0031460 * IPR004681\",\\n \"feature_label\": \"glycine betaine transport * TRAP transporter large membrane protein DctM\",\\n \"bio_property\": \"osmoprotection * transporter activity\",\\n \"env_property\": \"marine * high salinity\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Glycine betaine is transported through membrane proteins like DctM which aids in osmoprotection under high salinity conditions typical of marine environments.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR003563 * GO:0004638\",\\n \"feature_label\": \"Oxidized purine nucleoside triphosphate * phosphoribosylaminoimidazole carboxylase activity\",\\n \"bio_property\": \"nucleotide metabolism * DNA repair\",\\n \"env_property\": \"marine * UV exposure\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Marine environments typically have high UV exposure, which can lead to DNA damage. Enzymes involved in DNA repair and nucleotide metabolism help to mitigate this damage.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR007037 * GO:0018551\",\\n \"feature_label\": \"Siderophore-interacting protein, C-terminal domain * dissimilatory sulfite reductase activity\",\\n \"bio_property\": \"iron acquisition * sulfur metabolism\",\\n \"env_property\": \"marine * anoxic zones\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Sulfite reductase and siderophore-interacting proteins are crucial for iron and sulfur metabolism in anoxic zones often found in marine environments.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR011802 * GO:0018551\",\\n \"feature_label\": \"Adenylylsulphate reductase, beta subunit * dissimilatory sulfite reductase activity\",\\n \"bio_property\": \"sulfur metabolism\",\\n \"env_property\": \"marine * anoxic zones\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Both adenylylsulfate reductase and dissimilatory sulfite reductase are involved in sulfur metabolism, which is particularly important in anoxic marine zones.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR008557 * IPR010036\",\\n \"feature_label\": \"Alkaline phosphatase PhoX * Magnesium-dependent phosphatase-1, eukaryotic/archaeal-type\",\\n \"bio_property\": \"phosphatase activity * nutrient cycling\",\\n \"env_property\": \"marine * phosphorous limitation\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Phosphatases like PhoX and magnesium-dependent phosphatase play roles in nutrient cycling in marine environments, which are often limited by phosphorus.\"\\n },\\n \"6\": {\\n \"feature_id\": \"IPR014931 * IPR017813\",\\n \"feature_label\": \"Protein of unknown function DUF1805 * Mycothiol acetyltransferase\",\\n \"bio_property\": \"detoxification * unknown\",\\n \"env_property\": \"marine * pollution\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"The presence of mycothiol acetyltransferase suggests a role in detoxification which may be necessary in marine environments affected by pollution.\"\\n },\\n \"7\": {\\n \"feature_id\": \"IPR011868 * sk__Bacteria;k__;p__Chloroflexi;c__Thermoflexia;o__Thermoflexales;f__Thermoflexaceae;g__Thermoflexus\",\\n \"feature_label\": \"Molybdate ABC transporter, ATP-binding protein * Chloroflexi (Thermoflexia)\",\\n \"bio_property\": \"heavy metal transport * thermophilic adaptation\",\\n \"env_property\": \"marine * hydrothermal vents\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Molybdate transporters and thermophilic Chloroflexi are often found in hydrothermal vents, which are rich in heavy metals and temperature variations.\"\\n }\\n }\\n}\\n```\\n\\nThese results identify relationships between observed microscopic features and the environmental characteristics of marine ecosystems, supported by high or medium confidence level explanations based on known biological and environmental properties.', role='assistant', function_call=None, tool_calls=None))], created=1717631237, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=957, prompt_tokens=1228, total_tokens=2185))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -4381,18 +4383,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Environmental:Aquatic:Marine:Hydrothermal vents\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -4425,7 +4427,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 16:\n", - "ChatCompletion(id='chatcmpl-9WpG0kAndEeu5y4gDSpYG5Ub1uUDI', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='Here is the JSON output structured to include detailed and reliable information about the relationships between the observed features and the environmental properties of the Environmental:Aquatic:Marine:Hydrothermal vents ecosystem.\\n\\n```json\\n{\\n \"Environmental:Aquatic:Marine:Hydrothermal vents\": {\\n \"1\": {\\n \"feature_id\": \"GO:0018551\",\\n \"feature_label\": \"dissimilatory sulfite reductase activity\",\\n \"bio_property\": \"sulfur metabolism * energy acquisition\",\\n \"env_property\": \"high temperature * high pressure * high sulfur concentration * reduced oxygen levels\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Dissimilatory sulfite reductase activity is critical for sulfur metabolizing organisms found in sulfur-rich hydrothermal vent environments.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR002723\",\\n \"feature_label\": \"N(4)-bis(aminopropyl)spermidine synthase, C-terminal\",\\n \"bio_property\": \"polyamine synthesis * stress response\",\\n \"env_property\": \"extreme conditions * variable temperature * nutrient variability\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Polyamines like spermidine contribute to cellular stability and stress resistance, essential in fluctuating and extreme hydrothermal vent environments.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR007445\",\\n \"feature_label\": \"Type IV pilus inner membrane component PilO\",\\n \"bio_property\": \"motility * adhesion * biofilm formation\",\\n \"env_property\": \"high pressure * variable substrate * thermal gradients\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Type IV pili are involved in adherence to surfaces and motility, which are essential for colonization and survival in the diverse and variable substrates of hydrothermal vents.\"\\n },\\n \"4\": {\\n \"feature_id\": \"sk__Bacteria;k__;p__Aquificae;c__Aquificae;o__Desulfurobacteriales;f__Desulfurobacteriaceae;g__Desulfurobacterium\",\\n \"feature_label\": \"Desulfurobacterium genus\",\\n \"bio_property\": \"thermophily * sulfur reduction * chemolithoautotrophy\",\\n \"env_property\": \"high temperature * high sulfur concentration * reduced oxygen levels\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Members of the Desulfurobacterium genus thrive in high-temperature environments and utilize sulfur compounds as electron acceptors, common in hydrothermal vents.\"\\n },\\n \"5\": {\\n \"feature_id\": \"sk__Eukaryota;k__Metazoa;p__Annelida;c__Polychaeta;o__Terebellida\",\\n \"feature_label\": \"Terebellida order\",\\n \"bio_property\": \"filter feeding * burrowing * symbiotic relationships\",\\n \"env_property\": \"particulate matter availability * substrate variability * chemical gradients\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Polychaetes, particularly those in the Terebellida order, are adapted to the deposit of particulate matter and establish symbiotic relationships with microorganisms in hydrothermal vent environments.\"\\n }\\n }\\n}\\n```\\n\\n### Relationships Explained\\n\\n**Dissimilatory sulfite reductase activity (GO:0018551):**\\n- **Biological Properties:** Sulfur metabolism and energy acquisition.\\n- **Environmental Properties:** High temperature, high pressure, high sulfur concentration, and reduced oxygen levels.\\n- **Explanation:** Hydrothermal vents are rich in sulfur compounds. Organisms leveraging dissimilatory sulfite reductase activity can reduce sulfur compounds to derive energy, helping them thrive in the vent ecosystem.\\n\\n**N(4)-bis(aminopropyl)spermidine synthase, C-terminal (IPR002723):**\\n- **Biological Properties:** Polyamine synthesis, stress response.\\n- **Environmental Properties:** Extreme conditions, variable temperature, nutrient variability.\\n- **Explanation:** Hydrothermal vent ecosystems experience extreme and fluctuating conditions. Polyamines like spermidine stabilize cellular structures and are involved in stress responses, aiding microbial survival.\\n\\n**Type IV pilus inner membrane component PilO (IPR007445):**\\n- **Biological Properties:** Motility, adhesion, biofilm formation.\\n- **Environmental Properties:** High pressure, variable substrate, thermal gradients.\\n- **Explanation:** Type IV pili are crucial for bacterial motility and adhesion, facilitating colonization and biofilm formation on diverse surfaces in high-pressure, thermally varied hydrothermal vent environments.\\n\\n**Desulfurobacterium genus (sk__Bacteria;k__;p__Aquificae;c__Aquificae;o__Desulfurobacteriales;f__Desulfurobacteriaceae;g__Desulfurobacterium):**\\n- **Biological Properties:** Thermophily, sulfur reduction, chemolithoautotrophy.\\n- **Environmental Properties:** High temperature, high sulfur concentration, reduced oxygen levels.\\n- **Explanation:** Desulfurobacterium species are adapted to high-temperature and sulfur-rich environments of hydrothermal vents, utilizing sulfur compounds for energy in oxygen-poor conditions.\\n\\n**Terebellida order (sk__Eukaryota;k__Metazoa;p__Annelida;c__Polychaeta;o__Terebellida):**\\n- **Biological Properties:** Filter feeding, burrowing, symbiotic relationships.\\n- **Environmental Properties:** Particulate matter availability, substrate variability, chemical gradients.\\n- **Explanation:** Polychaetes of the Terebellida order utilize available particulate matter for nutrition and have adapted to the varied substrates and chemical environments found in hydrothermal vents. They may also engage in symbiotic relationships with vent microorganisms.', role='assistant', function_call=None, tool_calls=None))], created=1717610556, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=1188, prompt_tokens=741, total_tokens=1929))\n", + "ChatCompletion(id='chatcmpl-9Wudmq44fbZ79Tn8V6Xs7ph7RS23p', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='Here is the JSON output structure based on the observed features in the Environmental:Aquatic:Marine:Hydrothermal vents ecosystem.\\n\\n```json\\n{\\n \"Environmental:Aquatic:Marine:Hydrothermal vents\": {\\n \"1\": {\\n \"feature_id\": \"GO:0018551\",\\n \"feature_label\": \"dissimilatory sulfite reductase activity\",\\n \"bio_property\": \"sulfur metabolism\",\\n \"env_property\": \"high sulfur content\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Dissimilatory sulfite reductase is an enzyme involved in the reduction of sulfite to sulfide, which is crucial in environments with high sulfur content such as hydrothermal vents.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR002723\",\\n \"feature_label\": \"N(4)-bis(aminopropyl)spermidine synthase, C-terminal\",\\n \"bio_property\": \"polyamine biosynthesis\",\\n \"env_property\": \"extreme conditions\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Polyamines help stabilize DNA and proteins under extreme conditions, an adaptation seen in organisms living in harsh environments like hydrothermal vents.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR007445\",\\n \"feature_label\": \"Type IV pilus inner membrane component PilO\",\\n \"bio_property\": \"surface attachment, motility\",\\n \"env_property\": \"high temperature, high pressure\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Type IV pili are involved in surface attachment and motility which are essential for microbial colonization in the harsh conditions of hydrothermal vents characterized by high temperatures and pressures.\"\\n },\\n \"4\": {\\n \"feature_id\": \"sk__Bacteria;k__;p__Aquificae;c__Aquificae;o__Desulfurobacteriales;f__Desulfurobacteriaceae;g__Desulfurobacterium\",\\n \"feature_label\": \"Desulfurobacterium (Bacteria; Aquificae; Desulfurobacteriales)\",\\n \"bio_property\": \"sulfur reduction\",\\n \"env_property\": \"anaerobic, high sulfur\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Desulfurobacterium is known for its sulfur-reducing capabilities, making it well-suited for anaerobic environments rich in sulfur, such as hydrothermal vents.\"\\n },\\n \"5\": {\\n \"feature_id\": \"sk__Eukaryota;k__Metazoa;p__Annelida;c__Polychaeta;o__Terebellida\",\\n \"feature_label\": \"Polychaeta (e.g., Annelida; Polychaeta; Terebellida)\",\\n \"bio_property\": \"adaptation to hypoxic conditions\",\\n \"env_property\": \"hypoxic, high pressure\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Members of Polychaeta, such as Terebellida, are adapted to hypoxic conditions, which are typical of deep-sea hydrothermal vent ecosystems.\"\\n }\\n }\\n}\\n```\\n\\n### Explanation:\\n- **GO:0018551 - dissimilatory sulfite reductase activity**: Relates to sulfur metabolism in high sulfur content environments, typical of hydrothermal vents.\\n \\n- **IPR002723 - N(4)-bis(aminopropyl)spermidine synthase, C-terminal**: Associated with polyamine biosynthesis which stabilizes cells under extreme environmental conditions.\\n \\n- **IPR007445 - Type IV pilus inner membrane component PilO**: Facilitates microbial surface attachment and motility in high-temperature and high-pressure environments of hydrothermal vents.\\n \\n- **sk__Bacteria;k__;p__Aquificae;c__Aquificae;o__Desulfurobacteriales;f__Desulfurobacteriaceae;g__Desulfurobacterium**: Desulfurising bacteria that thrive in anaerobic, sulfur-rich environments like hydrothermal vents.\\n \\n- **sk__Eukaryota;k__Metazoa;p__Annelida;c__Polychaeta;o__Terebellida**: Annelida adapted to hypoxic and high-pressure conditions, as found in hydrothermal vent ecosystems.\\n\\nThis comprehensive analysis uses identifiers and contextual knowledge to explain the interplay between microbial and environmental properties, ensuring reliable inferences.', role='assistant', function_call=None, tool_calls=None))], created=1717631250, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=920, prompt_tokens=752, total_tokens=1672))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -4448,18 +4450,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Environmental:Aquatic:Marine:Intertidal zone:Coral reef\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -4493,7 +4495,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 17:\n", - "ChatCompletion(id='chatcmpl-9WpGQAKKNtp1dHUSKIZirGfjXilFk', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Environmental:Aquatic:Marine:Intertidal zone:Coral reef\": {\\n \"1\": {\\n \"feature_id\": \"GO:0004114 * IPR001320\",\\n \"feature_label\": \"3\\',5\\'-cyclic-nucleotide phosphodiesterase activity * Ionotropic glutamate receptor, C-terminal\",\\n \"bio_property\": \"signal transduction * ion transport\",\\n \"env_property\": \"variable light * varying nutrient availability\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Signal transduction and ion transport are critical for organisms in environments with fluctuating light and nutrient conditions, common in coral reefs.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR000263 * IPR003514\",\\n \"feature_label\": \"Geminivirus AR1/BR1 coat protein * Microviridae F protein\",\\n \"bio_property\": \"viral replication * host-pathogen interactions\",\\n \"env_property\": \"high biodiversity * varying pathogen load\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"The presence of viral proteins suggests a high level of viral-host interactions, which are influenced by the high biodiversity and pathogen load in coral reefs.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR033762 * sk__Eukaryota;k__;p__;c__Dinophyceae;o__Suessiales;f__Symbiodiniaceae;g__Symbiodinium\",\\n \"feature_label\": \"MCM OB domain * Dinoflagellates (Symbiodinium)\",\\n \"bio_property\": \"DNA replication * symbiosis\",\\n \"env_property\": \"high solar radiation * variable nutrient levels\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Dinoflagellates like Symbiodinium are symbionts in coral reefs, contributing to their energy needs through photosynthesis. DNA replication is crucial for their rapid growth in response to high solar radiation.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717610582, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=418, prompt_tokens=737, total_tokens=1155))\n", + "ChatCompletion(id='chatcmpl-9Wue1wFrYkZxxrSHKbhpSf671w3Vh', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Environmental:Aquatic:Marine:Intertidal zone:Coral reef\": {\\n \"1\": {\\n \"feature_id\": \"GO:0004114 * IPR000263\",\\n \"feature_label\": \"3\\',5\\'-cyclic-nucleotide phosphodiesterase activity * Geminivirus AR1/BR1 coat protein\",\\n \"bio_property\": \"signal transduction * viral infection\",\\n \"env_property\": \"high nutrient cycling * presence of viral pathogens\",\\n \"confidence\": \"high\",\\n \"explanation\": \"3\\',5\\'-cyclic-nucleotide phosphodiesterase activity is involved in breaking down cAMP which is crucial in signal transduction and nutrient cycling. Geminivirus AR1/BR1 coat proteins indicate the presence of viruses, which can infect both algae and corals, affecting the overall health of the reef ecosystem.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR001320 * IPR033762\",\\n \"feature_label\": \"Ionotropic glutamate receptor, C-terminal * MCM OB domain\",\\n \"bio_property\": \"neuronal signaling * DNA replication\",\\n \"env_property\": \"complex habitat structure * high biodiversity\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Ionotropic glutamate receptors are implicated in neuronal signaling, crucial in higher organisms\\' interaction within the habitat. MCM OB domain is found in proteins involved in DNA replication, indicating high cellular activity which correlates with the complex and biodiverse nature of coral reefs.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR003514 * sk__Eukaryota;k__;p__;c__Dinophyceae;o__Suessiales;f__Symbiodiniaceae;g__Symbiodinium\",\\n \"feature_label\": \"Microviridae F protein * Symbiodinium genus\",\\n \"bio_property\": \"viral assembly * symbiosis\",\\n \"env_property\": \"presence of viruses * mutualistic relationships * high sunlight exposure\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Microviridae F protein is a critical component of viral assembly, suggesting the presence of viruses in coral reefs. Symbiodinium (a genus of dinoflagellates) is involved in mutualistic relationships with coral, essential for nutrient exchange and high productivity in sunlight-rich environments.\"\\n }\\n }\\n}\\n```\\n\\n### Explanation:\\n1. **Feature: GO:0004114 (3\\',5\\'-cyclic-nucleotide phosphodiesterase activity) and IPR000263 (Geminivirus AR1/BR1 coat protein)**\\n - **Bio_property**: The involvement of 3\\',5\\'-cyclic-nucleotide phosphodiesterase in signal transduction highlights nutrient cycling processes. The Geminivirus AR1/BR1 coat protein indicates viral infection pathways.\\n - **Env_property**: The Coral reefs are high in nutrient cycling due to constant balance between organisms. The presence of viral pathogens often impacts the health and balance of the ecosystem.\\n - **Explanation**: These features highlight the dynamic nutrient cycles and the impact of viral presence on coral reef ecosystems.\\n\\n2. **Feature: IPR001320 (Ionotropic glutamate receptor, C-terminal) and IPR033762 (MCM OB domain)**\\n - **Bio_property**: Ionotropic glutamate receptors are essential for neuronal signaling, an indicator of complex organismal interactions. MCM OB domain\\'s role in DNA replication suggests high cellular proliferation.\\n - **Env_property**: Coral reefs are known for their complex habitat structure and high biodiversity.\\n - **Explanation**: These features represent the intricate ecological interactions and cellular activities that define coral reef environments.\\n\\n3. **Feature: IPR003514 (Microviridae F protein) and sk__Eukaryota;k__;p__;c__Dinophyceae;o__Suessiales;f__Symbiodiniaceae;g__Symbiodinium**\\n - **Bio_property**: The Microviridae F protein indicates viral assembly processes. Symbiodinium genus suggests symbiosis, critical for reef health.\\n - **Env_property**: The presence of viruses, mutualistic symbiotic relationships, and high levels of sunlight exposure are characteristic of coral reef environments.\\n - **Explanation**: These features indicate the presence of viruses and essential symbiotic relationships that contribute to the productivity and resilience of coral reefs.\\n\\nBy examining these relationships, we gain a more comprehensive understanding of the interplay between microbial features and environmental properties in coral reef ecosystems.', role='assistant', function_call=None, tool_calls=None))], created=1717631265, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=937, prompt_tokens=744, total_tokens=1681))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -4516,18 +4518,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Environmental:Aquatic:Marine:Intertidal zone:Estuary\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -4567,7 +4569,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 18:\n", - "ChatCompletion(id='chatcmpl-9WpGbGEKa7tc3ZdP6dUQ1C0kMvxdi', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='Sure, let\\'s organize and summarize the observed features and infer their relationships with the environmental properties of the specific ecosystem. Below is a JSON structure containing several examples of features and their relationships to the Environmental:Aquatic:Marine:Intertidal zone:Estuary ecosystem:\\n\\n```json\\n{\\n \"Environmental:Aquatic:Marine:Intertidal zone:Estuary\": {\\n \"1\": {\\n \"feature_id\": \"IPR004763 * IPR021552\",\\n \"feature_label\": \"Cation efflux system CzcA/CusA/SilA/NccA/HelA/CnrA * Putative, 10TM heavy-metal exporter\",\\n \"bio_property\": \"metal ion transport * detoxification\",\\n \"env_property\": \"high metal concentrations * pollution\",\\n \"confidence\": \"high\",\\n \"explanation\": \"These features are related to the transport and removal of heavy metals, suggesting an adaptation to environments with high metal concentrations and possible pollution.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR017559\",\\n \"feature_label\": \"Alkyl hydroperoxide reductase subunit C\",\\n \"bio_property\": \"oxidative stress response * detoxification\",\\n \"env_property\": \"high oxygen levels * oxidative stress\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Alkyl hydroperoxide reductase is involved in the reduction of peroxides, indicating an adaptation to environments with oxidative stress.\"\\n },\\n \"3\": {\\n \"feature_id\": \"GO:0046797\",\\n \"feature_label\": \"viral procapsid maturation\",\\n \"bio_property\": \"viral infection * capsid assembly\",\\n \"env_property\": \"presence of viral pathogens * microbial interactions\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"The presence of viral procapsid maturation involves viral infection processes, suggesting an environment with active viral-microbial interactions.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR001360\",\\n \"feature_label\": \"Glycoside hydrolase family 1\",\\n \"bio_property\": \"carbohydrate metabolism * degradation of polysaccharides\",\\n \"env_property\": \"high organic matter * nutrient cycling\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Glycoside hydrolase enzymes break down complex sugars, indicating the presence of organic matter and active nutrient cycling within the ecosystem.\"\\n },\\n \"5\": {\\n \"feature_id\": \"sk__Bacteria;k__;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Candidatus_Pelagibacter;s__Candidatus_Pelagibacter_ubique\",\\n \"feature_label\": \"Candidatus Pelagibacter ubique\",\\n \"bio_property\": \"photoheterotrophy * organic carbon utilization\",\\n \"env_property\": \"nutrient-poor * stable marine environment\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Candidatus Pelagibacter ubique is known for their ability to utilize dissolved organic carbon in nutrient-poor marine environments, indicative of specific stable estuarine conditions.\"\\n },\\n \"6\": {\\n \"feature_id\": \"IPR017813\",\\n \"feature_label\": \"Mycothiol acetyltransferase\",\\n \"bio_property\": \"mycothiol biosynthesis * redox regulation\",\\n \"env_property\": \"variable nutrient conditions * fluctuating redox states\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Presence of mycothiol biosynthesis suggests adaptation to varying nutrient and redox conditions in the estuarine ecosystem.\"\\n }\\n }\\n}\\n```\\n\\n**Key Points:**\\n\\n1. **Metal ion transport and detoxification**: Presence of heavy metal transport systems is highly correlated with environments featuring high metal concentrations.\\n2. **Oxidative stress response**: Enzymes involved in reducing oxidative stress indicate adaptation to areas with high oxygen levels.\\n3. **Viral processes**: Activities related to viral capsid formation suggest environmental interactions involving viruses.\\n4. **Carbohydrate metabolism**: Glycoside hydrolases point to a high organic matter content and active nutrient cycling within the ecosystem.\\n5. **Specific microbial taxa**: Special adaptations like those seen in \"Candidatus Pelagibacter ubique\" include utilization of organic carbon in nutrient-poor conditions.\\n6. **Redox regulation**: Enzymes like mycothiol acetyltransferase indicate adaptation to fluctuating redox conditions.\\n\\nEach of these inferences serves to illuminate how specific molecular and biological functions of microbes are directly influenced by their environmental properties in the described estuarine ecosystem.', role='assistant', function_call=None, tool_calls=None))], created=1717610593, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=983, prompt_tokens=865, total_tokens=1848))\n", + "ChatCompletion(id='chatcmpl-9WueGQr95eCxKE2NCUQTwZm9YN2iD', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Environmental:Aquatic:Marine:Intertidal zone:Estuary\": {\\n \"1\": {\\n \"feature_id\": \"GO:0046797 * IPR017559\",\\n \"feature_label\": \"Viral procapsid maturation * Alkyl hydroperoxide reductase subunit C\",\\n \"bio_property\": \"viral lifecycle * oxidative stress response\",\\n \"env_property\": \"variable salinity * high UV exposure\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Viral procapsid maturation is essential in viral lifecycles occurring in estuaries, which often have fluctuating salinity. Alkyl hydroperoxide reductase is involved in reducing oxidative stress, an important response to high UV exposure typical of intertidal zones.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR001360 * IPR004763 * IPR017813\",\\n \"feature_label\": \"Glycoside hydrolase family 1 * Cation efflux system CzcA/CusA/SilA/NccA/HelA/CnrA * Mycothiol acetyltransferase\",\\n \"bio_property\": \"carbohydrate metabolism * heavy metal resistance * mycothiol biosynthesis\",\\n \"env_property\": \"organic matter enrichment * heavy metal contamination\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Glycoside hydrolases participate in the breakdown of complex carbohydrates, prevalent in estuaries due to organic matter enrichment. The cation efflux system is crucial for heavy metal resistance, often necessary in estuaries with varying levels of pollutant contamination. Mycothiol biosynthesis is another adaptive response to oxidative and chemically stressful conditions.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR002723 * IPR017813\",\\n \"feature_label\": \"N(4)-bis(aminopropyl)spermidine synthase, C-terminal * Mycothiol acetyltransferase\",\\n \"bio_property\": \"polyamine biosynthesis * mycothiol biosynthesis\",\\n \"env_property\": \"high bacterial activity\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Both polyamine biosynthesis and mycothiol biosynthesis are indicative of high microbial activity and stress adaptation, common in nutrient-rich and bacteria-dense environments like estuarine intertidal zones.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR014580 * IPR014931\",\\n \"feature_label\": \"Uncharacterised conserved protein UCP033199 * Protein of unknown function DUF1805\",\\n \"bio_property\": \"unknown specific function but likely involved in stress response or general metabolic activity\",\\n \"env_property\": \"varied environmental conditions\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"The presence of uncharacterized proteins often correlates with organisms adapted to varied and fluctuating conditions, such as those in estuarine environments.\"\\n },\\n \"5\": {\\n \"feature_id\": \"sk__Bacteria;k__;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Candidatus_Pelagibacter;s__Candidatus_Pelagibacter_ubique * IPR026395\",\\n \"feature_label\": \"Candidatus Pelagibacter ubique * CshA domain\",\\n \"bio_property\": \"high competitive fitness * cold-shock adaptation\",\\n \"env_property\": \"seasonal temperature fluctuations\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Candidatus Pelagibacter ubique is known for its competitive fitness in nutrient-limited environments, aligned with the dynamic nutrient deposition found in estuaries. The CshA domain is associated with cold-shock adaptation, relevant to the temperature variability in intertidal zones.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631280, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_aa87380ac5', usage=CompletionUsage(completion_tokens=818, prompt_tokens=873, total_tokens=1691))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -4590,18 +4592,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Environmental:Aquatic:Marine:Oceanic\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -4646,7 +4648,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 19:\n", - "ChatCompletion(id='chatcmpl-9WpGvqQpbeyADCXir3n6wcLXgW6Up', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='Here is the detailed JSON output with the required results:\\n\\n```json\\n{\\n \"Environmental:Aquatic:Marine:Oceanic\": {\\n \"1\": {\\n \"feature_id\": \"GO:0031460 * IPR007210\",\\n \"feature_label\": \"glycine betaine transport * Glycine betaine/proline betaine transport system ATP-binding protein ProV-like\",\\n \"bio_property\": \"osmoprotection * stress response\",\\n \"env_property\": \"marine * high salinity\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Glycine betaine is a known osmoprotectant in high osmolarity environments, and its transport is vital for organism survival in marine environments with high salinity.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR010518 * IPR032830\",\\n \"feature_label\": \"Flagellar regulatory FleQ * Helicase XPB/Ssl2, N-terminal domain\",\\n \"bio_property\": \"motility * DNA repair\",\\n \"env_property\": \"high nutrient turnover * moderate UV exposure\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"The flagellar regulatory protein and helicase are associated with motility and genomic integrity, respectively. Both properties are essential in environments with high nutrient turnover where movement is necessary and moderate UV exposure likely causing DNA damage requires efficient repair mechanisms.\"\\n },\\n \"3\": {\\n \"feature_id\": \"GO:0004114 * IPR025479\",\\n \"feature_label\": \"3\\',5\\'-cyclic-nucleotide phosphodiesterase activity * Domain of unknown function DUF4329\",\\n \"bio_property\": \"signal transduction * unknown\",\\n \"env_property\": \"variable extracellular signals * high environmental diversity\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"The 3\\',5\\'-cyclic-nucleotide phosphodiesterase activity suggests involvement in signal transduction processes, which is crucial in an environment with variable extracellular signals and high diversity. The associated domain of unknown function (DUF4329) might indicate a yet unidentified role in adapting to such an environment.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR000938 * GO:0006928\",\\n \"feature_label\": \"CAP Gly-rich domain * obsolete movement of cell or subcellular component\",\\n \"bio_property\": \"stress response * cell motility\",\\n \"env_property\": \"dynamic water currents * mechanical stress\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"The CAP Gly-rich domain is associated with stress response, which could be due to mechanical stress from dynamic water currents, implying these features contribute to cellular adaptations that allow movement or resilience in such conditions.\"\\n },\\n \"5\": {\\n \"feature_id\": \"sk__Bacteria;k__;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Candidatus_Pelagibacter;s__Candidatus_Pelagibacter_ubique\",\\n \"feature_label\": \"Candidatus Pelagibacter ubique\",\\n \"bio_property\": \"oligotrophy * carbon cycling\",\\n \"env_property\": \"low nutrient * open ocean\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Candidatus Pelagibacter ubique is known for its oligotrophic lifestyle, adapted to low nutrient conditions prevalent in the open ocean, playing a significant role in carbon cycling.\"\\n }\\n }\\n}\\n```\\n\\nIn this JSON output, we are reporting on relationships between specific feature identifiers, their biological properties, and relevant environmental properties in the marine ecosystem. The confidence level varies based on how well-established the connections are in scientific literature, with detailed explanations provided for each feature subset.', role='assistant', function_call=None, tool_calls=None))], created=1717610613, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=782, prompt_tokens=886, total_tokens=1668))\n", + "ChatCompletion(id='chatcmpl-9WueTUBB0Yu6qEi4d8xUBo71u93aR', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Environmental:Aquatic:Marine:Oceanic\": {\\n \"1\": {\\n \"feature_id\": \"GO:0031460 * IPR007210\",\\n \"feature_label\": \"glycine betaine transport * Glycine betaine/proline betaine transport system ATP-binding protein ProV-like\",\\n \"bio_property\": \"osmoprotection * stress response\",\\n \"env_property\": \"marine * high salinity\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Glycine betaine is a known osmoprotectant that helps microorganisms survive in high osmolarity environments such as marine ecosystems.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR001208 * IPR032830\",\\n \"feature_label\": \"MCM domain * Helicase XPB/Ssl2, N-terminal domain\",\\n \"bio_property\": \"DNA replication * DNA repair\",\\n \"env_property\": \"marine * high UV exposure\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Marine environments often have high UV exposure, which can damage DNA. MCM domains and helicase XPB/Ssl2 are involved in DNA repair and replication mechanisms that would be essential in such conditions.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR010518 * IPR001320\",\\n \"feature_label\": \"Flagellar regulatory FleQ * Ionotropic glutamate receptor, C-terminal\",\\n \"bio_property\": \"motility * signal transduction\",\\n \"env_property\": \"marine * nutrient gradient\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Motility and chemotaxis signal transduction are vital for navigating nutrient gradients in marine environments. Flagellar regulatory proteins and ionotropic receptors play crucial roles in these processes.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR014984 * IPR011946\",\\n \"feature_label\": \"HopJ type III effector protein * Integrase, integron-type\",\\n \"bio_property\": \"pathogenicity * horizontal gene transfer\",\\n \"env_property\": \"marine * microbial interaction\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Marine ecosystems often involve complex microbial interactions. Pathogenicity-related proteins and integrases facilitate these interactions via horizontal gene transfer, enhancing adaptive capabilities.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR028282 * sk__Bacteria;k__;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Candidatus_Pelagibacter;s__Candidatus_Pelagibacter_ubique\",\\n \"feature_label\": \"WASH complex subunit 7, central domain * Candidatus Pelagibacter ubique\",\\n \"bio_property\": \"actin cytoskeleton organization * oligotrophy\",\\n \"env_property\": \"marine * nutrient poor\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Candidatus Pelagibacter ubique is known for its oligotrophic lifestyle, thriving in nutrient-poor conditions typical of many marine environments. The WASH complex involvement in actin cytoskeleton organization aids in cellular maintenance and adaptation in such nutrient-limited environments.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631293, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=684, prompt_tokens=899, total_tokens=1583))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -4669,18 +4671,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Environmental:Aquatic:Marine:Sediment\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -4710,7 +4712,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 20:\n", - "ChatCompletion(id='chatcmpl-9WpHAehVrxgzfWsoyEz7AqRaAmNEj', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Environmental:Aquatic:Marine:Sediment\": {\\n \"1\": {\\n \"feature_id\": \"GO:0046797\",\\n \"feature_label\": \"viral procapsid maturation\",\\n \"bio_property\": \"viral life cycle * structural biology\",\\n \"env_property\": \"marine * high particle suspension\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Marine sediments can be high in particulate matter, providing habitats for various viruses that infect marine organisms. Viral procapsid maturation is a crucial step in the viral life cycle, suggesting that viral activity is prevalent in this environment.\"\\n },\\n \"2\": {\\n \"feature_id\": \"sk__Eukaryota;k__Metazoa;p__Arthropoda;c__Ostracoda;o__Halocyprida\",\\n \"feature_label\": \"Eukaryota * Metazoa * Arthropoda * Ostracoda * Halocyprida\",\\n \"bio_property\": \"biotic complexity * ecological interactions\",\\n \"env_property\": \"marine * anoxic layers\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Halocyprida (a type of Ostracoda) are small crustaceans often found in anoxic layers of marine sediments where they play a key role in the benthic food web, interacting with diverse microorganisms.\"\\n }\\n }\\n}\\n```\\n\\n### Notes:\\n1. Only observed features with high confidence and relevant associations are included.\\n2. The relationship between the microbiology features and the environment properties focuses on specific environmental situations such as high particle suspension and anoxic layers, which are characteristic of marine sediments.\\n3. The explanations are concise, carefully linking biological properties to specific environmental conditions.', role='assistant', function_call=None, tool_calls=None))], created=1717610628, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=355, prompt_tokens=646, total_tokens=1001))\n", + "ChatCompletion(id='chatcmpl-9WuebIfDAdUrryCWfDRRogJchwhvX', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Environmental:Aquatic:Marine:Sediment\": {\\n \"1\": {\\n \"feature_id\": \"GO:0046797\",\\n \"feature_label\": \"viral procapsid maturation\",\\n \"bio_property\": \"viral replication * capsid formation\",\\n \"env_property\": \"sediment * viral prevalence * nutrient cycling\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The presence of genes involved in viral procapsid maturation in marine sediment ecosystems suggests significant viral activity. Viruses are crucial players in nutrient cycling as they lyse microbial cells, releasing nutrients back into the environment.\"\\n },\\n \"2\": {\\n \"feature_id\": \"sk__Eukaryota;k__Metazoa;p__Arthropoda;c__Ostracoda;o__Halocyprida\",\\n \"feature_label\": \"sk__Eukaryota;k__Metazoa;p__Arthropoda;c__Ostracoda;o__Halocyprida\",\\n \"bio_property\": \"biodiversity * detritus processing\",\\n \"env_property\": \"sediment * benthic zone * organic matter richness\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Ostracods are known for their role in breaking down organic matter in sediment. Their presence indicates a sediment environment rich in organic material, which they help decompose and recycle, maintaining sediment health.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631301, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=299, prompt_tokens=659, total_tokens=958))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -4733,18 +4735,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -4775,7 +4777,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 21:\n", - "ChatCompletion(id='chatcmpl-9WpHJdoNOvfRooOOq6GbW7duXR1bJ', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond\": { \\n \"1\": {\\n \"feature_id\": \"IPR006093 * GO:0034614\",\\n \"feature_label\": \"Oxygen oxidoreductase covalent FAD-binding site * cellular response to oxidative stress\",\\n \"bio_property\": \"oxidative stress resistance * energy generation\",\\n \"env_property\": \"high salinity * high sunlight exposure\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Oxidative enzymes with FAD-binding sites are crucial for detoxifying reactive oxygen species (ROS) prevalent in high saline environments exposed to intense sunlight.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR011946 * GO:0006310\",\\n \"feature_label\": \"Integrase, integron-type * DNA integration\",\\n \"bio_property\": \"genomic rearrangement * horizontal gene transfer\",\\n \"env_property\": \"variable nutrient conditions\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Integron-type integrases facilitate the capture and rearrangement of gene cassettes, helping microorganisms adapt to the fluctuating nutrient availability in salt crystallizer ponds.\"\\n }, \\n \"3\": {\\n \"feature_id\": \"GO:0004638 * IPR004831\",\\n \"feature_label\": \"Phosphoribosylaminoimidazole carboxylase activity * PurM-like domain\",\\n \"bio_property\": \"nucleotide biosynthesis * metabolic adaptation\",\\n \"env_property\": \"nutrient poor * high pH\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Phosphoribosylaminoimidazole carboxylase is pivotal in purine biosynthesis, a pathway critical for nucleotide metabolism, which is especially crucial in nutrient-poor and high pH conditions of saline-alkaline environments.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717610637, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=405, prompt_tokens=693, total_tokens=1098))\n", + "ChatCompletion(id='chatcmpl-9WuefeRjWpSRFbatVuXY9YpumiAMo', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='Sure, let\\'s identify and explain the relationships between the observed microbial metagenomic features and the specific environmental properties of the \"Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond\" ecosystem.\\n\\nHere\\'s the structured JSON format with the observation results:\\n\\n```json\\n{\\n \"Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond\": {\\n \"1\": {\\n \"feature_id\": \"GO:0004638\",\\n \"feature_label\": \"phosphoribosylaminoimidazole carboxylase activity\",\\n \"bio_property\": \"purine metabolism\",\\n \"env_property\": \"high salinity * high pH\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Phosphoribosylaminoimidazole carboxylase is involved in purine biosynthesis, which is crucial for the synthesis of nucleotides. In extreme conditions like high salinity and pH, the adaptation of nucleotide synthesis pathways can be a critical survival mechanism for organisms.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR006093\",\\n \"feature_label\": \"Oxygen oxidoreductase covalent FAD-binding site\",\\n \"bio_property\": \"oxidative stress response * flavoproteins\",\\n \"env_property\": \"high salinity * high pH * oxidative stress\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The oxygen oxidoreductase enzymes, which contain covalent FAD-binding sites, are vital for cellular responses to oxidative stress. These enzymes help protect cells from oxidative damage, which could be prevalent in salt crystallizer ponds due to high salinity and alkalinity conditions that could generate reactive oxygen species.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR011946\",\\n \"feature_label\": \"Integrase, integron-type\",\\n \"bio_property\": \"horizontal gene transfer\",\\n \"env_property\": \"high salinity * high pH * genetic diversity\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Integrases, particularly the integron-type, are enzymes that facilitate horizontal gene transfer, allowing bacteria to acquire new genes, including those providing resistance to harsh environmental conditions such as high salinity and high pH. This mechanism significantly contributes to genetic diversity and adaptability in extreme environments.\"\\n }\\n }\\n}\\n```\\n\\nIn these results:\\n1. **Feature GO:0004638 (phosphoribosylaminoimidazole carboxylase activity)** is primarily involved in purine metabolism, which is essential for nucleotide synthesis. The adaptation of these metabolic pathways is crucial in environments with high salinity and high pH, providing a means for organisms to survive and proliferate in such harsh conditions.\\n\\n2. **Feature IPR006093 (Oxygen oxidoreductase covalent FAD-binding site)** is linked with the oxidative stress response. Flavoproteins play key roles in managing oxidative stress, especially in environments that pose extreme oxidative challenges, such as salt crystallizer ponds with high salinity and pH levels.\\n\\n3. **Feature IPR011946 (Integrase, integron-type)** facilitates horizontal gene transfer, which enhances genetic diversity and evolution, critical for survival in extreme environmental conditions like high salinity and high pH. This genetic adaptability can provide essential functions enabling microbes to thrive in such challenging ecosystems.\\n\\nThese explanations firmly link the metagenomic features to specific biophysical adaptations required to endure the harsh conditions of the salt crystallizer pond ecosystem.', role='assistant', function_call=None, tool_calls=None))], created=1717631305, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=726, prompt_tokens=696, total_tokens=1422))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -4798,18 +4800,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Environmental:Terrestrial:Soil\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -4851,7 +4853,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 22:\n", - "ChatCompletion(id='chatcmpl-9WpHSbv9vXITS6KYvP4cEqnoxRgG4', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Environmental:Terrestrial:Soil\": {\\n \"1\": {\\n \"feature_id\": \"GO:0008918 * IPR011735\",\\n \"feature_label\": \"lipopolysaccharide 3-alpha-galactosyltransferase activity * WlaTC/HtrL glycosyltransferase\",\\n \"bio_property\": \"lipopolysaccharide biosynthesis * glycosylation\",\\n \"env_property\": \"microbial diversity * nutrient cycles\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Lipopolysaccharides are key components of the outer membrane of Gram-negative bacteria, influencing microbial diversity and playing roles in nutrient cycling in soil ecosystems.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR000522 * IPR031834\",\\n \"feature_label\": \"ABC transporter, permease protein, BtuC-like * Antitoxin RnlB/LsoB\",\\n \"bio_property\": \"nutrient uptake * toxin-antitoxin systems\",\\n \"env_property\": \"nutrient availability * competition\",\\n \"confidence\": \"high\",\\n \"explanation\": \"ABC transporters facilitate the uptake of essential nutrients in nutrient-limited soil environments, while toxin-antitoxin systems play roles in microbial competition and survival.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR000036 * IPR028955\",\\n \"feature_label\": \"Peptidase A26, omptin * Immunity protein 57\",\\n \"bio_property\": \"proteolysis * immune evasion\",\\n \"env_property\": \"microbial interactions * pathogen resistance\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Peptidase activity contributes to protein turnover and microbial interactions in the soil, while immunity proteins can be linked to microbial defense mechanisms against pathogens.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR006949 * IPR007210\",\\n \"feature_label\": \"Baseplate protein J-like * Glycine betaine/proline betaine transport system ATP-binding protein ProV-like\",\\n \"bio_property\": \"phage structure * osmoprotection\",\\n \"env_property\": \"soil moisture * microbial population dynamics\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Baseplate proteins are components of bacteriophages influencing microbial population dynamics, and osmoprotection systems help bacteria survive in varying soil moisture conditions.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR003791 * IPR025123\",\\n \"feature_label\": \"Protein of unknown function UPF0178 * Domain of unknown function DUF4049\",\\n \"bio_property\": \"functional novelty\",\\n \"env_property\": \"unknown\",\\n \"confidence\": \"low\",\\n \"explanation\": \"Proteins of unknown function may represent novel enzymatic or structural adaptations specific to soil environments, but further characterization is needed.\"\\n },\\n \"6\": {\\n \"feature_id\": \"IPR010856 * IPR020497\",\\n \"feature_label\": \"Gig2-like * Domain of unknown function DUF5440\",\\n \"bio_property\": \"unknown\",\\n \"env_property\": \"unknown\",\\n \"confidence\": \"unknown\",\\n \"explanation\": \"Insufficient data to establish a relationship.\"\\n },\\n \"7\": {\\n \"feature_id\": \"IPR020484 * IPR021239\",\\n \"feature_label\": \"Protein of unknown function DUF5503 * Protein of unknown function DUF2625\",\\n \"bio_property\": \"unknown\",\\n \"env_property\": \"unknown\",\\n \"confidence\": \"unknown\",\\n \"explanation\": \"Insufficient data to establish a relationship.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717610646, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=777, prompt_tokens=798, total_tokens=1575))\n", + "ChatCompletion(id='chatcmpl-9WuepNVsTbHcJMQWuFqPog5z7egik', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Environmental:Terrestrial:Soil\": {\\n \"1\": {\\n \"feature_id\": \"GO:0008918 * IPR011735\",\\n \"feature_label\": \"lipopolysaccharide 3-alpha-galactosyltransferase activity * WlaTC/HtrL glycosyltransferase\",\\n \"bio_property\": \"cell wall synthesis * lipopolysaccharide biosynthesis\",\\n \"env_property\": \"nutrient-rich * microbial diversity\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Lipopolysaccharide biosynthesis is crucial for microbial cell wall formation, which is especially important in nutrient-rich environments with high microbial competition and diversity.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR000036 * IPR025123\",\\n \"feature_label\": \"Peptidase A26, omptin * Domain of unknown function DUF4049\",\\n \"bio_property\": \"proteolysis * defensive enzymatic activity\",\\n \"env_property\": \"organic matter decomposition * nutrient cycling\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Peptidases such as omptin are involved in the breakdown of proteins, aiding in the decomposition of organic matter and subsequent nutrient cycling within the soil.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR000522 * IPR021239\",\\n \"feature_label\": \"ABC transporter, permease protein, BtuC-like * Protein of unknown function DUF2625\",\\n \"bio_property\": \"transportation of molecules * transmembrane movement\",\\n \"env_property\": \"complex soil matrix * nutrient availability\",\\n \"confidence\": \"high\",\\n \"explanation\": \"ABC transporters are crucial for moving various molecules across cellular membranes, a vital function in the complex soil matrix where access to nutrients can vary significantly.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR010856 * IPR028955\",\\n \"feature_label\": \"Gig2-like * Immunity protein 57\",\\n \"bio_property\": \"immune response * pathogen defense\",\\n \"env_property\": \"competitive microbial habitats * pathogen presence\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Proteins involved in the immune response are important in soil environments that are competitive and host to various pathogens, aiding in microbe survival and dominance.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR031834 * IPR003791\",\\n \"feature_label\": \"Antitoxin RnlB/LsoB * Protein of unknown function UPF0178\",\\n \"bio_property\": \"toxin-antitoxin systems * stress response\",\\n \"env_property\": \"microbial interaction networks * environmental stress\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Antitoxin proteins are involved in stress responses and managing toxin exposure from other microbes or environmental sources, crucial in microbial-rich soil environments.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631315, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=620, prompt_tokens=813, total_tokens=1433))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -4874,18 +4876,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Host-associated:Birds\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -4949,7 +4951,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 23:\n", - "ChatCompletion(id='chatcmpl-9WpHgsMTjbtCAc4qRH3Tvmll1OPxp', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Birds\": {\\n \"1\": {\\n \"feature_id\": \"IPR007037 * IPR007925 * GO:0000502\",\\n \"feature_label\": \"Siderophore-interacting protein, C-terminal domain * Relaxosome protein TraM * proteasome complex\",\\n \"bio_property\": \"iron transport * conjugative transfer * protein degradation\",\\n \"env_property\": \"microbiota-rich * nutrient variable\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Siderophores are critical in iron transport, essential in nutrient-variable environments. Relaxosome proteins facilitate DNA conjugation, prevalent in mixed microbial populations. Proteasomes are involved in protein regulation and degradation, important in dense microbiota where protein turnover is high.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR004759 * GO:0015307\",\\n \"feature_label\": \"Glutamate:g-aminobutyrate antiporter * obsolete drug:proton antiporter activity\",\\n \"bio_property\": \"amino acid transport * membrane transport\",\\n \"env_property\": \"gut-associated * variable pH\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Antiporters, such as the Glutamate:g-aminobutyrate antiporter, are vital in amino acid transport and pH balance within the gut, which hosts a variable pH environment.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR007210 * GO:0031460\",\\n \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\\n \"bio_property\": \"osmoprotection * stress response\",\\n \"env_property\": \"marine * high salinity\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Glycine betaine is a known osmoprotectant, providing resistance to high salinity environments typically observed in marine settings.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR002723 * IPR019895 * GO:0008861\",\\n \"feature_label\": \"N(4)-bis(aminopropyl)spermidine synthase, C-terminal * Putative bacteriocin export ABC transporter, lactococcin 972 group * formate C-acetyltransferase activity\",\\n \"bio_property\": \"polyamine biosynthesis * bacteriocin transport * metabolic enzyme\",\\n \"env_property\": \"competing microbial community * nutrient recycling\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Polyamine biosynthesis and bacteriocin transport are important in densely packed microbial communities, facilitating competitive interactions. Formate C-acetyltransferases are involved in metabolic pathways crucial for nutrient recycling.\"\\n },\\n \"5\": {\\n \"feature_id\": \"sk__Bacteria * sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales\",\\n \"feature_label\": \"Bacteria * Firmicutes; Clostridia; Clostridiales\",\\n \"bio_property\": \"phylogeny * population structure\",\\n \"env_property\": \"high microbial diversity * anaerobic\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Firmicutes, particularly Clostridiales, are common in high-diversity, anaerobic environments like bird guts, impacting digestion and health.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717610660, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=721, prompt_tokens=1190, total_tokens=1911))\n", + "ChatCompletion(id='chatcmpl-9WuezyrVDH1T4M3dLwtnON6QLnGld', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Birds\": {\\n \"1\": {\\n \"feature_id\": \"GO:0000502 * GO:0008772 * IPR007925 * IPR009677\",\\n \"feature_label\": \"proteasome complex * isocitrate dehydrogenase (NADP+) kinase activity * Relaxosome protein TraM * Protein of unknown function DUF1266\",\\n \"bio_property\": \"protein degradation * metabolism regulation * protein interaction\",\\n \"env_property\": \"host immunity * nutrient cycling\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The proteasome complex is involved in protein degradation, key for cellular maintenance and host immunity. Isocitrate dehydrogenase kinase activity affects metabolism regulation. Relaxosome protein TraM and DUF1266 (unknown function) suggest interactions important for horizontal gene transfer, which may aid in adaptability to host environments.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR004759 * IPR007037 * IPR007920 * IPR035286 * sk__Bacteria;k__;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales\",\\n \"feature_label\": \"Glutamate:g-aminobutyrate antiporter * Siderophore-interacting protein, C-terminal domain * Protein of unknown function UPF0223 * Protein of unknown function DUF5361 * Bacteroidetes\",\\n \"bio_property\": \"amino acid transport * iron acquisition * protein function\",\\n \"env_property\": \"gut microbiota * nutrient uptake * low oxygen environment\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Bacteroidetes are prevalent in the gut microbiota of birds, contributing to nutrient uptake and low oxygen environments. Glutamate:g-aminobutyrate antiporter is involved in amino acid transport critical in nutrient-rich environments. Siderophore-interacting proteins aid in iron acquisition required for growth in the gut.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR019895 * IPR007037 * IPR031010 * sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae\",\\n \"feature_label\": \"Putative bacteriocin export ABC transporter, lactococcin 972 group * Siderophore-interacting protein, C-terminal domain * Radical SAM mobile pair protein A * Firmicutes; Ruminococcaceae\",\\n \"bio_property\": \"bacteriocin export * iron acquisition * radical SAM reactions\",\\n \"env_property\": \"gut microbiota * antibacterial activity\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Firmicutes, like Ruminococcaceae, are gut-associated. Bacteriocin export mechanisms suggest a role in inter-bacterial interactions and competitive inhibition. Iron acquisition remains crucial in these environments, while radical SAM enzymes are involved in diverse biosynthetic processes.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631325, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=629, prompt_tokens=1207, total_tokens=1836))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -4972,18 +4974,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Host-associated:Human\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -5057,7 +5059,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 24:\n", - "ChatCompletion(id='chatcmpl-9WpHuejz1X5yl5mkdmfiqkpNb5XiF', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Human\": {\\n \"1\": {\\n \"feature_id\": \"GO:0004984 * GO:0016032\",\\n \"feature_label\": \"olfactory receptor activity * viral process\",\\n \"bio_property\": \"chemosensation * infection\",\\n \"env_property\": \"high host interaction\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Olfactory receptors are crucial in sensing the environment, while viral processes are indicative of host-pathogen interactions.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0019512 * GO:0033920 * IPR004300 * IPR013148\",\\n \"feature_label\": \"lactose catabolic process via tagatose-6-phosphate * 6-phospho-beta-galactosidase activity * Glycoside hydrolase family 57, N-terminal domain * Glycosyl hydrolase family 32, N-terminal\",\\n \"bio_property\": \"carbohydrate metabolism\",\\n \"env_property\": \"nutrient availability and utilization\",\\n \"confidence\": \"high\",\\n \"explanation\": \"These features are linked to carbohydrate metabolism, specifically in the breakdown and utilization of lactose, which reflects the nutrient profile directly available in the human gastrointestinal tract.\"\\n },\\n \"3\": {\\n \"feature_id\": \"GO:0004352 * IPR010945 * IPR017821\",\\n \"feature_label\": \"glutamate dehydrogenase (NAD+) activity * Malate dehydrogenase, type 2 * Succinate CoA transferase\",\\n \"bio_property\": \"energy metabolism\",\\n \"env_property\": \"metabolically active\",\\n \"confidence\": \"high\",\\n \"explanation\": \"These enzymes play a critical role in energy metabolism by participating in the Krebs cycle and amino acid metabolism, indicative of a metabolically active environment within the human host.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR006322 * IPR015304 * IPR018470\",\\n \"feature_label\": \"Glutathione reductase, eukaryote/bacterial * ZinT domain * Periplasmic metal-binding protein Tp34-type\",\\n \"bio_property\": \"oxidative stress response * metal ion regulation\",\\n \"env_property\": \"metal ion fluctuations\",\\n \"confidence\": \"high\",\\n \"explanation\": \"These features are involved in maintaining cellular redox balance and regulating metal ions, reflecting the host environment where metal homeostasis and oxidative stress are significant concerns.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR004868 * IPR008016 * IPR012969\",\\n \"feature_label\": \"DNA-directed DNA polymerase, family B, mitochondria/virus * Portal protein Gp10 * Fibrinogen binding protein\",\\n \"bio_property\": \"genetic replication and host interaction\",\\n \"env_property\": \"infection and immune response\",\\n \"confidence\": \"high\",\\n \"explanation\": \"These features relate to viral DNA replication and interaction with host proteins, indicating an environment where host-pathogen interactions and immune responses are prevalent.\"\\n },\\n \"6\": {\\n \"feature_id\": \"GO:0019068 * IPR007119 * IPR021505\",\\n \"feature_label\": \"virion assembly * Phage minor structural protein, N-terminal domain * Bacteriophage B3, Orf6\",\\n \"bio_property\": \"bacteriophage activity\",\\n \"env_property\": \"bacteriophage presence\",\\n \"confidence\": \"high\",\\n \"explanation\": \"These features are linked to bacteriophage activities, reflecting an environment where phage-bacteria interactions are occurring, which is common in the human microbiome.\"\\n },\\n \"7\": {\\n \"feature_id\": \"IPR008981 * IPR010024 * IPR028049\",\\n \"feature_label\": \"F-MuLV receptor-binding * Conserved hypothetical protein CHP1671 * NTF2 fold immunity protein\",\\n \"bio_property\": \"host-pathogen interactions\",\\n \"env_property\": \"variable immune pressure\",\\n \"confidence\": \"high\",\\n \"explanation\": \"These protein domains are associated with pathogen recognition and immune responses, indicating an environment where host immune response plays a significant role.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717610674, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=905, prompt_tokens=1276, total_tokens=2181))\n", + "ChatCompletion(id='chatcmpl-9Wuf7OaFKO56xoar7yPiQCvhWbkkq', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Human\": {\\n \"1\": {\\n \"feature_id\": \"GO:0016032 * GO:0019068 * IPR007119 * IPR008016 * IPR010960 * IPR011868\",\\n \"feature_label\": \"viral process * virion assembly * Phage minor structural protein, N-terminal domain * Portal protein Gp10 * Flavocytochrome c * Molybdate ABC transporter, ATP-binding protein\",\\n \"bio_property\": \"viral infection and replication * phage formation * virion structural integrity * metabolic adaptation\",\\n \"env_property\": \"high infection pressure * diverse microbial interactions * variable nutrient availability\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Several features related to viral processes indicate a high infection pressure environment that requires significant microbial adaptation mechanisms, which align with human host-associated ecosystems where various viruses co-exist and interact with the host and microbial flora.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0004352 * GO:0004638 * GO:0019512 * GO:0033920 * IPR004300 * IPR013148 * IPR035364 * IPR005126 * IPR017821 * IPR006322\",\\n \"feature_label\": \"glutamate dehydrogenase (NAD+) activity * phosphoribosylaminoimidazole carboxylase activity * lactose catabolic process via tagatose-6-phosphate * 6-phospho-beta-galactosidase activity * Glycoside hydrolase family 57, N-terminal domain * Glycosyl hydrolase family 32, N-terminal * Glycosyl hydrolase 101, beta-sandwich domain * NapC/NirT cytochrome c, N-terminal * Succinate CoA transferase * Glutathione reductase, eukaryote/bacterial\",\\n \"bio_property\": \"carbohydrate metabolism * energy production * nitrogen metabolism * antioxidant activity\",\\n \"env_property\": \"nutrient availability * redox dynamics * gastrointestinal tract conditions\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The features are rich in enzymes involved in carbohydrate metabolism and energy production, reflecting the nutrient-dense and metabolically active environment of the human gastrointestinal tract, which supports complex microbial and host metabolic interactions.\"\\n },\\n \"3\": {\\n \"feature_id\": \"GO:0004521 * IPR002631 * IPR004868 * IPR012706 * IPR026345 * IPR028049\",\\n \"feature_label\": \"RNA endonuclease activity * Plasmid replication protein * DNA-directed DNA polymerase, family B, mitochondria/virus * Rib/alpha/Esp surface antigen * Adhesin isopeptide-forming adherence domain * NTF2 fold immunity protein\",\\n \"bio_property\": \"nucleic acid metabolism * genetic material replication and repair * immune evasion * surface adhesion\",\\n \"env_property\": \"intestinal mucosal surfaces * homeostatic and inflammatory conditions * microbial competition\",\\n \"confidence\": \"high\",\\n \"explanation\": \"These features indicate nucleic acid processing and interaction with the host\\'s immune system, highlighting the dynamic and competitive environment of intestinal mucosal surfaces, where microbes adapt and compete for adhesion and immune evasion.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR004764 * IPR019895 * IPR005126 * IPR004868 * IPR010945 * IPR010960\",\\n \"feature_label\": \"Hydrophobe/amphiphile efflux-1 HAE1 * Putative bacteriocin export ABC transporter, lactococcin 972 group * NapC/NirT cytochrome c, N-terminal * DNA-directed DNA polymerase, family B, mitochondria/virus * Malate dehydrogenase, type 2 * Flavocytochrome c\",\\n \"bio_property\": \"antibiotic resistance * metabolite transport * energy production\",\\n \"env_property\": \"antibiotic exposure * microbial community interactions * variable redox potential\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The presence of efflux and transport-related proteins, combined with enzymes involved in energy generation, suggests an environment where antibiotic pressure and complex metabolic interactions are prevalent, consistent with the human host-associated ecosystem.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631333, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=915, prompt_tokens=1294, total_tokens=2209))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -5080,18 +5082,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Host-associated:Human:Digestive system\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -5219,7 +5221,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 25:\n", - "ChatCompletion(id='chatcmpl-9WpIFRMBfBRMh4iDheB6ZDTAAfDxZ', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='Sure, let\\'s analyze the given features and align them with the environmental properties of the human digestive system. I\\'ll generate the JSON output as requested, focusing on features with well-supported relationships.\\n\\n```json\\n{\\n \"Host-associated:Human:Digestive system\": {\\n \"1\": {\\n \"feature_id\": \"GO:0004122 * IPR004642\",\\n \"feature_label\": \"cystathionine beta-synthase activity * Serine dehydratase, alpha subunit\",\\n \"bio_property\": \"sulfur amino acid metabolism * amino acid metabolism\",\\n \"env_property\": \"nutrient-rich * variable pH\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Enzymes involved in amino acid metabolism are essential for the breakdown and assimilation of dietary proteins, which are abundant in the human digestive system.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0015858 * GO:0022857 * IPR000522\",\\n \"feature_label\": \"nucleoside transport * transmembrane transporter activity * ABC transporter, permease protein, BtuC-like\",\\n \"bio_property\": \"nutrient uptake * membrane transport\",\\n \"env_property\": \"nutrient-rich * variable pH\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The digestive system is nutrient-rich, requiring efficient transport systems for uptake of nucleosides and other nutrients. Transport proteins facilitate these processes.\"\\n },\\n \"3\": {\\n \"feature_id\": \"GO:0019512 * IPR010945\",\\n \"feature_label\": \"lactose catabolic process via tagatose-6-phosphate * Malate dehydrogenase, type 2\",\\n \"bio_property\": \"carbohydrate metabolism * energy production\",\\n \"env_property\": \"nutrient-rich * microbial fermentation\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Lactose metabolism and fermentation are crucial in the gut where lactose from dairy intake is broken down by gut bacteria. Malate dehydrogenase is involved in the TCA cycle, essential for energy production.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR003514 * IPR004975 * IPR008016\",\\n \"feature_label\": \"Microviridae F protein * Poxvirus VLTF2, trans-activator * Portal protein Gp10\",\\n \"bio_property\": \"viral replication * viral assembly\",\\n \"env_property\": \"high microbial diversity * phage-rich environments\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"The human gut harbors a diverse range of microbes including bacteriophages and viruses that can infect bacteria. These proteins are involved in viral replication and assembly processes.\"\\n },\\n \"5\": {\\n \"feature_id\": \"GO:0046797 * IPR021505\",\\n \"feature_label\": \"viral procapsid maturation * Bacteriophage B3, Orf6\",\\n \"bio_property\": \"viral life cycle * bacteriophage development\",\\n \"env_property\": \"high microbial diversity * phage-rich environments\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Phages play a critical role in microbial dynamics within the gut. Proteins related to the phage life cycle, such as those involved in procapsid maturation, are important in this context.\"\\n },\\n \"6\": {\\n \"feature_id\": \"IPR012672 * IPR012673 * IPR035576\",\\n \"feature_label\": \"Type III secretion system YscX * Type III secretion system chaperone SycN * Type VI secretion system TssC\",\\n \"bio_property\": \"host-pathogen interaction * secretion system\",\\n \"env_property\": \"high microbial competition * host immune environment\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Secretion systems are used by gut bacteria to inject effector proteins into host cells or other bacteria, playing a key role in microbial competition and interactions with the host.\"\\n },\\n \"7\": {\\n \"feature_id\": \"IPR014154 * IPR017813\",\\n \"feature_label\": \"Global transcriptional regulator CodY * Mycothiol acetyltransferase\",\\n \"bio_property\": \"regulation of gene expression * stress response\",\\n \"env_property\": \"nutrient-rich * variable pH\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Regulatory proteins like CodY and mycothiol-related enzymes are crucial for bacteria to adapt to changing nutrient conditions and stress in the gut.\"\\n },\\n \"8\": {\\n \"feature_id\": \"sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae\",\\n \"feature_label\": \"Lachnospiraceae family\",\\n \"bio_property\": \"butyrate production * fiber degradation\",\\n \"env_property\": \"anaerobic * carbohydrate-rich\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Members of the Lachnospiraceae family are known for their ability to produce butyrate, a beneficial short-chain fatty acid, through fermentation of dietary fibers.\"\\n }\\n }\\n}\\n```\\n\\nThis JSON output includes high-confidence relationships between microbial metagenomic features and environmental properties relevant to the human digestive system. It prioritizes multiple feature subsets where possible and ensures thorough, reliable annotations.', role='assistant', function_call=None, tool_calls=None))], created=1717610695, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=1132, prompt_tokens=2522, total_tokens=3654))\n", + "ChatCompletion(id='chatcmpl-9WufTNr8OFd83lcoQpdxwewn2EyKk', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Human:Digestive system\": {\\n \"1\": {\\n \"feature_id\": \"GO:0015858 * GO:0022857 * IPR000522\",\\n \"feature_label\": \"nucleoside transport * transmembrane transporter activity * ABC transporter, permease protein, BtuC-like\",\\n \"bio_property\": \"nutrient uptake * transmembrane transport\",\\n \"env_property\": \"nutrient-rich\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The extensive presence of transporters, including nucleoside and other ABC transporters, is indicative of nutrient assimilation processes critical in a nutrient-rich environment like the human digestive system.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0019068 * GO:0046797 * IPR004975 * IPR008016\",\\n \"feature_label\": \"virion assembly * viral procapsid maturation * Poxvirus VLTF2, trans-activator * Portal protein Gp10\",\\n \"bio_property\": \"viral replication * virion formation\",\\n \"env_property\": \"host-associated\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Viral-related proteins and activities suggest active viral replication within the digestive system, which is a known host-associated environment where viruses interact with host cells for their life cycles.\"\\n },\\n \"3\": {\\n \"feature_id\": \"GO:0019512 * IPR004501\",\\n \"feature_label\": \"lactose catabolic process via tagatose-6-phosphate * Phosphotransferase system, EIIC component, type 3\",\\n \"bio_property\": \"carbohydrate metabolism\",\\n \"env_property\": \"nutrient-rich * varied diet\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The presence of genes involved in lactose catabolism and the phosphotransferase system suggests adaptation to a varied, carbohydrate-rich diet in the human digestive system.\"\\n },\\n \"4\": {\\n \"feature_id\": \"GO:0004352 * IPR010945\",\\n \"feature_label\": \"glutamate dehydrogenase (NAD+) activity * Malate dehydrogenase, type 2\",\\n \"bio_property\": \"amino acid metabolism * intermediary metabolism\",\\n \"env_property\": \"nutrient-rich * metabolically active\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The activities related to amino acid and intermediary metabolism are essential for handling the diverse range of nutrients available in the human gut.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR005126 * IPR008016\",\\n \"feature_label\": \"NapC/NirT cytochrome c, N-terminal * Portal protein Gp10\",\\n \"bio_property\": \"electron transport * viral replication\",\\n \"env_property\": \"anaerobic * host-associated\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Electron transport is crucial for energy production in anaerobic conditions, typical of parts of the digestive system. Concurrently, viral proteins indicate ongoing viral activity, relevant in host-associated environments.\"\\n },\\n \"6\": {\\n \"feature_id\": \"IPR012672 * IPR035576 * IPR035177\",\\n \"feature_label\": \"Type III secretion system YscX * Type VI secretion system TssC * Type VI secretion system TssN\",\\n \"bio_property\": \"secretion of effector proteins * bacterial competition\",\\n \"env_property\": \"microbiome interaction * host-associated\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The presence of secretion systems indicates complex microbial interactions and competition within the microbiome, typical in the densely populated human digestive tract.\"\\n },\\n \"7\": {\\n \"feature_id\": \"sk__Bacteria;k__;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella * sk__Bacteria;k__;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides\",\\n \"feature_label\": \"Collinsella * Bacteroides\",\\n \"bio_property\": \"fiber degradation * niche adaptation\",\\n \"env_property\": \"high fiber diet\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Collinsella and Bacteroides are known to be involved in polysaccharide metabolism, fitting well in an environment where plant-derived fibers are abundant, such as in human digestive systems with a high-fiber diet.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631355, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=975, prompt_tokens=2536, total_tokens=3511))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -5242,18 +5244,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Host-associated:Human:Digestive system:Large intestine\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -5338,7 +5340,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 26:\n", - "ChatCompletion(id='chatcmpl-9WpIZLZtgM1f3WNh5a5dm0i9K1g0k', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='Sure, let\\'s delve into the relationships between the observed microbial metagenomic features and the environmental properties of the Host-associated:Human:Digestive system:Large intestine ecosystem. \\n\\nI\\'ll provide a thorough and reliable analysis for each feature or feature subset:\\n\\n```json\\n{\\n \"Host-associated:Human:Digestive system:Large intestine\": {\\n \"1\": {\\n \"feature_id\": \"GO:0001510\",\\n \"feature_label\": \"RNA methylation\",\\n \"bio_property\": \"gene expression regulation * RNA stability\",\\n \"env_property\": \"nutritionally rich * low redox potential\",\\n \"confidence\": \"high\",\\n \"explanation\": \"RNA methylation in the gut helps in regulating gene expression and maintaining RNA stability, which is crucial for host-microbe interactions in a nutritionally rich environment with low oxidative stress.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0019317 * IPR004300\",\\n \"feature_label\": \"Fucose catabolic process * Glycoside hydrolase family 57, N-terminal domain\",\\n \"bio_property\": \"fucose utilization * carbohydrate metabolism\",\\n \"env_property\": \"high fiber diet * complex carbohydrate availability\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Fucose catabolism and glycoside hydrolase are involved in breaking down complex carbohydrates in the large intestine, where a high fiber diet provides diverse polysaccharides.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR005126\",\\n \"feature_label\": \"NapC/NirT cytochrome c, N-terminal\",\\n \"bio_property\": \"electron transport * oxidative stress response\",\\n \"env_property\": \"anaerobic conditions * low oxygen\",\\n \"confidence\": \"high\",\\n \"explanation\": \"NapC/NirT cytochrome c is crucial for electron transport under anaerobic conditions found in the large intestine, aiding in maintaining redox balance.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR017559 * IPR017821\",\\n \"feature_label\": \"Alkyl hydroperoxide reductase subunit C * Succinate CoA transferase\",\\n \"bio_property\": \"detoxification * energy production\",\\n \"env_property\": \"high oxidative stress * nutrient metabolism\",\\n \"confidence\": \"high\",\\n \"explanation\": \"These enzymes help in detoxifying reactive oxygen species and in energy production processes, addressing the high oxidative stress and diverse metabolic needs in the gut.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR012770\",\\n \"feature_label\": \"Trehalose operon transcriptional repressor\",\\n \"bio_property\": \"osmoprotection * sugar metabolism regulation\",\\n \"env_property\": \"osmotic stress * variable sugar availability\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Trehalose operon regulation provides osmoprotection and adapts sugar metabolism in response to varying osmotic conditions and sugar availability in the large intestine.\"\\n },\\n \"6\": {\\n \"feature_id\": \"IPR001101\",\\n \"feature_label\": \"Plectin repeat\",\\n \"bio_property\": \"structural stability * cytoskeletal interactions\",\\n \"env_property\": \"mechanical stress * host cell interaction\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Plectin repeats provide structural stability and facilitate cytoskeletal interactions, which are essential in the large intestine for withstanding mechanical stress and maintaining host-microbe interactions.\"\\n },\\n \"7\": {\\n \"feature_id\": \"IPR023972\",\\n \"feature_label\": \"Conserved hypothetical protein CHP04069, acyl carrier-related\",\\n \"bio_property\": \"lipid metabolism * protein-protein interaction\",\\n \"env_property\": \"lipid-rich diet * microbial community interactions\",\\n \"confidence\": \"high\",\\n \"explanation\": \"This conserved protein related to acyl carriers is involved in lipid metabolism and protein interactions, important for managing a lipid-rich diet and microbial interactions in the large intestine.\"\\n },\\n \"8\": {\\n \"feature_id\": \"IPR006541 * IPR008016\",\\n \"feature_label\": \"Bacteriocin-associated integral membrane protein * Portal protein Gp10\",\\n \"bio_property\": \"antimicrobial activity * viral infection\",\\n \"env_property\": \"microbial competition * pathogen presence\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Bacteriocin-associated proteins provide antimicrobial functions, and portal proteins are involved in viral infections. Both play roles in maintaining microbial competition and managing pathogen presence in the gut.\"\\n },\\n \"9\": {\\n \"feature_id\": \"sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnospira\",\\n \"feature_label\": \"Lachnospira species\",\\n \"bio_property\": \"butyrate production * fiber degradation\",\\n \"env_property\": \"high fiber diet * butyrate-rich environment\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Lachnospira species are known for their ability to degrade fiber and produce butyrate, which is prevalent in a high fiber diet and contributes to a butyrate-rich environment in the large intestine.\"\\n },\\n \"10\": {\\n \"feature_id\": \"sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Subdoligranulum\",\\n \"feature_label\": \"Subdoligranulum species\",\\n \"bio_property\": \"short-chain fatty acid production * polysaccharide degradation\",\\n \"env_property\": \"dietary polysaccharides * short-chain fatty acid availability\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Subdoligranulum species are involved in degrading dietary polysaccharides and producing short-chain fatty acids, which are abundant in the large intestine due to diet.\"\\n }\\n }\\n}\\n```\\n\\nThis structured JSON outlines the relationship between microbial features and the environmental context within the large intestine with clear biological properties, environmental properties, and high-confidence explanations for each feature.', role='assistant', function_call=None, tool_calls=None))], created=1717610715, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=1296, prompt_tokens=1541, total_tokens=2837))\n", + "ChatCompletion(id='chatcmpl-9WufiVX1LpWDpt8pOlbmPS05eeiHr', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Human:Digestive system:Large intestine\": {\\n \"1\": {\\n \"feature_id\": \"GO:0019317 * IPR004300 * sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae\",\\n \"feature_label\": \"fucose catabolic process * Glycoside hydrolase family 57, N-terminal domain * Lachnospiraceae family\",\\n \"bio_property\": \"fucose metabolism * carbohydrate processing * specific microbiota\",\\n \"env_property\": \"nutrient-rich * low oxygen * moderate pH\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Fucose is found in the mucus of the gut lining, providing a substrate that supports specific carbohydrate processing abilities. Lachnospiraceae family bacteria are known to be prevalent in the human gut and capable of utilizing such oligosaccharides.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR017559 * IPR012770 * sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae\",\\n \"feature_label\": \"Alkyl hydroperoxide reductase subunit C * Trehalose operon transcriptional repressor * Ruminococcaceae family\",\\n \"bio_property\": \"antioxidant activity * carbohydrate metabolism regulation\",\\n \"env_property\": \"low oxygen * intermediate moisture\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Alkyl hydroperoxide reductase offers protection against oxidative stress, which is essential in low-oxygen environments like the large intestine. The Trehalose operon is involved in carbohydrate metabolism, crucial for the digestibility of dietary fibers, a primary function of the Ruminococcaceae family in the gut.\"\\n },\\n \"3\": {\\n \"feature_id\": \"GO:0015858 * IPR009677 * IPR006541 * sk__Bacteria;k__;p__Firmicutes;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium\",\\n \"feature_label\": \"nucleoside transport * DUF1266 * Bacteriocin-associated integral membrane protein * Phascolarctobacterium genus\",\\n \"bio_property\": \"nucleoside uptake * bacteriocin production * specific microbiota\",\\n \"env_property\": \"nutrient recycling * competitive environment\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Phascolarctobacterium species participate in the recycling of nucleosides and nucleotides, which are key for microbial community balance and competition within the gut. Bacteriocin production helps these microorganisms prevail in such a competitive ecosystem.\"\\n },\\n \"4\": {\\n \"feature_id\": \"GO:0008918 * IPR014234 * IPR006391 * sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Subdoligranulum\",\\n \"feature_label\": \"lipopolysaccharide 3-alpha-galactosyltransferase activity * N-acetylmuramoyl-L-alanine amidase CwlD * P-type ATPase, B chain, subfamily IA * Subdoligranulum genus\",\\n \"bio_property\": \"lipopolysaccharide modification * cell wall remodeling * ion transport\",\\n \"env_property\": \"microbial community stability * nutrient-rich\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The presence of enzymes involved in lipopolysaccharide modification, cell wall remodeling, and ion transport suggests a role for Subdoligranulum in maintaining cell integrity and microbial community stability in the nutrient-rich environment of the large intestine.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR008016 * IPR010960 * IPR017821 * sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales\",\\n \"feature_label\": \"Portal protein Gp10 * Flavocytochrome c * Succinate CoA transferase\",\\n \"bio_property\": \"virus-like particle assembly * electron transfer * succinate metabolism\",\\n \"env_property\": \"variable nutrient levels * controlled competition\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"These features suggest the presence of complex microbial interactions, including virus-like particle assembly (Gp10), efficient electron transfer (Flavocytochrome c), and succinate metabolism. Such functionalities are critical in a dynamic gut environment with varying nutrient levels.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631370, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=994, prompt_tokens=1552, total_tokens=2546))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -5361,18 +5363,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Host-associated:Human:Digestive system:Large intestine:Fecal\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -5435,7 +5437,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 27:\n", - "ChatCompletion(id='chatcmpl-9WpIw8ynK3ZACEloAaEtdHfIzueQA', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Human:Digestive system:Large intestine:Fecal\": {\\n \"1\": {\\n \"feature_id\": \"GO:0015858 * IPR004501\",\\n \"feature_label\": \"nucleoside transport * Phosphotransferase system, EIIC component, type 3\",\\n \"bio_property\": \"nucleoside transport across membranes * carbohydrate transport system\",\\n \"env_property\": \"nutrient-rich * low pH\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Nucleoside transport and phosphotransferase systems are critical in nutrient absorption and carbohydrate metabolism, which is essential in the nutrient-rich, low-pH environment of the large intestine.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0019512 * GO:0033920\",\\n \"feature_label\": \"lactose catabolic process via tagatose-6-phosphate * 6-phospho-beta-galactosidase activity\",\\n \"bio_property\": \"lactose metabolism * carbohydrate breakdown\",\\n \"env_property\": \"high lactose diet * anaerobic conditions\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Lactose catabolic pathways are particularly relevant in environments where a high lactose diet is present, and the activity of these enzymes supports carbohydrate breakdown under anaerobic conditions typical of the large intestine.\"\\n },\\n \"3\": {\\n \"feature_id\": \"GO:0019317 * IPR026366\",\\n \"feature_label\": \"fucose catabolic process * Putative selenium metabolism protein, YedE family\",\\n \"bio_property\": \"fucose metabolism * selenium utilization\",\\n \"env_property\": \"complex carbohydrate diet * presence of trace elements\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The fucose catabolic process and selenium metabolism are crucial for breaking down complex carbohydrates and utilizing trace elements that are often found in complex diets, characteristic of the large intestine environment.\"\\n },\\n \"4\": {\\n \"feature_id\": \"GO:0008743 * IPR019646\",\\n \"feature_label\": \"L-threonine 3-dehydrogenase activity * Aminoglycoside-2\\'\\'-adenylyltransferase\",\\n \"bio_property\": \"amino acid catabolism * antibiotic resistance\",\\n \"env_property\": \"protein-rich diet * exposure to antibiotic residues\",\\n \"confidence\": \"high\",\\n \"explanation\": \"L-threonine dehydrogenase plays a role in amino acid catabolism which is essential in a protein-rich diet, while aminoglycoside transferases confer antibiotic resistance, important in environments where antibiotic residues might be present.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR016041 * IPR024264\",\\n \"feature_label\": \"CO dehydrogenase/acetyl-CoA synthase delta subunit, TIM barrel * Domain of unknown function DUF3786\",\\n \"bio_property\": \"carbon utilization * unknown function possibly related to carbon metabolism\",\\n \"env_property\": \"presence of short-chain fatty acids (SCFAs) * fermentative conditions\",\\n \"confidence\": \"high\",\\n \"explanation\": \"CO dehydrogenase/acetyl-CoA synthase is key for carbon utilization under fermentative conditions producing SCFAs in the gut, and DUF3786 may play an associated unknown role in these processes.\"\\n },\\n \"6\": {\\n \"feature_id\": \"sk__Bacteria;k__;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella * sk__Bacteria;k__;p__Firmicutes;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium\",\\n \"feature_label\": \"Collinsella * Phascolarctobacterium\",\\n \"bio_property\": \"gut microbiota composition * SCFA production\",\\n \"env_property\": \"fiber-rich diet * low oxygen availability\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Both Collinsella and Phascolarctobacterium are integral components of gut microbiota associated with the production of short-chain fatty acids (SCFAs) under low oxygen conditions typical in a fiber-rich diet.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717610738, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=918, prompt_tokens=1259, total_tokens=2177))\n", + "ChatCompletion(id='chatcmpl-9WufvNCfids4AXWHvmOdy94NF1IOX', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='Given the context and requirements of the task, the following JSON object outlines the relationships between microbial metagenomic features and environmental properties in the Host-associated:Human:Digestive system:Large intestine:Fecal ecosystem.\\n\\n```json\\n{\\n \"Host-associated:Human:Digestive system:Large intestine:Fecal\": {\\n \"1\": {\\n \"feature_id\": \"GO:0019317 * GO:0019512 * GO:0033920\",\\n \"feature_label\": \"fucose catabolic process * lactose catabolic process via tagatose-6-phosphate * 6-phospho-beta-galactosidase activity\",\\n \"bio_property\": \"carbohydrate metabolism * energy production\",\\n \"env_property\": \"nutrient-rich * complex carbohydrate substrate\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The large intestine is rich in complex carbohydrates from dietary fibers. These features are involved in the breakdown of these compounds, aiding in energy production and nutrient absorption.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0015858 * IPR004501\",\\n \"feature_label\": \"nucleoside transport * Phosphotransferase system, EIIC component, type 3\",\\n \"bio_property\": \"nucleotide metabolism * transport system\",\\n \"env_property\": \"dynamic nutrient availability * competitive microbial environment\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Efficient transport and utilization of nucleosides are crucial in an environment with varying nutrient availability. The phosphotransferase system indicates structured nutrient uptake pathways to manage competition.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR007920 * IPR010360 * IPR024264\",\\n \"feature_label\": \"Protein of unknown function UPF0223 * Protein of unknown function DUF956 * Domain of unknown function DUF3786\",\\n \"bio_property\": \"potential regulatory roles * hypothetical framework\",\\n \"env_property\": \"unknown specific, assumed complex microbial community interactions\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"While the exact functions are unknown, these proteins may play a role in regulatory processes or interactions within the complex microbial community of the large intestine.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR003563 * IPR009229\",\\n \"feature_label\": \"Oxidized purine nucleoside triphosphate * Staphylococcal AgrD\",\\n \"bio_property\": \"DNA repair * quorum sensing\",\\n \"env_property\": \"high microbial density * oxidative stress\",\\n \"confidence\": \"high\",\\n \"explanation\": \"In a dense microbial environment like the gut, DNA damage repair mechanisms are essential to maintain genomic integrity. Quorum sensing (e.g., AgrD) facilitates microbial communication in high-density settings.\"\\n },\\n \"5\": {\\n \"feature_id\": \"sk__Bacteria;k__;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella * sk__Bacteria;k__;p__Firmicutes;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium * sk__Bacteria;k__;p__Verrucomicrobia;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia\",\\n \"feature_label\": \"Collinsella * Phascolarctobacterium * Akkermansia\",\\n \"bio_property\": \"microbiota composition * host interaction\",\\n \"env_property\": \"anaerobic conditions * presence of mucus layer * dietary fibers\",\\n \"confidence\": \"high\",\\n \"explanation\": \"These genera are known colonizers of the gut, thriving in anaerobic conditions and utilizing dietary fibers and mucus for growth. They play significant roles in host digestion and health.\"\\n }\\n }\\n}\\n```\\n\\n**Explanation of Results:**\\n\\n1. **Carbohydrate Metabolism:** Features associated with fucose and lactose catabolism are crucial in the nutrient-rich environment of the large intestine that contains dietary fibers. These microbial activities are highly relevant for energy production and nutrient absorption.\\n\\n2. **Nucleotide Metabolism and Transport:** Features related to nucleoside transport and the phosphotransferase system demonstrate the importance of nutrient uptake and utilization in a competitive microbial setting, highlighting the need for structured nutrient acquisition strategies.\\n\\n3. **Hypothetical Functions:** Protein domains of unknown function are grouped to suggest potential regulatory or interaction roles within the complex microbial ecosystem, although these associations come with a medium confidence level due to the lack of specific functional information.\\n\\n4. **DNA Repair and Quorum Sensing:** Features for oxidized purine nucleoside triphosphate (DNA repair) and Staphylococcal AgrD (quorum sensing) underscore the significance of maintaining genomic integrity and microbial communication in high-density environments like the large intestine.\\n\\n5. **Microbiota Composition:** The presence of specific bacterial genera (Collinsella, Phascolarctobacterium, Akkermansia) is closely tied to the anaerobic conditions and the availability of dietary fibers and mucus in the large intestine, validating their role in the gut ecosystem and host interactions.\\n\\nThese relationships provide insight into how microbial genomic features correspond to the environmental characteristics and functionalities within the large intestine.', role='assistant', function_call=None, tool_calls=None))], created=1717631383, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=1131, prompt_tokens=1267, total_tokens=2398))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -5458,18 +5460,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Host-associated:Human:Digestive system:Large intestine:Sigmoid colon\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -5571,7 +5573,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 28:\n", - "ChatCompletion(id='chatcmpl-9WpJTqvrfIlHa2TBnDunonniYpMKQ', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Human:Digestive system:Large intestine:Sigmoid colon\": {\\n \"1\": {\\n \"feature_id\": \"GO:0031460 * IPR024735\",\\n \"feature_label\": \"glycine betaine transport * Conjugative transposon protein TcpC\",\\n \"bio_property\": \"osmoprotection * genetic exchange\",\\n \"env_property\": \"high osmolarity\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Glycine betaine acts as an osmoprotectant in high osmolarity environments often found in the gut. Conjugative transposons facilitate horizontal gene transfer, which may include genes for osmoprotection.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0015858 * IPR012727\",\\n \"feature_label\": \"nucleoside transport * Glycine oxidase ThiO\",\\n \"bio_property\": \"nucleotide metabolism * oxidative stress resistance\",\\n \"env_property\": \"low pH * anaerobic\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Nucleoside transport is crucial for nucleotide salvage in the metabolically demanding gut environment. Glycine oxidase is involved in oxidative stress resistance, crucial for survival in the low pH, anaerobic condition of the gut.\"\\n },\\n \"3\": {\\n \"feature_id\": \"GO:0043093 * IPR004759\",\\n \"feature_label\": \"FtsZ-dependent cytokinesis * Glutamate:g-aminobutyrate antiporter\",\\n \"bio_property\": \"bacterial cell division * neurotransmitter regulation\",\\n \"env_property\": \"rich in neurotransmitters * nutrient variability\",\\n \"confidence\": \"high\",\\n \"explanation\": \"FtsZ-dependent cytokinesis indicates active cell division, supported by the nutrient-rich environment of the gut. The Glutamate:g-aminobutyrate antiporter is involved in neurotransmitter regulation, relevant in an environment rich in these compounds.\"\\n },\\n \"4\": {\\n \"feature_id\": \"GO:0019512 * IPR006322\",\\n \"feature_label\": \"lactose catabolic process via tagatose-6-phosphate * Glutathione reductase, eukaryote/bacterial\",\\n \"bio_property\": \"carbohydrate metabolism * antioxidant defense\",\\n \"env_property\": \"high lactose content * oxidative stress\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The large intestine processes high levels of lactose, requiring specific catabolic pathways. Glutathione reductase provides protection against oxidative stress, which is prevalent in metabolically active environments.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR004763 * sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales\",\\n \"feature_label\": \"Cation efflux system CzcA/CusA/SilA/NccA/HelA/CnrA * Clostridiales\",\\n \"bio_property\": \"metal resistance * anaerobic metabolism\",\\n \"env_property\": \"metal exposure * anaerobic\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The cation efflux system is crucial for resisting toxic metals in the gut. Clostridiales\\' ability to thrive in anaerobic conditions complements the low oxygen environment of the large intestine.\"\\n },\\n \"6\": {\\n \"feature_id\": \"GO:0000502 * IPR035391\",\\n \"feature_label\": \"proteasome complex * Arylsulfotransferase, N-terminal domain\",\\n \"bio_property\": \"protein degradation * detoxification\",\\n \"env_property\": \"immune response * high sulfate levels\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Proteasomes are involved in degrading damaged proteins, supporting immune homeostasis. Arylsulfotransferase aids in detoxification of sulfate compounds, relevant in environments with high sulfate levels.\"\\n },\\n \"7\": {\\n \"feature_id\": \"GO:0004638 * IPR015304\",\\n \"feature_label\": \"phosphoribosylaminoimidazole carboxylase activity * ZinT domain\",\\n \"bio_property\": \"purine biosynthesis * zinc homeostasis\",\\n \"env_property\": \"nutrient-rich * presence of heavy metals\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Phosphoribosylaminoimidazole carboxylase is important for purine biosynthesis in nutrient-rich conditions. The ZinT domain helps in zinc homeostasis, crucial for metal presence in the gut.\"\\n },\\n \"8\": {\\n \"feature_id\": \"GO:0019512 * IPR007516\",\\n \"feature_label\": \"lactose catabolic process via tagatose-6-phosphate * Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal\",\\n \"bio_property\": \"carbohydrate metabolism * redox metabolism\",\\n \"env_property\": \"high lactose content * anaerobic\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Lactose metabolism is vital in the gut. Coenzyme F420 hydrogenase/dehydrogenase is involved in redox reactions, which are essential in the reducing environment of the large intestine.\"\\n }\\n }\\n}\\n```\\n\\nThis output structure provides detailed and reliable associations between observed microbiological features in the sigmoid colon environment and its corresponding biological and environmental properties with clearly defined confidence levels.', role='assistant', function_call=None, tool_calls=None))], created=1717610771, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=1145, prompt_tokens=1857, total_tokens=3002))\n", + "ChatCompletion(id='chatcmpl-9WugEOb9ibHMJFcn8d18YpKa6UTon', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Human:Digestive system:Large intestine:Sigmoid colon\": {\\n \"1\": {\\n \"feature_id\": \"GO:0015858 * IPR006322 * IPR011868\",\\n \"feature_label\": \"nucleoside transport * Glutathione reductase, eukaryote/bacterial * Molybdate ABC transporter, ATP-binding protein\",\\n \"bio_property\": \"transport processes * redox balance * nutrient acquisition\",\\n \"env_property\": \"nutrient-rich environment * low pH\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Nucleoside transport and nutrient acquisition are critical for microbial survival in the nutrient-rich sigmoid colon. The glutathione reductase and molybdate transporter help manage oxidative stress and nutrient acquisition in this low pH environment.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0019512 * GO:0033920 * IPR001360\",\\n \"feature_label\": \"lactose catabolic process via tagatose-6-phosphate * 6-phospho-beta-galactosidase activity * Glycoside hydrolase family 1\",\\n \"bio_property\": \"carbohydrate metabolism * energy generation\",\\n \"env_property\": \"presence of complex carbohydrates\",\\n \"confidence\": \"high\",\\n \"explanation\": \"These features are involved in the breakdown and metabolism of lactose and other carbohydrates prevalent in the diet. This highlights how the microbial community adapts to carbohydrate-rich conditions in the sigmoid colon.\"\\n },\\n \"3\": {\\n \"feature_id\": \"GO:0043093 * IPR004763 * IPR026345\",\\n \"feature_label\": \"FtsZ-dependent cytokinesis * Cation efflux system CzcA/CusA/SilA/NccA/HelA/CnrA * Adhesin isopeptide-forming adherence domain\",\\n \"bio_property\": \"cell division * ion transport * adherence\",\\n \"env_property\": \"high microbial density\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Features related to cell division, ion transport, and adherence reflect adaptation to a densely populated environment where microbes need to efficiently divide, manage ionic stress, and attach to surfaces.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR004764 * IPR005694 * IPR018721\",\\n \"feature_label\": \"Hydrophobe/amphiphile efflux-1 HAE1 * Efflux pump membrane protein * Protein of unknown function DUF2252\",\\n \"bio_property\": \"efflux systems * resistance mechanisms\",\\n \"env_property\": \"antibiotic presence * toxic compound presence\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Efflux systems are essential for dealing with toxic compounds and antibiotics that may be present in the large intestine, contributing to microbial resistance mechanisms in the gut environment.\"\\n },\\n \"5\": {\\n \"feature_id\": \"sk__Bacteria * sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales * sk__Bacteria;k__;p__Actinobacteria;c__Coriobacteriia;o__Eggerthellales\",\\n \"feature_label\": \"Bacteria * Firmicutes * Actinobacteria\",\\n \"bio_property\": \"microbial diversity * community structure\",\\n \"env_property\": \"anoxic conditions * presence of complex organic matter\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The presence of diverse bacterial groups such as Firmicutes and Actinobacteria indicates a complex, anoxic environment rich in organic matter that supports a diverse microbial community.\"\\n }\\n }\\n}\\n```\\nThis JSON output elucidates the relationships between various microbial metagenomic features and environmental properties in the sigmoid colon. Each feature or subset of features is thoroughly examined to provide a reliable association, with a focus on multiple features sharing biological properties, thereby enhancing the confidence of inferred relationships.', role='assistant', function_call=None, tool_calls=None))], created=1717631402, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=832, prompt_tokens=1864, total_tokens=2696))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -5594,18 +5596,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Host-associated:Human:Digestive system:Oral\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -5642,7 +5644,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 29:\n", - "ChatCompletion(id='chatcmpl-9WpKFBRbn2ZOlR0QKJBqDa1liDnuF', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Human:Digestive system:Oral\": {\\n \"1\": {\\n \"feature_id\": \"IPR001077 * GO:0008171\",\\n \"feature_label\": \"O-methyltransferase domain * O-methyltransferase activity\",\\n \"bio_property\": \"methanol biosynthesis * secondary metabolite biosynthesis\",\\n \"env_property\": \"variable pH * varied nutrient availability\",\\n \"confidence\": \"high\",\\n \"explanation\": \"O-methyltransferases are involved in the biosynthesis of various secondary metabolites and can affect the microbial ecology by altering organic compound profiles responsive to nutrient variability and pH changes in the oral cavity.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR008013 * GO:0070323\",\\n \"feature_label\": \"GATA-type transcription activator, N-terminal * DNA-binding transcription factor activity\",\\n \"bio_property\": \"gene expression regulation * cellular differentiation\",\\n \"env_property\": \"anaerobic pockets * host-microbe interface\",\\n \"confidence\": \"high\",\\n \"explanation\": \"GATA-type transcription factors regulate transcription in response to oxygen gradients within biofilms and anaerobic microenvironments in the oral ecosystem, crucial for microbial survival at the host interface.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR019108 * GO:0006123\",\\n \"feature_label\": \"Cytochrome c oxidase caa3-type, assembly factor CtaG-related * cytochrome-c oxidase activity\",\\n \"bio_property\": \"electron transport chain * aerobic respiration\",\\n \"env_property\": \"fluctuating oxygen levels * host-derived nutrients\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Cytochrome c oxidase is integral to the electron transport chain and aerobic respiration, allowing microbes to adapt to fluctuating oxygen levels and varying availability of nutrients derived from the host.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR026395 * GO:0031460\",\\n \"feature_label\": \"CshA domain * RNA helicase activity\",\\n \"bio_property\": \"RNA processing * translation regulation\",\\n \"env_property\": \"thermal gradients * salivary fluid dynamics\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"RNA helicases like CshA play a role in RNA metabolism and protein synthesis, allowing microbes to modulate gene expression in response to thermal changes and varying salivary fluid conditions.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR030985 * sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Eubacteriaceae;g__Eubacterium;s__Eubacterium_sp._oral_clone_FX028\",\\n \"feature_label\": \"Putative peptide maturation system protein * Eubacterium_sp._oral_clone_FX028\",\\n \"bio_property\": \"peptide modification * proteolysis\",\\n \"env_property\": \"nutrient gradients * interspecies interactions\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Peptide maturation systems and proteolysis are crucial for microbial interactions and nutrient acquisition, influencing microbial community dynamics within the complex nutrient gradients of the oral cavity.\"\\n },\\n \"6\": {\\n \"feature_id\": \"sk__Archaea;k__;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter;s__Methanobrevibacter_oralis * IPR021447\",\\n \"feature_label\": \"Methanobrevibacter_oralis * Protein of unknown function DUF3097\",\\n \"bio_property\": \"methanogenesis * unknown protein function\",\\n \"env_property\": \"anaerobic niches * biofilm formation\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Methanobrevibacter oralis is a key archaeon in anaerobic niches associated with methanogenesis, contributing to oral microbial ecology. The function of DUF3097 is unknown, but it may play a role in biofilm dynamics or methanogenic pathways.\"\\n },\\n \"7\": {\\n \"feature_id\": \"IPR032576 * GO:0006397\",\\n \"feature_label\": \"Domain of unknown function DUF4921 * mRNA processing\",\\n \"bio_property\": \"mRNA modification * genetic regulation\",\\n \"env_property\": \"biotic stress * nutrient variability\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Although the exact role of DUF4921 is unclear, its association with mRNA processing suggests it may help microbes respond to biotic stresses and environmental nutrient fluctuations in the oral cavity.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717610819, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=1003, prompt_tokens=818, total_tokens=1821))\n", + "ChatCompletion(id='chatcmpl-9WugSxgODPHIdL29z8x6GKjVj93Pu', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Human:Digestive system:Oral\": {\\n \"1\": {\\n \"feature_id\": \"IPR001077 * IPR021447\",\\n \"feature_label\": \"O-methyltransferase domain * Protein of unknown function DUF3097\",\\n \"bio_property\": \"methylation * structural function\",\\n \"env_property\": \"microbiome diversity * nutrient-rich\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The presence of the O-methyltransferase domain (involved in methylation processes) alongside proteins with unknown functions (DUF3097) indicates a diverse and complex microbial community with potentially unique metabolic capabilities in an environment like the oral cavity rich in various nutrients.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR008013 * sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Eubacteriaceae;g__Eubacterium;s__Eubacterium_sp._oral_clone_FX028\",\\n \"feature_label\": \"GATA-type transcription activator, N-terminal * Eubacterium sp. oral clone FX028\",\\n \"bio_property\": \"transcription regulation * bacterial component\",\\n \"env_property\": \"microbiome diversity * variable pH\",\\n \"confidence\": \"high\",\\n \"explanation\": \"GATA-type transcription activators play a role in regulating gene expression. In presence of Eubacterium species, these regulators can be crucial for adapting to the variable pH conditions of the oral cavity.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR019108 * sk__Archaea;k__;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter;s__Methanobrevibacter_oralis\",\\n \"feature_label\": \"Cytochrome c oxidase caa3-type, assembly factor CtaG-related * Methanobrevibacter oralis\",\\n \"bio_property\": \"electron transport chain * archaeal component\",\\n \"env_property\": \"anoxic microenvironments * nutrient-rich\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Cytochrome c oxidase assembly factors are essential for electron transport chains in Methanobrevibacter oralis, indicating adaptation to anoxic niches within the oral cavity, where nutrient availability facilitates diverse metabolic interactions.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR026395 * IPR030985\",\\n \"feature_label\": \"CshA domain * Putative peptide maturation system protein\",\\n \"bio_property\": \"RNA helicase activity * peptide processing\",\\n \"env_property\": \"microbiome diversity * temperature stable\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"The CshA domain is associated with RNA helicase activity which is vital for microbial RNA processing. Coupled with peptide maturation systems, it highlights the metabolic complexity and adaptability needed to thrive in the stable temperature conditions of the human oral cavity.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631416, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=659, prompt_tokens=829, total_tokens=1488))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -5665,18 +5667,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Host-associated:Human:Digestive system:Oral:Saliva\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -5724,7 +5726,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 30:\n", - "ChatCompletion(id='chatcmpl-9WpKcbtUE4RWad9ORiRc2lPKMOMxk', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Human:Digestive system:Oral:Saliva\": {\\n \"1\": {\\n \"feature_id\": \"GO:0004352 * GO:0033920 * IPR004868 * IPR012706\",\\n \"feature_label\": \"glutamate dehydrogenase (NAD+) activity * 6-phospho-beta-galactosidase activity * DNA-directed DNA polymerase, family B, mitochondria/virus * Rib/alpha/Esp surface antigen\",\\n \"bio_property\": \"amino acid metabolism * lactose degradation * DNA replication and repair * surface adherence\",\\n \"env_property\": \"moist * nutrient-rich\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The saliva environment is rich in nutrients, supporting diverse metabolic activities including amino acid metabolism and lactose degradation. DNA repair and replication are essential for maintaining integrity in a complex microbial community, and surface antigens assist in microbial adhesion to oral tissues.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR004300 * IPR010960 * IPR015304\",\\n \"feature_label\": \"Glycoside hydrolase family 57, N-terminal domain * Flavocytochrome c * ZinT domain\",\\n \"bio_property\": \"carbohydrate metabolism * electron transport * metal ion binding\",\\n \"env_property\": \"fluctuating oxygen levels * variable metal ion concentrations\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Glycoside hydrolases facilitate carbohydrate breakdown in the nutrient-rich oral environment. Flavocytochrome c is involved in electron transport processes under fluctuating oxygen levels. ZinT domain proteins help in metal ion homeostasis, adapting to variable concentrations.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR008016 * IPR021505 * IPR022458\",\\n \"feature_label\": \"Portal protein Gp10 * Bacteriophage B3, Orf6 * Conjugative coupling factor TraG/TraD\",\\n \"bio_property\": \"viral infection and propagation * conjugative transfer\",\\n \"env_property\": \"high microbial diversity\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The high microbial diversity in saliva supports viral replication and horizontal gene transfer, facilitated by bacteriophages and conjugative elements. These processes contribute to genetic variability and adaptation of the oral microbiome.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR007210 * GO:0031460\",\\n \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\\n \"bio_property\": \"osmoprotection * stress response\",\\n \"env_property\": \"saliva\\'s variable osmolarity\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Glycine betaine functions as an osmoprotectant in environments with variable osmolarity, as found in the oral cavity. This provides microbial protection against osmotic stress.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR011119 * IPR028962 * IPR031012\",\\n \"feature_label\": \"Uncharacterised domain, helicase/relaxase, putative * Immunity protein 10 * Radical SAM mobile pair protein B\",\\n \"bio_property\": \"genome stability * bacteriophage immunity * radical-mediated enzymatic activity\",\\n \"env_property\": \"dynamic microbial interactions\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"The dynamic microbial interactions within the oral cavity necessitate mechanisms for genome stability and bacteriophage immunity. Radical SAM proteins contribute to various enzymatic reactions critical for microbial survival.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717610842, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=778, prompt_tokens=911, total_tokens=1689))\n", + "ChatCompletion(id='chatcmpl-9WugaQNTniecEAWzKBPPaF6VDWsgF', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Human:Digestive system:Oral:Saliva\": {\\n \"1\": {\\n \"feature_id\": \"GO:0033920 * IPR004300\",\\n \"feature_label\": \"6-phospho-beta-galactosidase activity * Glycoside hydrolase family 57, N-terminal domain\",\\n \"bio_property\": \"carbohydrate metabolism * glycoside hydrolase activity\",\\n \"env_property\": \"nutrient-rich * variable pH * presence of dietary sugars\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The activity of 6-phospho-beta-galactosidase and glycoside hydrolase are crucial for the breakdown of dietary sugars in the nutrient-rich and variably pH-fluctuating environment of saliva.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR010960 * IPR028049\",\\n \"feature_label\": \"Flavocytochrome c * NTF2 fold immunity protein\",\\n \"bio_property\": \"electron transport chain * immune-related functions\",\\n \"env_property\": \"microbiome diversity * divergent redox conditions\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Flavocytochrome c is involved in the electron transport chain which can vary according to different redox conditions in the oral saliva. The NTF2 fold immunity protein plays a role in the microbial competition within a diverse microbiome.\"\\n },\\n \"3\": {\\n \"feature_id\": \"GO:0004352 * IPR022458\",\\n \"feature_label\": \"glutamate dehydrogenase (NAD+) activity * Conjugative coupling factor TraG/TraD\",\\n \"bio_property\": \"amino acid metabolism * DNA transfer and replication\",\\n \"env_property\": \"inter-organism interactions * high microbial turnover\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Glutamate dehydrogenase activity is indicative of amino acid metabolism that supports microbial growth, whereas conjugative coupling factors like TraG/TraD are critical for horizontal gene transfer in environments with high microbial turnover and diversity.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR004868 * IPR011119\",\\n \"feature_label\": \"DNA-directed DNA polymerase, family B, mitochondria/virus * Uncharacterised domain, helicase/relaxase, putative\",\\n \"bio_property\": \"DNA replication and repair * helicase activity\",\\n \"env_property\": \"genomic stability * environmental DNA flux\",\\n \"confidence\": \"high\",\\n \"explanation\": \"DNA-directed DNA polymerase and helicase/relaxase activity are essential for maintaining genomic stability and managing the high environmental DNA flux common in the complex oral microbiome.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR032576 * IPR028962\",\\n \"feature_label\": \"Domain of unknown function DUF4921 * Immunity protein 10\",\\n \"bio_property\": \"protein interaction * immunity functions\",\\n \"env_property\": \"microbial competition * host immune response\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"The prevalence of immunity-related proteins and various protein domains of unknown function suggests adaptation strategies to cope with microbial competition and host immune response in the oral environment.\"\\n },\\n \"6\": {\\n \"feature_id\": \"IPR035576 * IPR021505\",\\n \"feature_label\": \"Type VI secretion system TssC * Bacteriophage B3, Orf6\",\\n \"bio_property\": \"bacterial pathogenicity * phage interaction\",\\n \"env_property\": \"interspecies microbial warfare * dynamic microbial populations\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The Type VI secretion system (TssC) and bacteriophage proteins are indicative of interspecies microbial warfare and dynamic microbial population structures typical in the saliva ecosystem.\"\\n },\\n \"7\": {\\n \"feature_id\": \"IPR028962 * IPR015304\",\\n \"feature_label\": \"Immunity protein 10 * ZinT domain\",\\n \"bio_property\": \"immune defenses * zinc transport\",\\n \"env_property\": \"trace metal availability * host-microbe interactions\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Immunity protein and zinc transport-related domains reflect adaptation mechanisms to manage trace metal availability and enhanced host-microbe interactions within the oral environment.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631424, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=937, prompt_tokens=919, total_tokens=1856))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -5747,18 +5749,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Host-associated:Human:Skin\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -5812,7 +5814,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 31:\n", - "ChatCompletion(id='chatcmpl-9WpKzZ8oIdk6h9F2lAUlYyaAuYAiW', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='Below are the identified relationships between the microbial metagenomic features in the Host-associated:Human:Skin ecosystem and environmental properties. The relationships are focused on groups of features when possible and are presented with high confidence:\\n\\n```json\\n{\\n \"Host-associated:Human:Skin\": {\\n \"1\": {\\n \"feature_id\": \"IPR010706 * GO:0004037\",\\n \"feature_label\": \"Fatty acid cis-trans isomerase * allantoicase activity\",\\n \"bio_property\": \"membrane adaptation * nitrogen metabolism\",\\n \"env_property\": \"desiccation * nutrient variability\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Fatty acid cis-trans isomerase is involved in altering membrane fluidity under stress conditions like desiccation. Allantoicase participates in nitrogen metabolism, which can be crucial in environments with variable nutrient availability.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR017821 * IPR010945\",\\n \"feature_label\": \"Succinate CoA transferase * Malate dehydrogenase, type 2\",\\n \"bio_property\": \"metabolic versatility * energy metabolism\",\\n \"env_property\": \"nutrient variability * fluctuating moisture\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Both succinate CoA transferase and malate dehydrogenase type 2 are involved in metabolic processes that allow microbes to adapt to varying nutrient compositions and moisture levels in the skin environment.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR000938 * IPR014984\",\\n \"feature_label\": \"CAP Gly-rich domain * HopJ type III effector protein\",\\n \"bio_property\": \"transcriptional regulation * host interaction\",\\n \"env_property\": \"host immune evasion * inflammatory conditions\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The CAP Gly-rich domain is involved in transcriptional regulation, including stress responses, while HopJ effectors are known for manipulating host immune responses, relevant to managing inflammation and immune evasion on the skin surface.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR017523 * IPR032576\",\\n \"feature_label\": \"Conserved hypothetical protein CHP03089 * Domain of unknown function DUF4921\",\\n \"bio_property\": \"structural integrity * unknown function (potential stress response)\",\\n \"env_property\": \"physical abrasion * microenvironmental stress\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Conserved hypothetical proteins often play roles in maintaining cellular or structural integrity under various stressors, and domains of unknown function like DUF4921, often are later found to contribute to stress response mechanisms, helping microbes withstand skin surface conditions.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR012706 * IPR026359\",\\n \"feature_label\": \"Rib/alpha/Esp surface antigen * SasC/Mrp/FmtB intercellular aggregation domain\",\\n \"bio_property\": \"surface adhesion * biofilm formation\",\\n \"env_property\": \"biotic interactions * stable microbial communities\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Rib/alpha/Esp surface antigens and aggregation domains are known to facilitate surface adhesion and biofilm formation, essential for maintaining stable microbial communities on the skin by mediating interactions between microbial populations and with the host cells.\"\\n }\\n }\\n}\\n```\\n\\n### Summary:\\n- The listed features demonstrate significant relationships between microbial genetic expressions and adaptations necessary for surviving and thriving in the unique environment of human skin, correlating with various environmental stresses and nutrient dynamics.\\n- The confidence levels for associations between features and environmental properties are all high, ensuring reliable data for understanding these relationships.\\n\\nThis dataset provides insight into the resilience and adaptability of skin-associated microbial communities, emphasizing the biological properties aligning with specific environmental conditions.', role='assistant', function_call=None, tool_calls=None))], created=1717610865, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=799, prompt_tokens=1020, total_tokens=1819))\n", + "ChatCompletion(id='chatcmpl-9Wugq1dGMaz6J6RapXh6uQfz7EMpr', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Human:Skin\": {\\n \"1\": {\\n \"feature_id\": \"IPR010706 * GO:0004037 * IPR010945 * IPR010518 * IPR017821\",\\n \"feature_label\": \"Fatty acid cis-trans isomerase * allantoicase activity * Malate dehydrogenase, type 2 * Flagellar regulatory protein FleQ * Succinate CoA transferase\",\\n \"bio_property\": \"fatty acid metabolism * allantoate degradation * malate oxidation * flagellar regulation * succinate conversion\",\\n \"env_property\": \"exposure to UV radiation * presence of fatty acids * need for motility * variable hydration levels\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Fatty acid cis-trans isomerase and malate dehydrogenase are involved in fatty acid metabolism and oxidation essential for energy production in fluctuating hydration levels. Flagellar regulatory protein FleQ is important for motility, aiding bacteria to navigate the host skin\\'s complex environment. Succinate CoA transferase is significant for succinate conversion in energy pathways. Allantoate degradation is pertinent due to the breakdown of nitrogenous compounds on skin.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR000938 * IPR009272 * IPR012706 * IPR022387 * IPR031631\",\\n \"feature_label\": \"CAP Gly-rich domain * Protein of unknown function DUF929 * Rib/alpha/Esp surface antigen * Carbohydrate ABC transporter substrate-binding, CPR0540 * Glycosyl hydrolase family 63, N-terminal\",\\n \"bio_property\": \"adhesion * unknown function * antigenic variation * carbohydrate transport * carbohydrate metabolism\",\\n \"env_property\": \"host immune response * nutrient utilization * microbial community interaction\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The CAP Gly-rich domain is crucial for adhesion, aiding microbial persistence in the host habitat. The Rib/alpha/Esp surface antigen participates in immune evasion through antigenic variation. Carbohydrate ABC transporters and glycosyl hydrolases are essential for nutrient acquisition and metabolism on the skin, supporting microbial survival and growth.\"\\n },\\n \"3\": {\\n \"feature_id\": \"sk__Bacteria;k__;p__Proteobacteria;c__Betaproteobacteria;o__Neisseriales;f__Neisseriaceae;g__Neisseria;s__Neisseria_meningitidis * IPR019949 * IPR032124 * IPR032191 * IPR032193\",\\n \"feature_label\": \"Neisseria meningitidis * Luciferase family oxidoreductase, group 1 * Bacteriophage F116-like holin * CCR4-NOT transcription complex subunit 1, CAF1-binding domain * CCR4-NOT transcription complex subunit 1, TTP binding domain\",\\n \"bio_property\": \"pathogenicity * bioluminescence * phage function * transcriptional regulation\",\\n \"env_property\": \"pathogenic potential * interaction with viruses\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Neisseria meningitidis is a known pathogen with the ability to evade host defenses. Luciferase family oxidoreductases contribute to oxidative stress responses. Bacteriophage holins are important for phage cycle regulation, impacting bacterial-viral interactions on the skin. CCR4-NOT transcription complex is involved in transcriptional regulation, crucial for bacterial adaptability in response to environmental stressors.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR014984 * IPR017523 * IPR031636\",\\n \"feature_label\": \"HopJ type III effector protein * Conserved hypothetical protein CHP03089 * Protein kinase G, tetratricopeptide repeat containing domain\",\\n \"bio_property\": \"effector function * conserved protein function * phosphorylation signaling\",\\n \"env_property\": \"bacterial-host interaction * signal transduction\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"HopJ type III effector proteins play a role in pathogenicity via manipulation of host processes. Conserved hypothetical proteins suggest essential but unknown functions. Protein kinase G with TPR domains is involved in signal transduction, essential for microbial responses to environmental cues on the skin.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR032576 * IPR021250 * IPR018067\",\\n \"feature_label\": \"Domain of unknown function DUF4921 * Protein of unknown function DUF2789 * Protein phosphatase 2A regulatory subunit PR55, conserved site\",\\n \"bio_property\": \"unknown function * regulatory function\",\\n \"env_property\": \"desiccation resistance * nutrient variability\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"While functions of DUF4921 and DUF2789 remain unknown, their presence indicates potential roles in stress response and survival. Protein phosphatase 2A regulatory subunits are involved in regulatory activities, suggesting a response to nutrient variability and environmental stress on the skin.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631440, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=1067, prompt_tokens=1036, total_tokens=2103))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -5835,18 +5837,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Host-associated:Human:Skin:Naris\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -5898,7 +5900,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 32:\n", - "ChatCompletion(id='chatcmpl-9WpLI85WQ3ETQ97acr7BGxXMsxzMb', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Human:Skin:Naris\": {\\n \"1\": {\\n \"feature_id\": \"GO:0019317 * GO:0019512 * GO:0033920\",\\n \"feature_label\": \"fucose catabolic process * lactose catabolic process via tagatose-6-phosphate * 6-phospho-beta-galactosidase activity\",\\n \"bio_property\": \"catabolism of sugars * carbohydrate metabolism\",\\n \"env_property\": \"nutrient-rich * chemically complex\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The presence of genes involved in the catabolism of fucose, lactose, and other carbohydrates indicates the ability of the microbial community to utilize a variety of sugars, which is consistent with an environment rich in diverse chemical substrates such as the human skin where various complex carbohydrates are available.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR007298 * IPR011868 * IPR007445\",\\n \"feature_label\": \"Copper resistance lipoprotein NlpE * Molybdate ABC transporter, ATP-binding protein * Type IV pilus inner membrane component PilO\",\\n \"bio_property\": \"metal resistance * nutrient uptake * surface adhesion\",\\n \"env_property\": \"metal availability * nutrient variability * high microbial interaction\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Copper resistance proteins and transport systems, along with surface adhesion components, suggest adaptations to an environment with variable metal concentrations and competitive microbial interactions, typical of the human skin where trace metals from sweat and environmental interactions are common.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR006541 * IPR010133 * IPR019895\",\\n \"feature_label\": \"Bacteriocin-associated integral membrane protein * Bacteriocin-type signal sequence * Putative bacteriocin export ABC transporter, lactococcin 972 group\",\\n \"bio_property\": \"bacteriocin production * antimicrobial competition\",\\n \"env_property\": \"competitive microbial community\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The presence of bacteriocin-related proteins suggests that the microbial community is engaged in competitive interactions through the production of antimicrobial peptides, a typical feature of densely populated environments such as the human skin.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR008557 * IPR017821 * IPR001096\",\\n \"feature_label\": \"Alkaline phosphatase PhoX * Succinate CoA transferase * Peptidase C13, legumain\",\\n \"bio_property\": \"phosphate metabolism * TCA cycle * proteolysis\",\\n \"env_property\": \"variable pH * nutrient processing\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The presence of proteins involved in phosphate metabolism, the TCA cycle, and proteolysis indicates adaptations to an environment where pH and nutrient availability may vary, reflecting the dynamic conditions of the human skin.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR012770 * IPR035364\",\\n \"feature_label\": \"Trehalose operon transcriptional repressor * Glycosyl hydrolase 101, beta-sandwich domain\",\\n \"bio_property\": \"sugar signaling and regulation * carbohydrate breakdown\",\\n \"env_property\": \"nutrient variability\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Components involved in sugar regulation and breakdown suggest the ability to adapt to fluctuating nutrient conditions, indicating that the microbial community can efficiently manage and recycle nutrients on the human skin.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717610884, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=754, prompt_tokens=991, total_tokens=1745))\n", + "ChatCompletion(id='chatcmpl-9Wuh3gTDzLV0F44ZbBemkwa2jEgef', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Human:Skin:Naris\": {\\n \"1\": {\\n \"feature_id\": \"GO:0019317 * GO:0019512 * GO:0033920\",\\n \"feature_label\": \"fucose catabolic process * lactose catabolic process via tagatose-6-phosphate * 6-phospho-beta-galactosidase activity\",\\n \"bio_property\": \"carbohydrate metabolism\",\\n \"env_property\": \"nutrient-rich\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The skin has a variety of oligosaccharides and polysaccharides derived from human secretion and microbial sources. These enzymes indicate the presence of catabolic pathways to utilize these complex carbohydrates as nutrient sources.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR007298 * IPR008557\",\\n \"feature_label\": \"Copper resistance lipoprotein NlpE * Alkaline phosphatase PhoX\",\\n \"bio_property\": \"metal ion homeostasis * phosphate metabolism\",\\n \"env_property\": \"high metal ion concentration * nutrient availability\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Copper and phosphate regulation are crucial for microbial survival in the skin environment, which is known to contain various metal ions and nutrient levels from sweat and other secretions.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR006541 * IPR010133 * IPR019895\",\\n \"feature_label\": \"Bacteriocin-associated integral membrane protein * Bacteriocin-type signal sequence * Putative bacteriocin export ABC transporter, lactococcin 972 group\",\\n \"bio_property\": \"bacteriocin production and export\",\\n \"env_property\": \"competitive microbial environment\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Bacteriocins are antimicrobial peptides produced to inhibit the growth of competing bacteria, which is significant in the dense and competitive microbial communities on human skin.\"\\n },\\n \"4\": {\\n \"feature_id\": \"GO:0004352 * IPR010945 * IPR017821\",\\n \"feature_label\": \"glutamate dehydrogenase (NAD+) activity * Malate dehydrogenase, type 2 * Succinate CoA transferase\",\\n \"bio_property\": \"amino acid metabolism * TCA cycle\",\\n \"env_property\": \"oxygen availability * metabolic flexibility\",\\n \"confidence\": \"high\",\\n \"explanation\": \"These enzymes participate in the TCA cycle and amino acid metabolism which are crucial for energy production and metabolic adaptability in the fluctuating aerobic-anaerobic conditions present on the skin.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR011868 * IPR018148 * IPR026359\",\\n \"feature_label\": \"Molybdate ABC transporter, ATP-binding protein * Methylglyoxal synthase, active site * SasC/Mrp/FmtB intercellular aggregation domain\",\\n \"bio_property\": \"molybdate transport * stress response * cell aggregation\",\\n \"env_property\": \"trace element presence * cellular stress * biofilm formation\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Transport of trace elements like molybdate, stress response mechanisms, and cell aggregation are critical for survival and persistence in the skin ecosystem, which is exposed to environmental stressors and requires microbial aggregation for biofilm formation.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631453, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=722, prompt_tokens=1005, total_tokens=1727))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -5921,18 +5923,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Host-associated:Mammals:Digestive system\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -5991,7 +5993,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 33:\n", - "ChatCompletion(id='chatcmpl-9WpLcBSlxoyFieJRYaRqAgBo8TXap', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Mammals:Digestive system\": {\\n \"1\": {\\n \"feature_id\": \"GO:0004352\",\\n \"feature_label\": \"glutamate dehydrogenase (NAD+) activity\",\\n \"bio_property\": \"amino acid metabolism * nitrogen metabolism\",\\n \"env_property\": \"high protein diet * nitrogen rich\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Glutamate dehydrogenase plays a key role in the catabolism of amino acids, converting glutamate to α-ketoglutarate and ammonia. High activity correlates with nitrogen-rich environments due to protein degradation.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR007210 * GO:0031460\",\\n \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\\n \"bio_property\": \"osmoprotection * stress response\",\\n \"env_property\": \"high osmolarity * fluctuating moisture levels\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Glycine betaine is a known osmoprotectant in high osmolarity environments, aiding microbial cells in coping with osmotic stress.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR000036 * GO:0006928\",\\n \"feature_label\": \"Peptidase A26, omptin * obsolete movement of cell or subcellular component\",\\n \"bio_property\": \"protein degradation * movement regulation\",\\n \"env_property\": \"microbial competition * dense microbial communities\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Omptins are proteases that modulate cell surfaces and can play roles in microbial interactions and competition, which is significant in densely populated microbial environments.\"\\n },\\n \"4\": {\\n \"feature_id\": \"GO:0016539\",\\n \"feature_label\": \"intein-mediated protein splicing\",\\n \"bio_property\": \"post-translational modification * protein processing\",\\n \"env_property\": \"fluctuating environmental conditions * stress adaptation\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Intein-mediated protein splicing is important for protein maturation processes, which can be critical in environments where adaptive response to stress and fluctuating conditions is necessary.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR014983\",\\n \"feature_label\": \"GAD-related\",\\n \"bio_property\": \"glutamate metabolism * neurotransmitter regulation\",\\n \"env_property\": \"high protein diet * gut-brain axis\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The glutamate decarboxylase (GAD)-related proteins are crucial in the conversion of glutamate to GABA, linking amino acid metabolism to gut-brain interactions and nutrient processing.\"\\n },\\n \"6\": {\\n \"feature_id\": \"IPR014580\",\\n \"feature_label\": \"Uncharacterised conserved protein UCP033199\",\\n \"bio_property\": \"unknown conservation\",\\n \"env_property\": \"stable long-term conditions * co-evolution with host\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"While its function is unknown, conserved proteins may indicate stable, co-evolved symbiotic relationships within the host environment.\"\\n },\\n \"7\": {\\n \"feature_id\": \"IPR021505 * sk__Bacteria;k__;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae\",\\n \"feature_label\": \"Bacteriophage B3, Orf6 * Prevotellaceae\",\\n \"bio_property\": \"phage-host interaction * microbial regulation\",\\n \"env_property\": \"microbiome diversity * phage impact on microbial communities\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Bacteriophages like B3 can influence microbial population dynamics, impacting species like Prevotellaceae within the gut microbiome.\"\\n },\\n \"8\": {\\n \"feature_id\": \"IPR022380 * IPR019235\",\\n \"feature_label\": \"Glutamyl-Q tRNA(Asp) synthetase * Protein of unknown function DUF2178, transmembrane\",\\n \"bio_property\": \"tRNA aminoacylation * transmembrane protein function\",\\n \"env_property\": \"nutrient absorption * cellular communication\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Glutamyl-Q tRNA synthetase and transmembrane proteins are essential for proper functioning of translation processes and nutrient transport across cell membranes in nutrient-rich environments.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717610904, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=981, prompt_tokens=1147, total_tokens=2128))\n", + "ChatCompletion(id='chatcmpl-9WuhHSO12FDf9aQQPAUFTK6JZYevN', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Mammals:Digestive system\": {\\n \"1\": {\\n \"feature_id\": \"GO:0004352 * IPR003563\",\\n \"feature_label\": \"glutamate dehydrogenase (NAD+) activity * Oxidized purine nucleoside triphosphate\",\\n \"bio_property\": \"amino acid metabolism * nucleic acid repair\",\\n \"env_property\": \"nutrient-rich * variable pH\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Glutamate dehydrogenase activity is involved in amino acid metabolism, important in nutrient-rich environments like the digestive system where amino acids are abundant. Oxidized purine nucleoside triphosphate repair is significant for maintaining genomic integrity in variable pH conditions.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR000036 * GO:0006928\",\\n \"feature_label\": \"Peptidase A26, omptin * obsolete movement of cell or subcellular component\",\\n \"bio_property\": \"proteolysis * cellular migration\",\\n \"env_property\": \"dynamic microbial communities * high microbial load\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Peptidase A26 is crucial for proteolysis and processing proteins in environments with high microbial interactions. Cellular migration, although obsolete, indicates a dynamic environment with constant microbial movement.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR007117 * IPR008983\",\\n \"feature_label\": \"Expansin, cellulose-binding-like domain * Tumour necrosis factor-like domain superfamily\",\\n \"bio_property\": \"cell wall degradation * immune response modulation\",\\n \"env_property\": \"high fiber diet * host immune interactions\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Expansins play roles in degrading cellulose in high fiber diets. Tumour necrosis factor-like domains suggest interactions with the host\\'s immune system.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR012657 * IPR014583\",\\n \"feature_label\": \"23S rRNA-intervening sequence protein * Uncharacterised conserved protein UCP033199\",\\n \"bio_property\": \"ribosome biogenesis * conserved domain functions\",\\n \"env_property\": \"complex microbial interactions * optimized protein synthesis\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Ribo-bases are essential for protein synthesis in environments with complex microbial interactions. Conserved proteins may play roles in maintaining essential functions amidst diverse microbial communities.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR014983 * GO:0017148\",\\n \"feature_label\": \"GAD-related * negative regulation of translation\",\\n \"bio_property\": \"glutamate regulation * translational control\",\\n \"env_property\": \"fluctuating nutrient availability * environmental stress\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"GAD-related proteins are involved in glutamate regulation under variable nutrient conditions. Negative regulation of translation responds to environmental stressors.\"\\n },\\n \"6\": {\\n \"feature_id\": \"sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae * sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae\",\\n \"feature_label\": \"Lachnospiraceae * Ruminococcaceae\",\\n \"bio_property\": \"polysaccharide fermentation * butyrate production\",\\n \"env_property\": \"high fiber diet * anaerobic conditions\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Lachnospiraceae and Ruminococcaceae members are key polysaccharide fermenters producing butyrate in high fiber diets typical of anaerobic environments in the digestive system.\"\\n },\\n \"7\": {\\n \"feature_id\": \"IPR024405 * IPR035408\",\\n \"feature_label\": \"Prophage protein BhlA/UviB * Phage single-stranded DNA-binding protein\",\\n \"bio_property\": \"phage DNA integration * DNA stabilization\",\\n \"env_property\": \"high microbial turnover * phage-host interactions\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Prophage integrations and DNA-binding proteins are indicative of high microbial turnover rates and frequent phage-host interactions in the digestive system.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631467, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=944, prompt_tokens=1160, total_tokens=2104))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -6014,18 +6016,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Host-associated:Mammals:Digestive system:Fecal\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -6085,7 +6087,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 34:\n", - "ChatCompletion(id='chatcmpl-9WpM21tH1Ey5Q4p379Qnphor5kFHM', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Mammals:Digestive system:Fecal\": {\\n \"1\": {\\n \"feature_id\": \"GO:0019512 * IPR004300 * sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae\",\\n \"feature_label\": \"lactose catabolic process via tagatose-6-phosphate * Glycoside hydrolase family 57, N-terminal domain * Firmicutes clostridia\",\\n \"bio_property\": \"carbohydrate metabolism * glycoside hydrolase activity * lactose degradation\",\\n \"env_property\": \"high nutrient availability * presence of lactose\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Glycoside hydrolase family 57 enzymes are involved in breaking down polysaccharides, and this process is essential in environments rich in carbohydrates, like the mammalian fecal ecosystem where lactose is present.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0045151 * IPR000675 * sk__Bacteria;k__;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae\",\\n \"feature_label\": \"acetoin biosynthetic process * Cutinase/acetylxylan esterase * Bacteroidetes bacteroidia\",\\n \"bio_property\": \"acetoin production * esterase activity\",\\n \"env_property\": \"anaerobic conditions * presence of fermentation substrates\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Acetoin biosynthesis occurs under anaerobic conditions, common in the gut. The presence of cutinase/acetylxylan esterase hints at the ability to break down complex plant materials.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR007210 * sk__Bacteria;k__;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae\",\\n \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * Bacteroidetes bacteroidia\",\\n \"bio_property\": \"osmoprotection * betaine transport\",\\n \"env_property\": \"stress conditions * variable osmolarity\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Glycine betaine serves as an osmoprotectant, which helps microbes survive in variable osmotic conditions in the gut environment.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR003080 * sk__Bacteria;k__;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae\",\\n \"feature_label\": \"Glutathione S-transferase, alpha class * Bacteroidetes bacteroidia\",\\n \"bio_property\": \"detoxification * xenobiotic metabolism\",\\n \"env_property\": \"presence of xenobiotics * oxidative stress\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Glutathione S-transferases play a crucial role in detoxifying harmful compounds, which is important in an environment with dietary toxins and endogenous oxidative stress.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR019646 * sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Subdoligranulum\",\\n \"feature_label\": \"Aminoglycoside-2\\'\\'-adenylyltransferase * Firmicutes clostridia\",\\n \"bio_property\": \"antibiotic resistance * aminoglycoside modification\",\\n \"env_property\": \"presence of antibiotics * selective pressure\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Aminoglycoside-2\\'\\'-adenylyltransferase confers resistance to aminoglycoside antibiotics, highlighting selective pressure due to antibiotic exposure in the gut.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717610930, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=845, prompt_tokens=1273, total_tokens=2118))\n", + "ChatCompletion(id='chatcmpl-9WuhU1fYifeaLF1oN6bVK1igePAQI', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Mammals:Digestive system:Fecal\": {\\n \"1\": {\\n \"feature_id\": \"GO:0019512 * IPR004501\",\\n \"feature_label\": \"lactose catabolic process via tagatose-6-phosphate * Phosphotransferase system, EIIC component, type 3\",\\n \"bio_property\": \"Carbohydrate metabolism * Lactose degradation\",\\n \"env_property\": \"high nutrient availability * anaerobic conditions\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The lactose catabolic process via tagatose-6-phosphate and Phosphotransferase system EIIC component are involved in carbohydrate metabolism that is essential in the mammalian gut where lactose from diet is metabolized.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR000675 * IPR004300\",\\n \"feature_label\": \"Cutinase/acetylxylan esterase * Glycoside hydrolase family 57, N-terminal domain\",\\n \"bio_property\": \"Polysaccharide degradation * Xenobiotic degradation\",\\n \"env_property\": \"high fiber diet * complex carbohydrate presence\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The presence of Cutinase/acetylxylan esterase and Glycoside hydrolase family 57 domains indicates a system specialized in breaking down complex polysaccharides likely derived from a high fiber diet found in fecal matter.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR003080 * IPR010106\",\\n \"feature_label\": \"Glutathione S-transferase, alpha class * Recombination-promoting nuclease RpnA\",\\n \"bio_property\": \"Detoxification * DNA repair\",\\n \"env_property\": \"fluctuating toxicity levels * reactive oxygen species\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Glutathione S-transferase, alpha class enzyme, and RpnA provide defense against oxidative stress and DNA damage, vital in environments like the gut where reactive oxygen species and other toxins can be present.\"\\n },\\n \"4\": {\\n \"feature_id\": \"GO:0045151 * IPR019646\",\\n \"feature_label\": \"acetoin biosynthetic process * Aminoglycoside-2\\'\\'-adenylyltransferase\",\\n \"bio_property\": \"Fermentation * antibiotic resistance\",\\n \"env_property\": \"anaerobic conditions * presence of antibiotics\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Acetoin biosynthesis is involved in anaerobic fermentation processes in the gut, and Aminoglycoside-2\\'\\'-adenylyltransferase indicates resistance to antibiotics, reflecting the selective pressures of such compounds in this environment.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR022339 * GO:0017148\",\\n \"feature_label\": \"MHC class II-associated invariant chain * negative regulation of translation\",\\n \"bio_property\": \"Immune modulation * gene expression control\",\\n \"env_property\": \"immune system interaction * microbial competition\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"The MHC class II-associated invariant chain and regulatory translation processes underline the dynamic interaction between the gut microbiota and the host immune system, as well as competitive interactions among microbial species.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631480, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=706, prompt_tokens=1283, total_tokens=1989))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -6108,18 +6110,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Host-associated:Mammals:Digestive system:Large intestine\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -6161,7 +6163,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 35:\n", - "ChatCompletion(id='chatcmpl-9WpMNgu3wlxUXTixTIPCo6OHjaZ7E', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Mammals:Digestive system:Large intestine\": {\\n \"1\": {\\n \"feature_id\": \"IPR010106 * IPR026935\",\\n \"feature_label\": \"Recombination-promoting nuclease RpnA * Butirosin biosynthesis protein H, N-terminal\",\\n \"bio_property\": \"DNA double-strand break repair * Antibiotic biosynthesis\",\\n \"env_property\": \"low oxygen * nutrient rich\",\\n \"confidence\": \"high\",\\n \"explanation\": \"In the large intestine, the DNA double-strand break repair system is critical for maintaining genetic stability in an anaerobic (low oxygen) yet nutrient-rich environment, where horizontal gene transfer can also occur. The presence of antibiotic biosynthesis-related proteins suggests an ongoing microbial competition for resources.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR022225 * IPR021725\",\\n \"feature_label\": \"Phage tail fibre protein * Pathogenicity locus\",\\n \"bio_property\": \"Phage infection system * Pathogenesis\",\\n \"env_property\": \"high microbial diversity * high cell density\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The interaction between phage proteins and pathogen-related loci indicates a dynamic environment where bacteriophages may contribute to regulating microbial populations within the high-density and diverse microbial ecosystem of the large intestine.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR023972 * IPR023812\",\\n \"feature_label\": \"Conserved hypothetical protein CHP04069, acyl carrier-related * Conserved hypothetical protein CHP04002\",\\n \"bio_property\": \"Lipid metabolism * conserved microbial functions\",\\n \"env_property\": \"high organic matter\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Proteins involved in acyl carrier-related functions suggest important roles in lipid metabolism, which is crucial in environments rich in organic matter like the large intestine.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR024522 * IPR032318 * IPR032480 * IPR032511\",\\n \"feature_label\": \"Protein of unknown function DUF3789 * Protein of unknown function DUF4848 * Domain of unknown function DUF5057 * Protein of unknown function DUF4971\",\\n \"bio_property\": \"Uncharacterized microbial functions\",\\n \"env_property\": \"variable nutrient availability * microbial community stability\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Multiple DUF (domain of unknown function) proteins are likely involved in various uncharacterized but essential processes, which ensure stability and adaptation within the microbial community in the large intestine ecosystem where nutrient availability fluctuates.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR028049\",\\n \"feature_label\": \"NTF2 fold immunity protein\",\\n \"bio_property\": \"Immunity-related processes\",\\n \"env_property\": \"immune pressure * host-microbe interactions\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Proteins with NTF2 fold are often involved in immunity-related processes, which are crucial for microbial survival in the large intestine faced with host immune defenses.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717610951, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=667, prompt_tokens=830, total_tokens=1497))\n", + "ChatCompletion(id='chatcmpl-9WuhdVy2KjYvlB0bo884oTG71sEvs', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Mammals:Digestive system:Large intestine\": {\\n \"1\": {\\n \"feature_id\": \"IPR010106 * IPR021725 * IPR022225\",\\n \"feature_label\": \"Recombination-promoting nuclease RpnA * Pathogenicity locus * Phage tail fibre protein\",\\n \"bio_property\": \"genomic recombination * pathogenicity * viral infection mechanisms\",\\n \"env_property\": \"complex microbiome * high bacterial diversity * immune interaction\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Recombination-promoting nucleases and pathogenicity loci are often associated with gene transfer and bacterial adaptation in diverse microbial communities, while phage tail fiber proteins are indicative of presence of bacteriophages which interact with host immunity and microbial competition.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR014580 * IPR023812 * IPR023972 * IPR024522 * IPR032318 * IPR032480 * IPR032511\",\\n \"feature_label\": \"Uncharacterised conserved protein UCP033199 * Conserved hypothetical protein CHP04002 * Conserved hypothetical protein CHP04069, acyl carrier-related * Protein of unknown function DUF3789 * Protein of unknown function DUF4848 * Domain of unknown function DUF5057 * Protein of unknown function DUF4971\",\\n \"bio_property\": \"conserved protein functions * potential biosynthetic pathways * unknown cellular roles\",\\n \"env_property\": \"complex nutrient interactions * high microbial metabolism\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Many conserved and hypothetical proteins suggest the presence of unique or specialized metabolic processes that are not fully understood but are likely to play a role in the high metabolic activity and nutrient processing typical of the large intestine environment.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR028049\",\\n \"feature_label\": \"NTF2 fold immunity protein\",\\n \"bio_property\": \"immune response modulation\",\\n \"env_property\": \"immune interaction * microbial homeostasis\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"NTF2 fold immunity proteins are implicated in immune responses, which are crucial in maintaining microbial balance and preventing overgrowth of harmful bacteria in the host-associated gut environment.\"\\n },\\n \"4\": {\\n \"feature_id\": \"sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae\",\\n \"feature_label\": \"Bacterial taxonomy: Firmicutes; Clostridia; Clostridiales; Ruminococcaceae\",\\n \"bio_property\": \"fermentation * short-chain fatty acids production\",\\n \"env_property\": \"anaerobic conditions * fiber-rich diet\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The Ruminococcaceae family is well-known for its role in fermenting complex carbohydrates and producing short-chain fatty acids under anaerobic conditions, which are typical properties of the large intestine environment enriched with dietary fibers.\"\\n }\\n }\\n}\\n```\\n\\nI have compiled and analyzed the relationships between observed microbial metagenomic features and environmental properties specific to the Host-associated:Mammals:Digestive system:Large intestine ecosystem. The focus was on interpreting the implications of these features regarding the biological activities and environmental conditions characteristic of this niche. Each relationship is supported by well-established associations and is presented with a confidence estimation based on the strength of available evidence.', role='assistant', function_call=None, tool_calls=None))], created=1717631489, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=725, prompt_tokens=840, total_tokens=1565))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -6184,18 +6186,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Host-associated:Mammals:Digestive system:Large intestine:Fecal\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -6252,7 +6254,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 36:\n", - "ChatCompletion(id='chatcmpl-9WpMeaRNNQ7LJqvB3qUej5vPcQe9Z', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='Certainly! Let\\'s dive into the observed features in the Host-associated:Mammals:Digestive system:Large intestine:Fecal ecosystem, their biological properties, and how these properties relate to their environment. Below is the analyzed data in JSON format.\\n\\n```json\\n{\\n \"Host-associated:Mammals:Digestive system:Large intestine:Fecal\": {\\n \"1\": {\\n \"feature_id\": \"GO:0008740 * IPR004759 * IPR006879\",\\n \"feature_label\": \"L-rhamnose isomerase activity * Glutamate:g-aminobutyrate antiporter * Carbohydrate deacetylase YdjC-like\",\\n \"bio_property\": \"carbohydrate metabolism * nutrient assimilation * stress response\",\\n \"env_property\": \"nutrient rich * acidic pH\",\\n \"confidence\": \"high\",\\n \"explanation\": \"These features are involved in carbohydrate metabolism and nutrient assimilation, processes that are crucial in the nutrient-rich but acidic environment of the large intestine.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR004813 * IPR025479 * GO:0015307\",\\n \"feature_label\": \"Oligopeptide transporter, OPT superfamily * Domain of unknown function DUF4329 * obsolete drug:proton antiporter activity\",\\n \"bio_property\": \"peptide transport * stress response\",\\n \"env_property\": \"high microbial competition * anaerobic condition\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Peptide transport systems help bacteria survive in competitive environments like the gut, where anaerobic conditions prevail.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR007210 * GO:0031460 * IPR016300\",\\n \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport * Arsenical pump ATPase, ArsA/GET3\",\\n \"bio_property\": \"osmoprotection * detoxification * stress response\",\\n \"env_property\": \"high osmolarity * presence of xenobiotics\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Features related to osmoprotection and detoxification indicate adaptation to high osmolarity and presence of harmful substances in the gut.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR012706 * IPR018669 * IPR012657\",\\n \"feature_label\": \"Rib/alpha/Esp surface antigen * carbohydrate-binding protein * 23S rRNA-intervening sequence protein\",\\n \"bio_property\": \"immune system interaction * cellular adhesion\",\\n \"env_property\": \"high bacterial load * host immune activity\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Surface antigens and carbohydrate-binding proteins enable microorganisms to interact with the host\\'s immune system and adhere to gut surfaces.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR025123 * IPR025399 * IPR025479\",\\n \"feature_label\": \"Domain of unknown function DUF4049 * Domain of unknown function DUF4372 * Domain of unknown function DUF4329\",\\n \"bio_property\": \"potential regulatory function\",\\n \"env_property\": \"variable environmental conditions\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"While their exact functions are unknown, domains of unknown function (DUFs) likely serve regulatory roles that allow adaptation to the variable conditions in the gut.\"\\n },\\n \"6\": {\\n \"feature_id\": \"IPR030984 * IPR032507\",\\n \"feature_label\": \"Bacterial microcompartment shell protein PduB * GH32, BT1760-like, C-terminal domain\",\\n \"bio_property\": \"compartmentalization * polysaccharide degradation\",\\n \"env_property\": \"high polysaccharide content\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Bacterial microcompartments and polysaccharide degrading enzymes are crucial for breaking down complex carbohydrates present in the gut.\"\\n },\\n \"7\": {\\n \"feature_id\": \"sk__Bacteria;k__;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae * sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae\",\\n \"feature_label\": \"Prevotellaceae * Ruminococcaceae\",\\n \"bio_property\": \"cellulose metabolism * short-chain fatty acid production\",\\n \"env_property\": \"fiber-rich diet\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Prevotellaceae and Ruminococcaceae are known for their capacity to metabolize cellulose and produce short-chain fatty acids, key processes in fiber-rich diets.\"\\n }\\n }\\n}\\n```\\n\\n### Summary\\n\\nIn the Host-associated:Mammals:Digestive system:Large intestine:Fecal ecosystem, the data show several key relationships between the identified features and the environmental conditions. Features related to carbohydrate metabolism, osmoprotection, detoxification, immune system interaction, and microbial competition are prevalent. These features support the high microbial diversity, high osmolarity, the presence of xenobiotics, and high competition for resources characteristic of the large intestine environment. This curated digest provides comprehensive and reliable associations with a high level of confidence.', role='assistant', function_call=None, tool_calls=None))], created=1717610968, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=1118, prompt_tokens=1109, total_tokens=2227))\n", + "ChatCompletion(id='chatcmpl-9Wuht4iVoIFXeGaoIryuD4aCy0HDT', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Mammals:Digestive system:Large intestine:Fecal\": {\\n \"1\": {\\n \"feature_id\": \"GO:0008740 * IPR004759 * IPR026419\",\\n \"feature_label\": \"L-rhamnose isomerase activity * Glutamate:g-aminobutyrate antiporter * Glycosyltransferase, GG-Bacteroidales peptide system\",\\n \"bio_property\": \"carbohydrate metabolism * amino acid metabolism * glycosylation\",\\n \"env_property\": \"nutrient-rich * anaerobic\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The large intestine is rich in diverse carbohydrates which require specific enzymes for their metabolism. These microbial features support the digestion and absorption of diverse nutrients in an anaerobic environment.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR004813 * IPR008016 * IPR030984\",\\n \"feature_label\": \"Oligopeptide transporter, OPT superfamily * Portal protein Gp10 * Bacterial microcompartment shell protein PduB\",\\n \"bio_property\": \"peptide transport * viral assembly * microcompartment formation\",\\n \"env_property\": \"host-associated * high bacterial density\",\\n \"confidence\": \"high\",\\n \"explanation\": \"These features highlight the complex roles of transport systems, bacterial microcompartments, and interactions with bacteriophages in a densely populated gut environment.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR006879 * IPR009677 * IPR032830\",\\n \"feature_label\": \"Carbohydrate deacetylase YdjC-like * Protein of unknown function DUF1266 * Helicase XPB/Ssl2, N-terminal domain\",\\n \"bio_property\": \"carbohydrate processing * protein function unknown * DNA repair\",\\n \"env_property\": \"biotic interactions * chemical signal processing\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Carbohydrate deacetylases and helicases play essential roles in processing and modifying polysaccharides and DNA, vital in the microbe-rich and chemically dynamic environment of the large intestine.\"\\n },\\n \"4\": {\\n \"feature_id\": \"GO:0005871 * GO:0015307 * IPR031636\",\\n \"feature_label\": \"kinesin complex * obsolete drug:proton antiporter activity * Protein kinase G, tetratricopeptide repeat containing domain\",\\n \"bio_property\": \"cellular transport * ion transport * protein phosphorylation\",\\n \"env_property\": \"fluid-dynamic conditions * chemical gradients\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Kinesin complexes and antiporters are crucial for maintaining cellular and ionic balance, driven by the dynamic fluid environment and chemical gradients in the gut.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631505, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=598, prompt_tokens=1116, total_tokens=1714))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -6275,18 +6277,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Host-associated:Mammals:Respiratory system\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -6333,7 +6335,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 37:\n", - "ChatCompletion(id='chatcmpl-9WpMzluo5UDZF7LI2zxdhQQDUwAPU', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Mammals:Respiratory system\": {\\n \"1\": {\\n \"feature_id\": \"GO:0004144 * IPR006322\",\\n \"feature_label\": \"diacylglycerol O-acyltransferase activity * Glutathione reductase, eukaryote/bacterial\",\\n \"bio_property\": \"lipid metabolism * oxidative stress response\",\\n \"env_property\": \"low oxygen * variable nutrient levels\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Diacylglycerol O-acyltransferase is involved in lipid biosynthesis which is crucial in bacteria thriving in nutrient-variable environments like the mammalian respiratory tract. Glutathione reductase plays a key role in protecting cells from oxidative damage, hinting at low oxygen conditions where oxidative stress management is critical.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0019512 * IPR007037\",\\n \"feature_label\": \"lactose catabolic process via tagatose-6-phosphate * Siderophore-interacting protein, C-terminal domain\",\\n \"bio_property\": \"carbohydrate metabolism * iron acquisition\",\\n \"env_property\": \"high nutrient variability * iron limitation\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The ability to catabolize lactose via the tagatose-6-phosphate pathway indicates adaptation to utilize diverse carbon sources, a necessity in the variable nutrient conditions of the respiratory tract. Siderophore-interacting proteins are essential for acquiring iron in iron-limited environments, which is a common challenge in host-associated locales.\"\\n },\\n \"3\": {\\n \"feature_id\": \"GO:0045151 * IPR007445\",\\n \"feature_label\": \"acetoin biosynthetic process * Type IV pilus inner membrane component PilO\",\\n \"bio_property\": \"secondary metabolite production * cell adhesion\",\\n \"env_property\": \"mucosal surfaces * host interaction\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Acetoin biosynthesis is part of the metabolic complexity needed for survival in diverse conditions. Type IV pili are essential for bacterial adhesion to host cells and mucosal surfaces, facilitating colonization and persistence in the respiratory system.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR007210 * GO:0046797\",\\n \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * viral procapsid maturation\",\\n \"bio_property\": \"osmoprotection * viral assembly\",\\n \"env_property\": \"high osmolarity * host immune response\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The ProV-like protein is associated with compatibility solutes transport that helps in osmoprotection, essential in fluctuating osmolarity conditions. Viral procapsid maturation refers to the assembly stages of viral replication, which are relevant in understanding host-pathogen dynamics and immune evasion strategies in the respiratory system.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR012706 * IPR011118\",\\n \"feature_label\": \"Rib/alpha/Esp surface antigen * Tannase/feruloyl esterase\",\\n \"bio_property\": \"surface antigens * degradation of complex organic compounds\",\\n \"env_property\": \"host immune evasion * complex nutrient environment\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Surface antigens like Rib/alpha/Esp play roles in immune evasion and modulation, which are crucial for persistence in the respiratory system. Tannase/feruloyl esterase indicates the ability to degrade complex organic compounds, suggesting adaptation to a nutrient-diverse environment.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717610989, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=779, prompt_tokens=889, total_tokens=1668))\n", + "ChatCompletion(id='chatcmpl-9Wui25EJzpFkkFlPd6b9WPg9C9acC', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Mammals:Respiratory system\": {\\n \"1\": {\\n \"feature_id\": \"GO:0004144 * IPR007037 * IPR007445\",\\n \"feature_label\": \"diacylglycerol O-acyltransferase activity * Siderophore-interacting protein, C-terminal domain * Type IV pilus inner membrane component PilO\",\\n \"bio_property\": \"lipid metabolism * iron acquisition * bacterial adhesion\",\\n \"env_property\": \"mucosal surfaces * competitive microenvironment * host immune interactions\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Diacylglycerol O-acyltransferase is involved in lipid metabolism crucial for microbial energy storage and membrane fluidity. Siderophore-interacting proteins mediate iron acquisition, critical in the iron-limited environments of respiratory mucosa. Type IV pili are implicated in bacterial adhesion to mucosal surfaces, aiding colonization in the competitive and immune-challenging respiratory tract.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0019512 * IPR011118 * IPR004624\",\\n \"feature_label\": \"lactose catabolic process via tagatose-6-phosphate * Tannase/feruloyl esterase * Protein YjdM\",\\n \"bio_property\": \"carbohydrate metabolism * aromatic compound degradation * protein function unknown\",\\n \"env_property\": \"mucosal surfaces * presence of host sugars * variable nutrient availability\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"The lactose catabolic process facilitates utilization of host-derived sugars, crucial for microbial survival in mucosa. Tannase/feruloyl esterase degrades aromatic compounds, potentially sourced from dietary elements. Protein YjdM functionality remains unclear but may play a regulatory or structural role in such an environment.\"\\n },\\n \"3\": {\\n \"feature_id\": \"GO:0046797 * IPR032124 * IPR014984\",\\n \"feature_label\": \"viral procapsid maturation * Bacteriophage F116-like holin * HopJ type III effector protein\",\\n \"bio_property\": \"viral replication * bacteriophage function * immune system evasion\",\\n \"env_property\": \"host-virus interaction * microbial ecosystem dynamics * immune evasion\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Viral procapsid maturation is critical for virus assembly within host cells. Bacteriophage-associated holins regulate host cell lysis, influencing bacterial population dynamics. Type III effector proteins enable bacteria to manipulate host immune responses, vital for survival within the immune-active respiratory tract.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR007920 * IPR021250 * IPR021361 * IPR023845\",\\n \"feature_label\": \"Protein of unknown function UPF0223 * Protein of unknown function DUF2789 * Protein of unknown function DUF2829 * Domain of unknown function DUF3817, transmembrane\",\\n \"bio_property\": \"unknown protein functions * potential structural roles * possible regulatory functions\",\\n \"env_property\": \"highly dynamic * host-derived nutrient conditions * microbial competition\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"These proteins of unknown function likely contribute to structural, regulatory, or adaptive responses essential for survival and competition within the respiratory tract’s dynamic and nutrient-variable environment.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631514, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=718, prompt_tokens=901, total_tokens=1619))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -6356,18 +6358,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Host-associated:Plants\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -6409,7 +6411,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 38:\n", - "ChatCompletion(id='chatcmpl-9WpNKKa2OYjuAafXkBILPidGcFmM6', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Plants\": {\\n \"1\": {\\n \"feature_id\": \"GO:0017148 * GO:0042176 * IPR001208 * IPR032191 * IPR032193\",\\n \"feature_label\": \"negative regulation of translation * regulation of protein catabolic process * MCM domain * CCR4-NOT transcription complex subunit 1, CAF1-binding domain * CCR4-NOT transcription complex subunit 1, TTP binding domain\",\\n \"bio_property\": \"protein regulation * transcription regulation * protein degradation\",\\n \"env_property\": \"nutrient variation * biotic stress\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Protein and transcription regulation mechanisms, including the CCR4-NOT complex, are crucial adaptations for plants facing fluctuating nutrients and biotic stress from pathogens or symbionts.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR018040\",\\n \"feature_label\": \"Pectinesterase, Tyr active site\",\\n \"bio_property\": \"cell wall modification * pectin degradation\",\\n \"env_property\": \"biotic stress * symbiosis\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Pectinesterase enzymes play a key role in modifying plant cell walls, often in response to pathogen attack or during interactions with symbiotic organisms.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR004813\",\\n \"feature_label\": \"Oligopeptide transporter, OPT superfamily\",\\n \"bio_property\": \"nutrient uptake * peptide transport\",\\n \"env_property\": \"nutrient poor\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Oligopeptide transporters facilitate the uptake of peptides, a crucial adaptation for plants in nutrient-limited environments to maximize available resources.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR001096 * IPR033126\",\\n \"feature_label\": \"Peptidase C13, legumain * Glycosyl hydrolases family 9, Asp/Glu active sites\",\\n \"bio_property\": \"protein degradation * carbohydrate degradation\",\\n \"env_property\": \"nutrient cycling * decomposition\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Peptidases and glycosyl hydrolases are essential for breaking down proteins and carbohydrates, respectively, contributing to nutrient cycling and decomposition in soil associated with plants.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717611010, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=517, prompt_tokens=821, total_tokens=1338))\n", + "ChatCompletion(id='chatcmpl-9WuiGhYIRZw9yGhE0f4Or2BlA0ua5', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Plants\": {\\n \"1\": {\\n \"feature_id\": \"IPR018040 * IPR033126\",\\n \"feature_label\": \"Pectinesterase, Tyr active site * Glycosyl hydrolases family 9, Asp/Glu active sites\",\\n \"bio_property\": \"polysaccharide degradation * cell wall modification * carbohydrate metabolism\",\\n \"env_property\": \"rich in plant cell wall materials * varied carbohydrate availability\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Pectinesterase and Glycosyl hydrolases are involved in the degradation and modification of plant cell wall components, commonly found in plant-associated environments.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR000477 * IPR004264\",\\n \"feature_label\": \"Reverse transcriptase domain * Transposase, Tnp1/En/Spm-like\",\\n \"bio_property\": \"genetic element mobility * genome maintenance * DNA recombination\",\\n \"env_property\": \"dynamic genomic environment * presence of mobile genetic elements\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Reverse transcriptase and Transposase domains are associated with the mobility of genetic elements, which is crucial in dynamic plant-associated environments where genetic adaptations can be advantageous.\"\\n },\\n \"3\": {\\n \"feature_id\": \"GO:0017148 * GO:0042176\",\\n \"feature_label\": \"negative regulation of translation * regulation of protein catabolic process\",\\n \"bio_property\": \"protein homeostasis * stress response * cellular regulation\",\\n \"env_property\": \"variable nutrient conditions * fluctuating environmental stressors\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Regulatory processes like the negative regulation of translation and protein catabolism are important in maintaining cellular homeostasis under variable nutrient conditions and environmental stress commonly encountered in plant-associated environments.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR001096 * IPR032191\",\\n \"feature_label\": \"Peptidase C13, legumain * CCR4-NOT transcription complex subunit 1, CAF1-binding domain\",\\n \"bio_property\": \"protein degradation * mRNA regulation * post-transcriptional modification\",\\n \"env_property\": \"nutrient cycling * high symbiotic activity\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Enzymes like Peptidase legumain and components of the CCR4-NOT complex are involved in protein degradation and mRNA regulation, which are key in nutrient cycling and maintaining symbiotic interactions in plant-associated environments.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR001320 * IPR004813\",\\n \"feature_label\": \"Ionotropic glutamate receptor, C-terminal * Oligopeptide transporter, OPT superfamily\",\\n \"bio_property\": \"signal transduction * nutrient uptake * intercellular communication\",\\n \"env_property\": \"rich in signaling molecules * diverse nutrient availability\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Ionotropic glutamate receptors and oligopeptide transporters play roles in signal transduction and nutrient uptake, which are essential in environments rich in signaling molecules and diverse nutrients, typical of plant-associated ecosystems.\"\\n }\\n }\\n}\\n```\\n\\n**Explanation**:\\n- The selected features and their subsets were chosen based on their biological properties and relevance to the plant-associated environment.\\n- The relationships between features and environmental properties were inferred based on known functions of the features and characteristics of plant-associated ecosystems.\\n- Only medium to high confidence associations were reported, ensuring reliability.\\n- This JSON structure groups the features by their shared biological and environmental properties, providing a thorough and exhaustive list of reliable relationships.', role='assistant', function_call=None, tool_calls=None))], created=1717631528, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=773, prompt_tokens=839, total_tokens=1612))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -6432,18 +6434,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Host-associated:Plants:Phylloplane\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -6479,7 +6481,7 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 39:\n", - "ChatCompletion(id='chatcmpl-9WpNUxnRZh9H12bdCKNAzoqMYwKgi', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Plants:Phylloplane\": {\\n \"1\": {\\n \"feature_id\": \"GO:0042176 * IPR006652\",\\n \"feature_label\": \"regulation of protein catabolic process * Kelch repeat type 1\",\\n \"bio_property\": \"protein degradation * structural protein interactions\",\\n \"env_property\": \"nutrient limited * exposure to microbial competition\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The regulation of protein catabolic processes and Kelch repeat proteins are essential for maintaining protein turnover and structural functions in nutrient-limited environments where efficient resource utilization is critical.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR000036 * GO:0033890\",\\n \"feature_label\": \"Peptidase A26, omptin * ribonuclease D activity\",\\n \"bio_property\": \"protein degradation * RNA processing\",\\n \"env_property\": \"high microbial diversity * exposure to pathogenic attack\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Peptidases and ribonucleases are necessary for breaking down proteins and RNA, respectively, providing a quick response to microbial competition and pathogen attacks in a diverse microbial environment.\"\\n },\\n \"3\": {\\n \"feature_id\": \"GO:0003950 * IPR033126\",\\n \"feature_label\": \"NAD+ ADP-ribosyltransferase activity * Glycosyl hydrolases family 9, Asp/Glu active sites\",\\n \"bio_property\": \"DNA repair * carbohydrate metabolism\",\\n \"env_property\": \"exposure to UV light * abundant plant polysaccharides\",\\n \"confidence\": \"high\",\\n \"explanation\": \"NAD+ ADP-ribosyltransferase activity is key for DNA repair mechanisms, which is critical in environments exposed to UV light, while glycosyl hydrolases aid in polysaccharide breakdown, prevalent on plant surfaces.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR033762\",\\n \"feature_label\": \"MCM OB domain\",\\n \"bio_property\": \"DNA replication\",\\n \"env_property\": \"high cellular turnover * exposure to DNA-damaging agents\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The MCM OB domain is integral to DNA replication processes, necessary for maintaining genomic stability in environments with high cellular turnover and exposure to DNA-damaging agents.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717611020, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=516, prompt_tokens=720, total_tokens=1236))\n", + "ChatCompletion(id='chatcmpl-9WuiVMNPKYNz6QhlqSczcGIMVJpWR', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Plants:Phylloplane\": {\\n \"1\": {\\n \"feature_id\": \"GO:0003950 * IPR033126\",\\n \"feature_label\": \"NAD+ ADP-ribosyltransferase activity * Glycosyl hydrolases family 9, Asp/Glu active sites\",\\n \"bio_property\": \"post-translational modification * carbohydrate metabolism\",\\n \"env_property\": \"high nutrient availability * complex organic matter\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The NAD+ ADP-ribosyltransferase activity relates to post-translational modifications, which are critical for regulating intracellular processes in a nutrient-rich environment like the phylloplane. Glycosyl hydrolases are involved in breaking down complex carbohydrates, indicating the presence of diverse organic matter on plant surfaces.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0033890 * IPR000036\",\\n \"feature_label\": \"ribonuclease D activity * Peptidase A26, omptin\",\\n \"bio_property\": \"RNA processing * protein degradation\",\\n \"env_property\": \"microbial community complexity * organic matter turnover\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Ribonuclease D is involved in RNA processing, suggesting active turnover of genetic material, complemented by Omptin peptidases which degrade proteins, both pointing to high microbial community dynamics and organic matter turnover in the phylloplane.\"\\n },\\n \"3\": {\\n \"feature_id\": \"GO:0042176 * IPR033762\",\\n \"feature_label\": \"regulation of protein catabolic process * MCM OB domain\",\\n \"bio_property\": \"protein catabolism regulation * DNA replication initiation\",\\n \"env_property\": \"stress adaptation * dynamic microenvironment\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The regulation of protein catabolic process is crucial for managing cellular stress, while MCM OB domains are key in DNA replication initiation, indicating adaptation to environmental stress and a dynamic microenvironment on the plant surface.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR006652 * IPR019060\",\\n \"feature_label\": \"Kelch repeat type 1 * Domain of unknown function DUF2382\",\\n \"bio_property\": \"protein-protein interactions * unknown\",\\n \"env_property\": \"complex microbial interactions * potential novel functionalities\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Kelch repeats are involved in protein-protein interactions, suggesting complex microbial interactions within the phylloplane. The DUF2382 domain\\'s unknown function highlights potential novel functionalities adapted to this environment.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631543, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=573, prompt_tokens=733, total_tokens=1306))\n", "\n", "\n", "***Begin Environmental Ecology and Microbiology Prompt***\n", @@ -6502,18 +6504,18 @@ "For each feature or subset, report:\n", "- **Feature Identifier(s)**\n", "- **Feature Description(s)**\n", - "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating what the specific feature is.\n", + "- **Bio_property**: List all biological properties of the features (e.g., pathways, biological complexes) excluding generic biological terms or just reiterating information about individual feature is such as what type of organism it is.\n", "- **Env_property**: List all relevant environmental properties of the environment (e.g., nutrient poor,\n", "high pH) excluding biological terms like 'DNA damage repair' or 'cellular maintenance' or kinds of metabolism or biological functions.\n", "- **Confidence Level**: Estimate the confidence of the inferred association (unknown, low, medium, high).\n", "- **Brief Explanation**: Provide a concise explanation of the relationship.\n", "\n", "**JSON Output Structure:**\n", - "The results should be returned in the following JSON format, using '*' as the list delimiter:\n", + "The results should be returned in the following JSON format, using '*' as the list delimiter as in the example below for a Environmental:Marine ecosystem:\n", "\n", "```json\n", "{\n", - " \"Host-associated:Plants:Rhizosphere\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", " \"feature_id\": \"IPR007210 * GO:0031460\",\n", " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", @@ -6561,10 +6563,10 @@ "***End Environmental Ecology and Microbiology Prompt***\n", "\n", "Result for row 40:\n", - "ChatCompletion(id='chatcmpl-9WpNjZ8PbL1LHUtIdGQ1MqkJqsxea', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='Sure, let\\'s break this down based on the required analysis for the Host-associated:Plants:Rhizosphere ecosystem in your observed features. \\n\\n```json\\n{\\n \"Host-associated:Plants:Rhizosphere\": {\\n \"1\": {\\n \"feature_id\": \"IPR000675\",\\n \"feature_label\": \"Cutinase/acetylxylan esterase\",\\n \"bio_property\": \"cutin degradation * hydrolysis of plant cell wall polymers\",\\n \"env_property\": \"nutrient cycling * decomposing plant material\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Cutinases and esterases are crucial for breaking down plant cutin and other polymers, facilitating nutrient cycling and decomposition.\"\\n },\\n \"2\": {\\n \"feature_id\": \"GO:0005871\",\\n \"feature_label\": \"kinesin complex\",\\n \"bio_property\": \"microtubule-based movement * intracellular transport\",\\n \"env_property\": \"soil structure interaction\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Kinesin complexes are involved in cellular movement and transport, which could influence interactions within the complex soil matrix.\"\\n },\\n \"3\": {\\n \"feature_id\": \"GO:0006011\",\\n \"feature_label\": \"UDP-glucose metabolic process\",\\n \"bio_property\": \"carbohydrate metabolism * cell wall biosynthesis\",\\n \"env_property\": \"nutrient availability\",\\n \"confidence\": \"high\",\\n \"explanation\": \"UDP-glucose is a crucial intermediate in carbohydrate metabolism and is important for plant and microbial cell wall biosynthesis, affecting nutrient cycles.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR007312\",\\n \"feature_label\": \"Phosphoesterase\",\\n \"bio_property\": \"nucleotide metabolism * phosphorus cycle\",\\n \"env_property\": \"nutrient rich * decomposing organic material\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Phosphoesterases are involved in breaking down phosphoester bonds, playing a key role in phosphorus cycling in environments rich in organic matter.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR012727\",\\n \"feature_label\": \"Glycine oxidase ThiO\",\\n \"bio_property\": \"amino acid metabolism * detoxification\",\\n \"env_property\": \"high nitrogen * organic-rich\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Glycine oxidase is involved in amino acid metabolism and detoxification processes, which are significant in nitrogen-rich, organic-rich environments.\"\\n },\\n \"6\": {\\n \"feature_id\": \"IPR004300\",\\n \"feature_label\": \"Glycoside hydrolase family 57, N-terminal domain\",\\n \"bio_property\": \"polysaccharide degradation * metabolic flexibility\",\\n \"env_property\": \"plant root vicinity * decomposing cellulose/hemicellulose\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Glycoside hydrolases degrade complex polysaccharides like cellulose and hemicellulose, which are abundant near plant roots and decomposing organic matter.\"\\n },\\n \"7\": {\\n \"feature_id\": \"sk__Bacteria;k__;p__Verrucomicrobia;c__Spartobacteria;o__Chthoniobacterales;f__Chthoniobacteraceae;g__Candidatus_Udaeobacter\",\\n \"feature_label\": \"Candidatus_Udaeobacter (Verrucomicrobia)\",\\n \"bio_property\": \"soil bacterial community * organic matter breakdown\",\\n \"env_property\": \"decomposing organic matter * rhizosphere\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Candidatus_Udaeobacter is part of soil bacterial communities known for breaking down organic matter, which is essential for nutrient cycling in the rhizosphere.\"\\n }\\n }\\n}\\n```\\n\\nThis JSON structure provides an exhaustive summary linking observed microbial metagenomic features to biological properties and relevant environmental properties with varying levels of confidence. These associations form a foundational understanding of the interactions within the rhizosphere ecosystem, aiding in further environmental and ecological studies.', role='assistant', function_call=None, tool_calls=None))], created=1717611035, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=863, prompt_tokens=896, total_tokens=1759))\n", + "ChatCompletion(id='chatcmpl-9WuifY45pYMJT9vrz0RWzilzUNc6T', choices=[Choice(finish_reason='stop', index=0, logprobs=None, message=ChatCompletionMessage(content='```json\\n{\\n \"Host-associated:Plants:Rhizosphere\": {\\n \"1\": {\\n \"feature_id\": \"GO:0005871 * GO:0006011 * GO:0019068\",\\n \"feature_label\": \"kinesin complex * UDP-glucose metabolic process * virion assembly\",\\n \"bio_property\": \"microbial motility complex * carbohydrate metabolism * virus lifecycle\",\\n \"env_property\": \"nutrient-rich * high microbial diversity\",\\n \"confidence\": \"high\",\\n \"explanation\": \"The kinesin complex is vital for intracellular transport, including in plant root interactions. UDP-glucose metabolism fuels various biosynthetic processes that are crucial in a nutrient-rich rhizosphere. Virion assembly indicates the potential for viral interactions within a diverse microbial community.\"\\n },\\n \"2\": {\\n \"feature_id\": \"IPR000675 * IPR007941 * IPR012727\",\\n \"feature_label\": \"Cutinase/acetylxylan esterase * Protein of unknown function DUF726 * Glycine oxidase ThiO\",\\n \"bio_property\": \"plant polymer degradation * unknown protein function * amino acid metabolism\",\\n \"env_property\": \"organic matter-rich * nitrogen cycling\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Cutinase and acetylxylan esterase are essential for breaking down plant polymers, crucial in rhizospheres rich in organic matter from root exudates. Glycine oxidase participates in nitrogen cycling by degrading glycine.\"\\n },\\n \"3\": {\\n \"feature_id\": \"IPR001320 * IPR004264 * IPR007312\",\\n \"feature_label\": \"Ionotropic glutamate receptor, C-terminal * Transposase, Tnp1/En/Spm-like * Phosphoesterase\",\\n \"bio_property\": \"neurotransmitter-like signaling * genetic element mobility * phosphate metabolism\",\\n \"env_property\": \"microbe-plant signaling * high horizontal gene transfer * phosphorus availability\",\\n \"confidence\": \"high\",\\n \"explanation\": \"Ionotropic glutamate receptors, akin to plant signaling molecules, play a role in microbe-plant interactions. Transposases reflect high genetic mobility, common in microbe-rich environments like the rhizosphere. Phosphoesterase activity is related to phosphorus cycling, essential in soil ecosystems.\"\\n },\\n \"4\": {\\n \"feature_id\": \"IPR004300 * IPR014983 * IPR017523\",\\n \"feature_label\": \"Glycoside hydrolase family 57, N-terminal domain * GAD-related * Conserved hypothetical protein CHP03089\",\\n \"bio_property\": \"polysaccharide breakdown * putative decarboxylase activity * uncharacterized but conserved function\",\\n \"env_property\": \"carbohydrate-rich * multiple nutrient cycles\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Glycoside hydrolases break down polysaccharides, pivotal in a carbohydrate-rich rhizosphere. GAD-related proteins may be involved in amino acid metabolism, contributing to nutrient cycling. Conserved hypothetical proteins often have key ecological roles despite unknown specific functions.\"\\n },\\n \"5\": {\\n \"feature_id\": \"IPR028962 * sk__Bacteria;k__;p__Verrucomicrobia;c__Spartobacteria;o__Chthoniobacterales;f__Chthoniobacteraceae;g__Candidatus_Udaeobacter\",\\n \"feature_label\": \"Immunity protein 10 * Candidatus_Udaeobacter\",\\n \"bio_property\": \"microbial defense mechanisms * actinobacterium association\",\\n \"env_property\": \"pathogen-rich * microbe-microbe interactions\",\\n \"confidence\": \"medium\",\\n \"explanation\": \"Immunity protein 10 suggests microbial defense in pathogen-rich environments, common in the rhizosphere. Candidatus_Udaeobacter, part of Verrucomicrobia, indicates specific microbial associations beneficial to plant roots.\"\\n }\\n }\\n}\\n```', role='assistant', function_call=None, tool_calls=None))], created=1717631553, model='gpt-4o-2024-05-13', object='chat.completion', system_fingerprint='fp_319be4768e', usage=CompletionUsage(completion_tokens=838, prompt_tokens=910, total_tokens=1748))\n", "\n", - "CPU times: user 746 ms, sys: 78 ms, total: 824 ms\n", - "Wall time: 12min 28s\n" + "CPU times: user 724 ms, sys: 77.8 ms, total: 801 ms\n", + "Wall time: 8min 23s\n" ] } ], @@ -6613,7 +6615,7 @@ }, { "cell_type": "code", - "execution_count": 190, + "execution_count": 196, "id": "49005310-d335-4e99-bc70-f801f80f251a", "metadata": {}, "outputs": [ @@ -6621,376 +6623,91 @@ "name": "stdout", "output_type": "stream", "text": [ + "[{'ecosystem': 'Engineered:Bioreactor', 'feature_id': 'GO:0018551 * IPR005126', 'feature_label': 'dissimilatory sulfite reductase activity * NapC/NirT cytochrome c, N-terminal', 'bio_property': 'anaerobic respiration*sulfur metabolism', 'env_property': 'anoxic*sulfur-rich', 'confidence': 'high', 'explanation': 'Dissimilatory sulfite reductase and associated cytochrome c are indicative of microbial sulfur cycling, which occurs primarily in anoxic and sulfur-rich conditions typical of engineered bioreactors.'}, {'ecosystem': 'Engineered:Bioreactor', 'feature_id': 'GO:0031460 * IPR004763', 'feature_label': 'glycine betaine transport * Cation efflux system CzcA/CusA/SilA/NccA/HelA/CnrA', 'bio_property': 'osmoprotection*ion transport', 'env_property': 'osmotic stress*metal-rich', 'confidence': 'high', 'explanation': 'Glycine betaine transport and cation efflux systems are crucial in environments experiencing osmotic stress and the presence of heavy metals, both of which are often encountered in engineered bioreactors.'}, {'ecosystem': 'Engineered:Bioreactor', 'feature_id': 'IPR007117 * IPR011868', 'feature_label': 'Expansin, cellulose-binding-like domain * Molybdate ABC transporter, ATP-binding protein', 'bio_property': 'cell wall modification*molybdenum transport', 'env_property': 'organic-rich*high molybdate availability', 'confidence': 'medium', 'explanation': 'The presence of expansin for cell wall modification and molybdate transport proteins suggests an environment rich in organic materials and available molybdate, such as one found in engineered bioreactors.'}, {'ecosystem': 'Engineered:Bioreactor', 'feature_id': 'IPR016300 * IPR019949', 'feature_label': 'Arsenical pump ATPase, ArsA/GET3 * Luciferase family oxidoreductase, group 1', 'bio_property': 'arsenic resistance*oxidative stress response', 'env_property': 'toxic metal contamination*high oxidative stress', 'confidence': 'medium', 'explanation': 'Arsenical pump ATPase and luciferase family oxidoreductases denote resistance to toxic metals and oxidative stress management, relevant to bioreactor conditions that handle waste with heavy metal contaminants.'}, {'ecosystem': 'Engineered:Bioreactor', 'feature_id': 'GO:0008743 * IPR001360', 'feature_label': 'L-threonine 3-dehydrogenase activity * Glycoside hydrolase family 1', 'bio_property': 'amino acid metabolism*carbohydrate degradation', 'env_property': 'nutrient cycling*high organic load', 'confidence': 'medium', 'explanation': 'L-threonine 3-dehydrogenase and glycoside hydrolases are involved in the breakdown of amino acids and carbohydrates, respectively, indicating active nutrient cycling in environments with a high organic load, typical in engineered bioreactors.'}, {'ecosystem': 'Engineered:Bioreactor', 'feature_id': 'IPR014242 * IPR002723', 'feature_label': 'Spore cortex biosynthesis protein, YabQ * N(4)-bis(aminopropyl)spermidine synthase, C-terminal', 'bio_property': 'sporulation*polyamine biosynthesis', 'env_property': 'nutrient-limited*stress conditions', 'confidence': 'medium', 'explanation': 'Proteins involved in spore formation and polyamine biosynthesis correlate with nutrient limitation and high-stress conditions, commonly present in engineered bioreactors designed to manage waste and recycling processes.'}]\n", + "[{'ecosystem': 'Engineered:Bioremediation:Terephthalate:Wastewater', 'feature_id': 'GO:0008743 * IPR001360 * GO:0019512', 'feature_label': 'L-threonine 3-dehydrogenase activity * Glycoside hydrolase family 1 * lactose catabolic process via tagatose-6-phosphate', 'bio_property': 'amino acid metabolism*carbohydrate metabolism*glycoside hydrolase function', 'env_property': 'organic carbon-rich*nutrient recycling*pollutant-degrading', 'confidence': 'high', 'explanation': 'The presence of enzymes involved in the metabolism of amino acids and carbohydrates, such as L-threonine 3-dehydrogenase and glycoside hydrolases, indicates active nutrient recycling processes. In an environment rich with organic carbon, such as terephthalate wastewater, these enzymes contribute significantly to breaking down complex organic pollutants.'}, {'ecosystem': 'Engineered:Bioremediation:Terephthalate:Wastewater', 'feature_id': 'GO:0008901 * IPR009677 * IPR012441', 'feature_label': 'ferredoxin hydrogenase activity * Protein of unknown function DUF1266 * Protein of unknown function DUF1643', 'bio_property': 'electron transport*molecular function', 'env_property': 'anaerobic conditions*redox potential variations', 'confidence': 'medium', 'explanation': 'Ferredoxin hydrogenase activity plays a crucial role in electron transport under anaerobic conditions. Alongside proteins of unknown functions (DUF1266 and DUF1643), this suggests adaptation to varying redox conditions within the wastewater environment, facilitating the breakdown of pollutants without oxygen.'}, {'ecosystem': 'Engineered:Bioremediation:Terephthalate:Wastewater', 'feature_id': 'IPR000036 * IPR006391', 'feature_label': 'Peptidase A26, omptin * P-type ATPase, B chain, subfamily IA', 'bio_property': 'protein degradation*ion transport', 'env_property': 'high metal ion concentration', 'confidence': 'high', 'explanation': 'P-type ATPases are involved in ion transport and homeostasis. The presence of peptidase A26, which catalyzes protein degradation, suggests adaptation to an environment with high metal ion concentrations where maintaining ion balance is crucial.'}, {'ecosystem': 'Engineered:Bioremediation:Terephthalate:Wastewater', 'feature_id': 'IPR004840 * GO:0043462', 'feature_label': 'Amino acid permease, conserved site * regulation of ATP-dependent activity', 'bio_property': 'amino acid transport*enzymatic regulation', 'env_property': 'nutrient absorption challenges', 'confidence': 'medium', 'explanation': 'The amino acid permease site indicates efficient nutrient uptake mechanisms, crucial for survival in a bioremediation environment where resources may be unevenly distributed. Coupled with regulatory activity, this suggests an adaptable organism capable of optimizing metabolic functions in response to environmental nutrient availability.'}, {'ecosystem': 'Engineered:Bioremediation:Terephthalate:Wastewater', 'feature_id': 'IPR010106 * IPR017813', 'feature_label': 'Recombination-promoting nuclease RpnA * Mycothiol acetyltransferase', 'bio_property': 'DNA repair*antioxidative stress response', 'env_property': 'chemical stress*oxidative stress', 'confidence': 'high', 'explanation': 'These proteins are involved in cellular defense mechanisms against chemical and oxidative stress, common in polluted environments like terephthalate wastewater. In particular, mycothiol acetyltransferase plays a role in maintaining redox balance, crucial for microbial survival and pollutant degradation.'}, {'ecosystem': 'Engineered:Bioremediation:Terephthalate:Wastewater', 'feature_id': '1PR016300 * GO:0019068', 'feature_label': 'Arsenical pump ATPase, ArsA/GET3 * virion assembly', 'bio_property': 'heavy metal detoxification*viral replication', 'env_property': 'toxic compounds*microbial interaction', 'confidence': 'medium', 'explanation': 'Arsenical pump ATPase reflects adaptation to toxic environments with heavy metals, common in industrial wastewater. Virion assembly indicates viral influences in microbial communities within the ecosystem, potentially affecting microbial dynamics and biodegradation processes.'}]\n", + "[{'ecosystem': 'Engineered:Built', 'feature_id': 'IPR009413 * sk__Eukaryota;k__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Aspergillaceae', 'feature_label': 'Hemolysin, aegerolysin type * Fungi (Aspergillaceae)', 'bio_property': 'hemolysis*virulence factor', 'env_property': 'high human presence*possible contamination with organic material', 'confidence': 'high', 'explanation': 'Hemolysins are virulence factors in pathogenic fungi; their presence in built environments suggests potential contamination or human infection risk.'}, {'ecosystem': 'Engineered:Built', 'feature_id': 'IPR010960', 'feature_label': 'Flavocytochrome c', 'bio_property': 'electron transport*oxidative metabolism', 'env_property': 'nutrient cycling*redox potential', 'confidence': 'high', 'explanation': 'Flavocytochrome c is involved in electron transport and plays a role in oxidative metabolism, indicating active biochemical processes including nutrient cycling in the environment.'}, {'ecosystem': 'Engineered:Built', 'feature_id': 'IPR021822 * IPR022190', 'feature_label': 'Protein of unknown function DUF3405 * Protein of unknown function DUF3716', 'bio_property': 'unknown protein*possible role in stress response or environmental adaptation', 'env_property': 'variable environmental conditions*potential for diverse microbial adaptation', 'confidence': 'medium', 'explanation': 'Proteins of unknown function may imply unexplained or poorly understood adaptive mechanisms to variable conditions, common in built environments with fluctuating parameters.'}, {'ecosystem': 'Engineered:Built', 'feature_id': 'sk__Eukaryota;k__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Aspergillaceae', 'feature_label': 'Aspergillaceae (Fungi)', 'bio_property': 'decomposition*biofilm formation*allergen production', 'env_property': 'indoor air quality*humidity*presence of organic material', 'confidence': 'high', 'explanation': 'Aspergillaceae is known for their role in decomposition and biofilm formation, which impacts indoor air quality and sustainability in built environments.'}]\n", + "[{'ecosystem': 'Environmental:Engineered:Food production', 'feature_id': 'GO:0004638 * IPR022380', 'feature_label': 'phosphoribosylaminoimidazole carboxylase activity * Glutamyl-Q tRNA(Asp) synthetase', 'bio_property': 'nucleotide biosynthesis*protein synthesis', 'env_property': 'nutrient-rich*controlled conditions', 'confidence': 'high', 'explanation': 'Phosphoribosylaminoimidazole carboxylase activity is involved in nucleotide biosynthesis pathways, which are critical in nutrient-rich environments typical of food production systems. The Glutamyl-Q tRNA(Asp) synthetase is essential for protein translation, supporting efficient growth in controlled nutrient environments.'}, {'ecosystem': 'Environmental:Engineered:Food production', 'feature_id': 'IPR000477 * IPR004264 * IPR004501', 'feature_label': 'Reverse transcriptase domain * Transposase, Tnp1/En/Spm-like * Phosphotransferase system, EIIC component, type 3', 'bio_property': 'genetic element mobility*carbohydrate transport', 'env_property': 'genetically engineered*carbohydrate-rich', 'confidence': 'high', 'explanation': 'Reverse transcriptase and transposase are indicative of genome mobility mechanisms, commonly observed in genetically engineered organisms. The Phosphotransferase system (PTS) component is involved in carbohydrate transport systems, which are prevalent in carbohydrate-rich environments of food production.'}, {'ecosystem': 'Environmental:Engineered:Food production', 'feature_id': 'IPR018216 * IPR002914', 'feature_label': 'Cathelicidin, conserved site * Pollen allergen Poa p IX/Phl p VI', 'bio_property': 'antimicrobial peptide*allergen', 'env_property': 'controlled microbial populations*presence of plants', 'confidence': 'medium', 'explanation': 'Cathelicidins are antimicrobial peptides that play a role in controlling microbial populations, a necessary function in managing food production environments. The presence of pollen allergens suggests a coexistence with plant materials within the food production ecosystem.'}]\n", + "[{'ecosystem': 'Engineered:Food production:Dairy products', 'feature_id': 'GO:0008740 * IPR003491 * GO:0017148', 'feature_label': 'L-rhamnose isomerase activity * Replication initiation factor * Negative regulation of translation', 'bio_property': 'sugar metabolism*DNA replication*gene expression regulation', 'env_property': 'nutrient-rich*temperature-controlled*high microbial activity', 'confidence': 'high', 'explanation': 'Dairy production environments are nutrient-rich and foster diverse microbial activity. L-rhamnose isomerase facilitates sugar metabolism from plant-based ingredients. Replication initiation factors are crucial for microbial proliferation. Negative regulation of translation hints at complex gene expression regulation due to the diverse microbiota.'}, {'ecosystem': 'Engineered:Food production:Dairy products', 'feature_id': 'IPR001360 * IPR011735 * GO:0004638', 'feature_label': 'Glycoside hydrolase family 1 * WlaTC/HtrL glycosyltransferase * phosphoribosylaminoimidazole carboxylase activity', 'bio_property': 'polysaccharide degradation*cell wall synthesis*nucleotide biosynthesis', 'env_property': 'rich in polysaccharides*stable pH*anaerobic niches', 'confidence': 'high', 'explanation': 'Dairy environments are rich in lactose and other polysaccharides, necessitating glycoside hydrolase activity. WlaTC/HtrL glycosyltransferase is involved in cell wall formation, crucial in dense microbial environments. Phosphoribosylaminoimidazole carboxylase activity is part of purine biosynthesis, supporting rapid microbial growth.'}, {'ecosystem': 'Engineered:Food production:Dairy products', 'feature_id': 'IPR007464 * IPR010133 * IPR017559', 'feature_label': 'Bacteriocin, class IId * Bacteriocin-type signal sequence * Alkyl hydroperoxide reductase subunit C', 'bio_property': 'antimicrobial peptide production*stress response*oxidative stress defense', 'env_property': 'competitive microbial interactions*oxidative stress conditions*community-specific signaling', 'confidence': 'high', 'explanation': 'Bacteriocins are antimicrobial peptides produced by bacteria to inhibit competitors, relevant in densely populated dairy microbial communities. Alkyl hydroperoxide reductase alleviates oxidative stress, enhancing survival in the competitive, high-interaction environment.'}, {'ecosystem': 'Engineered:Food production:Dairy products', 'feature_id': 'IPR007210 * IPR028955', 'feature_label': 'Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * Immunity protein 57', 'bio_property': 'osmoprotection*microbial defense', 'env_property': 'variable osmolarity*potential for bacteriophage presence', 'confidence': 'medium', 'explanation': 'Glycine betaine transport systems provide osmoprotection in environments with varying osmolarity, which can occur with ingredient changes. Immunity proteins suggest defense mechanisms against bacteriophages, common in diverse microbial ecosystems such as dairy.'}, {'ecosystem': 'Engineered:Food production:Dairy products', 'feature_id': 'IPR004501 * IPR003491 * IPR010960', 'feature_label': 'Phosphotransferase system, EIIC component, type 3 * Replication initiation factor * Flavocytochrome c', 'bio_property': 'sugar transport*DNA replication*electron transport', 'env_property': 'nutrient-rich*redox-active', 'confidence': 'high', 'explanation': 'The phosphotransferase system is crucial for sugar uptake in nutrient-rich dairy environments. Replication initiation factors support active microbial growth. Flavocytochrome c is involved in electron transport, significant for redox processes critical in microbial metabolism in dairy production.'}]\n", + "[{'ecosystem': 'Engineered:Food production:Fermented beverages', 'feature_id': 'GO:0004114 * IPR004501 * IPR007354', 'feature_label': \"3',5'-cyclic-nucleotide phosphodiesterase activity * Phosphotransferase system, EIIC component, type 3 * Bisanhydrobacterioruberin hydratase CruF-like\", 'bio_property': 'signal transduction*carbohydrate uptake*carotenoid biosynthesis', 'env_property': 'nutrient-rich*low pH*anaerobic', 'confidence': 'high', 'explanation': 'The combination of these features suggests a complex system of signaling, carbohydrate uptake, and carotenoid biosynthesis highly adapted to the nutrient-rich, low pH, and anaerobic conditions commonly found in fermented beverage production.'}, {'ecosystem': 'Engineered:Food production:Fermented beverages', 'feature_id': 'GO:0004122 * IPR004642', 'feature_label': 'cystathionine beta-synthase activity * Serine dehydratase, alpha subunit', 'bio_property': 'amino acid metabolism*sulfur amino acid biosynthesis', 'env_property': 'nutrient-rich*stable temperature', 'confidence': 'medium', 'explanation': 'The presence of cystathionine beta-synthase and serine dehydratase indicates active amino acid metabolism and sulfur amino acid biosynthesis, processes vital in nutrient-rich and stable temperature conditions typical of fermentation environments.'}, {'ecosystem': 'Engineered:Food production:Fermented beverages', 'feature_id': 'GO:0005871 * IPR004868', 'feature_label': 'kinesin complex * DNA-directed DNA polymerase, family B, mitochondria/virus', 'bio_property': 'intracellular transport*DNA replication', 'env_property': 'controlled temperature*anaerobic', 'confidence': 'high', 'explanation': 'Kinesin complexes and mitochondrial/viral DNA polymerases are essential for intracellular transport and replication processes, crucial in the controlled temperature and anaerobic conditions of fermented beverage ecosystems.'}, {'ecosystem': 'Engineered:Food production:Fermented beverages', 'feature_id': 'IPR006541 * IPR007165 * IPR019895', 'feature_label': 'Bacteriocin-associated integral membrane protein * Mycobacterial 4 TMS phage holin, superfamily IV * Putative bacteriocin export ABC transporter, lactococcin 972 group', 'bio_property': 'antimicrobial activity*cell lysis*transporter activity', 'env_property': 'high microbial diversity*anaerobic', 'confidence': 'high', 'explanation': 'Features related to bacteriocin production, phage holins, and bacteriocin transporters are indicative of mechanisms to control microbial diversity and ensure survival in anaerobic conditions found in fermented habitats.'}, {'ecosystem': 'Engineered:Food production:Fermented beverages', 'feature_id': 'GO:0042176 * IPR002631', 'feature_label': 'regulation of protein catabolic process * Plasmid replication protein', 'bio_property': 'proteolysis regulation*plasmid maintenance', 'env_property': 'nutrient-rich*variable pH', 'confidence': 'medium', 'explanation': 'Regulation of protein catabolic processes and plasmid replication proteins are critical in maintaining plasmid integrity and protein turnover, which are vital in nutrient-rich and varying pH conditions seen in fermented beverages.'}]\n", + "[{'ecosystem': 'Engineered:Solid waste:Composting', 'feature_id': 'GO:0016999 * IPR002723', 'feature_label': 'antibiotic metabolic process * N(4)-bis(aminopropyl)spermidine synthase, C-terminal', 'bio_property': 'antibiotic production*polyamine biosynthesis', 'env_property': 'organic-rich*dynamic temperature', 'confidence': 'high', 'explanation': 'The antibiotic metabolic process is significant in composting as antibiotics can suppress harmful microbial species. N(4)-bis(aminopropyl)spermidine synthase is involved in polyamine synthesis, crucial for microbial cell growth under organic-rich conditions and dynamic temperatures.'}, {'ecosystem': 'Engineered:Solid waste:Composting', 'feature_id': 'GO:0004638 * IPR004501', 'feature_label': 'phosphoribosylaminoimidazole carboxylase activity * Phosphotransferase system, EIIC component, type 3', 'bio_property': 'purine biosynthesis*carbohydrate metabolism', 'env_property': 'nutrient-rich*fluctuating pH', 'confidence': 'high', 'explanation': 'Phosphoribosylaminoimidazole carboxylase is crucial for purine biosynthesis, supporting rapid microbial growth in nutrient-rich conditions. The phosphotransferase system aids in carbohydrate metabolism, essential for energy extraction in environments with fluctuating pH.'}, {'ecosystem': 'Engineered:Solid waste:Composting', 'feature_id': 'IPR008016 * IPR014242 * IPR014580', 'feature_label': 'Portal protein Gp10 * Spore cortex biosynthesis protein, YabQ * Uncharacterised conserved protein UCP033199', 'bio_property': 'phage infection*spore formation*unknown', 'env_property': 'diverse microbial population*high organic content', 'confidence': 'medium', 'explanation': 'Portal protein Gp10 links to viral infections prevalent in diverse microbial populations. The Spore cortex biosynthesis protein, YabQ, is vital for spore formation, crucial for microbial survival in high organic content environments. The function of UCP033199 is unknown but may have a role in adaptation.'}, {'ecosystem': 'Engineered:Solid waste:Composting', 'feature_id': 'IPR014931 * IPR019060 * IPR022343', 'feature_label': 'Protein of unknown function DUF1805 * Domain of unknown function DUF2382 * GCR1-cAMP receptor', 'bio_property': 'unknown*unknown*signal transduction', 'env_property': 'variable nutrient availability*anaerobic pockets', 'confidence': 'medium', 'explanation': 'Although DUF1805 and DUF2382 proteins have unknown functions, their presence in diverse environments suggests roles in adaptation to variable nutrient availability. The GCR1-cAMP receptor is involved in signal transduction, enabling microbial communication in anaerobic pockets.'}, {'ecosystem': 'Engineered:Solid waste:Composting', 'feature_id': 'GO:0004122 * IPR022380', 'feature_label': 'cystathionine beta-synthase activity * Glutamyl-Q tRNA(Asp) synthetase', 'bio_property': 'amino acid metabolism*protein synthesis', 'env_property': 'high nitrogen content*thermophilic conditions', 'confidence': 'high', 'explanation': 'Cystathionine beta-synthase activity is crucial for sulfur amino acid metabolism, significant in high nitrogen content environments. Glutamyl-Q tRNA(Asp) synthetase is vital for protein synthesis, supporting microbial activity in thermophilic conditions typical of composting.'}]\n", + "[{'ecosystem': 'Engineered:Wastewater', 'feature_id': 'GO:0018551 * IPR001613', 'feature_label': 'dissimilatory sulfite reductase activity * Flavin amine oxidase', 'bio_property': 'sulfate reduction*amine catabolism', 'env_property': 'anaerobic conditions*presence of organic amines', 'confidence': 'high', 'explanation': 'Dissimilatory sulfite reductase is crucial in anaerobic conditions for reducing sulfate to sulfide, common in wastewater environments. The presence of flavin amine oxidase indicates catabolism of organic amines which are typically found in wastewater.'}, {'ecosystem': 'Engineered:Wastewater', 'feature_id': 'GO:0003968 * GO:0080009 * IPR028962', 'feature_label': 'RNA-dependent RNA polymerase activity * mRNA methylation * Immunity protein 10', 'bio_property': 'viral replication*gene expression regulation*bacterial immunity', 'env_property': 'high viral load*presence of phages', 'confidence': 'high', 'explanation': 'RNA-dependent RNA polymerase indicates viral replication, mRNA methylation suggests viral or host gene expression regulation, and immunity protein points to bacterial immune response to phages, all indicative of environments with high viral presence as seen in wastewater.'}, {'ecosystem': 'Engineered:Wastewater', 'feature_id': 'GO:0008901 * IPR035576', 'feature_label': 'ferredoxin hydrogenase activity * Type VI secretion system TssC', 'bio_property': 'hydrogen production*bacterial competition', 'env_property': 'anaerobic conditions*microbial competition', 'confidence': 'high', 'explanation': 'Ferredoxin hydrogenase is involved in anaerobic hydrogen production, and Type VI secretion system TssC is associated with bacterial competition. Both processes are pertinent to the dynamic microbial communities in wastewater.'}, {'ecosystem': 'Engineered:Wastewater', 'feature_id': 'GO:0019068 * IPR021725', 'feature_label': 'virion assembly * Pathogenicity locus', 'bio_property': 'viral assembly*pathogenicity', 'env_property': 'high microbial diversity*presence of pathogens', 'confidence': 'high', 'explanation': 'Virion assembly is related to viral activity and pathogenicity loci indicate the presence of pathogenic bacteria. Wastewater is known for its diverse microbial population including pathogens.'}, {'ecosystem': 'Engineered:Wastewater', 'feature_id': 'IPR001360 * GO:0019512', 'feature_label': 'Glycoside hydrolase family 1 * lactose catabolic process via tagatose-6-phosphate', 'bio_property': 'carbohydrate metabolism*lactose catabolism', 'env_property': 'nutrient-rich*presence of organic compounds', 'confidence': 'high', 'explanation': 'Glycoside hydrolase family 1 enzymes are involved in breaking down complex carbohydrates, and lactose catabolism processes indicate the presence of lactose and other organic compounds, typical in nutrient-rich wastewater.'}]\n", + "[{'ecosystem': 'Engineered:Wastewater:Activated Sludge', 'feature_id': 'GO:0015444 * GO:0008901', 'feature_label': 'P-type magnesium transporter activity * ferredoxin hydrogenase activity', 'bio_property': 'metal ion transport*hydrogen metabolism', 'env_property': 'metal-rich*anaerobic', 'confidence': 'high', 'explanation': 'Activated sludge systems often contain high levels of various metals, and P-type magnesium transporters are important for managing magnesium ion concentrations. Ferredoxin hydrogenase activity is crucial in anaerobic conditions often found in wastewater treatment where hydrogen is involved in redox reactions.'}, {'ecosystem': 'Engineered:Wastewater:Activated Sludge', 'feature_id': 'GO:0018551 * IPR004462', 'feature_label': 'dissimilatory sulfite reductase activity * Desulfoferrodoxin, N-terminal domain', 'bio_property': 'sulfur metabolism*redox reactions', 'env_property': 'sulfate-rich*anaerobic', 'confidence': 'high', 'explanation': 'Dissimilatory sulfite reductase and the desulfoferrodoxin domain are involved in the reduction of sulfite to sulfide, a key process in anaerobic environments such as those found in activated sludge, which are commonly sulfate-rich.'}, {'ecosystem': 'Engineered:Wastewater:Activated Sludge', 'feature_id': 'IPR001360 * IPR010706', 'feature_label': 'Glycoside hydrolase family 1 * Fatty acid cis-trans isomerase', 'bio_property': 'polysaccharide degradation*fatty acid metabolism', 'env_property': 'organic-rich*diverse carbon substrates', 'confidence': 'high', 'explanation': 'Activated sludge contains diverse organic matter. Glycoside hydrolases break down complex carbohydrates while fatty acid cis-trans isomerases modify fatty acids, both of which are important for metabolizing the varied carbon sources present.'}, {'ecosystem': 'Engineered:Wastewater:Activated Sludge', 'feature_id': 'IPR035576 * IPR032830', 'feature_label': 'Type VI secretion system TssC * Helicase XPB/Ssl2, N-terminal domain', 'bio_property': 'bacterial competition*DNA repair', 'env_property': 'microbial diversity*high competition', 'confidence': 'high', 'explanation': 'The Type VI secretion system is used by bacteria to compete with others in densely populated environments. Helicase domains are involved in DNA repair mechanisms, which are crucial in high-stress, competitive environments like those found in activated sludge.'}, {'ecosystem': 'Engineered:Wastewater:Activated Sludge', 'feature_id': 'IPR008707 * GO:0019068', 'feature_label': 'PilC beta-propeller domain * virion assembly', 'bio_property': 'cell adhesion*viral life cycle', 'env_property': 'high microbial interaction*viral presence', 'confidence': 'high', 'explanation': 'PilC domains facilitate bacterial adhesion to surfaces and other cells, while virion assembly is indicative of viral activity. Both are integral in environments with high microbial interactions and viral presence, such as activated sludge.'}]\n", + "[{'ecosystem': 'Engineered:Wastewater:Water and sludge', 'feature_id': 'GO:0019512 * GO:0033920', 'feature_label': 'lactose catabolic process via tagatose-6-phosphate * 6-phospho-beta-galactosidase activity', 'bio_property': 'carbohydrate metabolism', 'env_property': 'high organic matter*nutrient-rich', 'confidence': 'high', 'explanation': 'Lactose catabolism and beta-galactosidase activity indicate the utilization of organic compounds prevalent in wastewater environments.'}, {'ecosystem': 'Engineered:Wastewater:Water and sludge', 'feature_id': 'IPR017821 * IPR011868', 'feature_label': 'Succinate CoA transferase * Molybdate ABC transporter, ATP-binding protein', 'bio_property': 'energy metabolism*nutrient transport', 'env_property': 'anaerobic conditions*high metal content', 'confidence': 'high', 'explanation': 'Succinate CoA transferase is involved in anaerobic energy production, and molybdate transporters assist in handling metal ions commonly found in wastewater.'}, {'ecosystem': 'Engineered:Wastewater:Water and sludge', 'feature_id': 'GO:0045151 * IPR017559', 'feature_label': 'acetoin biosynthetic process * Alkyl hydroperoxide reductase subunit C', 'bio_property': 'stress response*antioxidant activity', 'env_property': 'variable oxygen levels*oxidative stress', 'confidence': 'high', 'explanation': 'Acetoin biosynthesis and alkyl hydroperoxide reductase are responses to oxidative stress, a common condition in wastewater treatment processes due to fluctuating oxygen levels.'}, {'ecosystem': 'Engineered:Wastewater:Water and sludge', 'feature_id': 'IPR003491 * IPR010789 * IPR010517', 'feature_label': 'Replication initiation factor * Terminase small subunit, Skunalikevirus-type * Phage tail tube protein, Siphoviridae', 'bio_property': 'viral replication*phage assembly', 'env_property': 'high microbial diversity*high phage activity', 'confidence': 'high', 'explanation': 'Replication initiation factors and phage-related proteins are indicative of high microbial and phage activities, reflecting the microbial richness in wastewater.'}, {'ecosystem': 'Engineered:Wastewater:Water and sludge', 'feature_id': 'IPR008707 * IPR014984', 'feature_label': 'PilC beta-propeller domain * HopJ type III effector protein', 'bio_property': 'cell adhesion*pathogenicity', 'env_property': 'high microbial interaction*pathogen presence', 'confidence': 'medium', 'explanation': 'Proteins involved in cell adhesion and pathogenicity suggest interactions among microbes and potential pathogen prevalence in wastewater.'}, {'ecosystem': 'Engineered:Wastewater:Water and sludge', 'feature_id': 'GO:0019068 * IPR010789', 'feature_label': 'virion assembly * Terminase small subunit, Skunalikevirus-type', 'bio_property': 'viral assembly', 'env_property': 'high microbial diversity*high phage activity', 'confidence': 'high', 'explanation': 'The presence of proteins related to virion assembly is indicative of a dynamic virome in wastewater environments.'}, {'ecosystem': 'Engineered:Wastewater:Water and sludge', 'feature_id': 'IPR010945 * IPR017821', 'feature_label': 'Malate dehydrogenase, type 2 * Succinate CoA transferase', 'bio_property': 'energy metabolism', 'env_property': 'anaerobic conditions', 'confidence': 'high', 'explanation': 'Key enzymes of the TCA cycle and related anaerobic pathways are crucial under low oxygen conditions typical of sludge environments.'}, {'ecosystem': 'Engineered:Wastewater:Water and sludge', 'feature_id': 'GO:0004521 * IPR011119', 'feature_label': 'RNA endonuclease activity * Uncharacterised domain, helicase/relaxase, putative', 'bio_property': 'RNA processing*genetic regulation', 'env_property': 'dynamic nutrient changes', 'confidence': 'medium', 'explanation': 'RNA endonucleases and helicase-related domains play roles in genetic regulation, significant in environments with dynamic nutrient fluctuations.'}]\n", + "[{'ecosystem': 'Environmental:Aquatic:Estuary', 'feature_id': 'IPR011802 * IPR011946', 'feature_label': 'Adenylylsulphate reductase, beta subunit * Integrase, integron-type', 'bio_property': 'sulfur metabolism*genetic recombination', 'env_property': 'nutrient-rich*variable salinity', 'confidence': 'high', 'explanation': 'Adenylylsulphate reductase is critical in sulfur metabolism, a common process in nutrient-rich environments like estuaries. Integron-type integrases facilitate genetic exchange, which can offer adaptive advantages in the highly variable salinity and nutrient conditions of estuaries.'}, {'ecosystem': 'Environmental:Aquatic:Estuary', 'feature_id': 'GO:0046797 * IPR014984', 'feature_label': 'viral procapsid maturation * HopJ type III effector protein', 'bio_property': 'viral life cycle*host-pathogen interaction', 'env_property': 'high viral activity*microbial interactions', 'confidence': 'medium', 'explanation': 'The occurrence of viral procapsid maturation suggests high viral activity, a common aspect in estuary ecosystems due to their dynamic microbial communities. The HopJ type III effector protein indicates active host-pathogen interactions, which align with the high biodiversity and microbial interactions prevalent in estuaries.'}, {'ecosystem': 'Environmental:Aquatic:Estuary', 'feature_id': 'IPR028282 * sk__Bacteria;k__;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Candidatus_Pelagibacter;s__Candidatus_Pelagibacter_ubique', 'feature_label': 'WASH complex subunit 7, central domain * Candidatus Pelagibacter ubique', 'bio_property': 'cytoskeletal organization*abundant marine bacteria', 'env_property': 'low nutrient availability', 'confidence': 'high', 'explanation': 'WASH complex subunit 7 is involved in cytoskeletal organization, important for maintaining cellular structure in complex environments. Candidatus Pelagibacter ubique is one of the most abundant marine bacteria, well-adapted to low nutrient conditions, which can also be found in estuarine environments.'}]\n", + "[{'ecosystem': 'Environmental:Aquatic:Estuary:Sediment', 'feature_id': 'GO:0005471 * IPR007343', 'feature_label': 'ATP:ADP antiporter activity * Uncharacterised protein family, zinc metallopeptidase putative', 'bio_property': 'energy metabolism*enzymatic activity*metal ion binding', 'env_property': 'estuarine*nutrient cycling', 'confidence': 'high', 'explanation': 'The ATP:ADP antiporter is integral to energy metabolism, which is crucial in nutrient-rich estuarine environments. The presence of zinc metallopeptidase indicates enzymatic activity essential for nutrient degradation and metal ion binding, common in sediment ecosystems.'}, {'ecosystem': 'Environmental:Aquatic:Estuary:Sediment', 'feature_id': 'IPR010518 * IPR014984 * IPR021249', 'feature_label': 'Flagellar regulatory FleQ * HopJ type III effector protein * Protein of unknown function DUF2788', 'bio_property': 'motility regulation*pathogenesis*protein interaction', 'env_property': 'sediment*microbial community interaction', 'confidence': 'medium', 'explanation': 'The Flagellar regulatory FleQ is involved in motility, essential for bacteria navigating sedimentary environments. HopJ type III effector proteins often play roles in pathogenesis and interactions within microbial communities, while the DUF2788 protein likely contributes to yet unidentified microbial functions within the sediment.'}, {'ecosystem': 'Environmental:Aquatic:Estuary:Sediment', 'feature_id': 'IPR007343 * IPR021249', 'feature_label': 'Uncharacterised protein family, zinc metallopeptidase putative * Protein of unknown function DUF2788', 'bio_property': 'enzymatic activity*metal ion binding*unknown function', 'env_property': 'estuarine*metal-rich', 'confidence': 'medium', 'explanation': 'Zinc metallopeptidases play crucial roles in enzymatic activity, which is key in the nutrient-rich and often metal-rich environments found in estuarine sediments. Protein of unknown function DUF2788 suggests additional, unidentified roles that contribute to the complexity of this ecosystem.'}]\n", + "[{'ecosystem': 'Environmental:Aquatic:Freshwater:Lake', 'feature_id': 'IPR026395 * sk__Bacteria;k__;p__Actinobacteria;c__Actinobacteria;o__Micrococcales;f__Microbacteriaceae;g__Candidatus_Limnoluna', 'feature_label': 'CshA domain * Candidatus_Limnoluna', 'bio_property': 'RNA helicase activity*cold shock response', 'env_property': 'low temperature*freshwater', 'confidence': 'high', 'explanation': 'The CshA domain is associated with cold shock proteins which are crucial for cold shock response. Actinobacteria, specifically Candidatus_Limnoluna, are often found in freshwater environments where temperature can vary significantly.'}]\n", + "[{'ecosystem': 'Environmental:Aquatic:Freshwater:Lotic:Sediment', 'feature_id': 'IPR004813 * IPR022380', 'feature_label': 'Oligopeptide transporter, OPT superfamily * Glutamyl-Q tRNA(Asp) synthetase', 'bio_property': 'nutrient transport*protein synthesis', 'env_property': 'nutrient variable*fluctuating nutrient levels', 'confidence': 'high', 'explanation': 'Oligopeptide transporters are critical in the uptake of peptides from the environment, essential in nutrient-variable conditions such as those found in lotic freshwater sediments. The presence of Glutamyl-Q tRNA(Asp) synthetase supports active protein synthesis, necessary for metabolic adaptation to fluctuating nutrient levels.'}, {'ecosystem': 'Environmental:Aquatic:Freshwater:Lotic:Sediment', 'feature_id': 'IPR012657', 'feature_label': '23S rRNA-intervening sequence protein', 'bio_property': 'ribosomal function*gene regulation', 'env_property': 'high microbial activity*sediment-associated microbial community', 'confidence': 'high', 'explanation': '23S rRNA-intervening sequence proteins are involved in maintaining and modifying ribosomal function, which is crucial for high levels of microbial activity observed in sediment environments. These proteins reflect an adaptation to densely populated microbial communities within sediment layers.'}]\n", + "[{'ecosystem': 'Environmental:Aquatic:Lentic:Brackish', 'feature_id': 'GO:0017148 * GO:0043093', 'feature_label': 'negative regulation of translation * FtsZ-dependent cytokinesis', 'bio_property': 'cell cycle control*protein synthesis regulation*cell division', 'env_property': 'fluctuating nutrient levels', 'confidence': 'high', 'explanation': 'In brackish waters with fluctuating nutrient levels, there might be a need for stringent cell cycle control and protein synthesis regulation to optimize resource usage and division timing.'}, {'ecosystem': 'Environmental:Aquatic:Lentic:Brackish', 'feature_id': 'IPR000036 * IPR025123', 'feature_label': 'Peptidase A26, omptin * Domain of unknown function DUF4049', 'bio_property': 'protein degradation*stress response', 'env_property': 'variable salinity', 'confidence': 'high', 'explanation': 'Omptin peptidases are known to be involved in stress responses, which would be crucial in brackish environments with fluctuating salinity. Domain DUF4049 might also be implicated in stress-related functions.'}, {'ecosystem': 'Environmental:Aquatic:Lentic:Brackish', 'feature_id': 'IPR005126 * IPR011735', 'feature_label': 'NapC/NirT cytochrome c, N-terminal * WlaTC/HtrL glycosyltransferase', 'bio_property': 'electron transport*glycosylation processes', 'env_property': 'low oxygen levels', 'confidence': 'medium', 'explanation': 'NapC/NirT cytochrome c proteins are essential for electron transport in low oxygen conditions, common in lentic brackish environments. Glycosyltransferases like WlaTC/HtrL could play roles in modifying proteins for optimal function under these conditions.'}, {'ecosystem': 'Environmental:Aquatic:Lentic:Brackish', 'feature_id': 'IPR023870 * IPR028955', 'feature_label': 'Poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA * Immunity protein 57', 'bio_property': 'biofilm formation*antimicrobial resistance', 'env_property': 'microbial community interactions', 'confidence': 'high', 'explanation': 'Biofilms provide structural integrity and protection in brackish environments, supporting diverse microbial communities. Immunity proteins contribute to the defense against competing organisms or phages.'}, {'ecosystem': 'Environmental:Aquatic:Lentic:Brackish', 'feature_id': 'IPR031834', 'feature_label': 'Antitoxin RnlB/LsoB', 'bio_property': 'toxin-antitoxin systems', 'env_property': 'variable pH', 'confidence': 'medium', 'explanation': 'Toxin-antitoxin systems help bacteria survive harsh conditions, such as variable pH levels found in brackish waters, by regulating cell death and survival.'}]\n", "JSON decode error for result: Expecting value: line 1 column 1 (char 0)\n", - "Content that caused the error: Sure. Below is the detailed relationships between observed features and environmental properties of the Engineered:Bioreactor ecosystem, represented in the desired JSON format:\n", + "Content that caused the error: Given the observed features in the Environmental:Aquatic:Marine ecosystem, let us identify and explain relationships between these features and the environmental properties of the marine ecosystem.\n", "\n", "\n", "{\n", - " \"Engineered:Bioreactor\": {\n", + " \"Environmental:Marine\": {\n", " \"1\": {\n", - " \"feature_id\": \"GO:0018551 * IPR005126\",\n", - " \"feature_label\": \"dissimilatory sulfite reductase activity * NapC/NirT cytochrome c, N-terminal\",\n", - " \"bio_property\": \"sulfate reduction * anaerobic respiration\",\n", - " \"env_property\": \"anaerobic * high sulfate\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Dissimilatory sulfite reductase is essential for the reduction of sulfates in anaerobic conditions where high sulfate concentration is prevalent.\"\n", - " },\n", - " \"2\": {\n", - " \"feature_id\": \"IPR004763 * IPR016300\",\n", - " \"feature_label\": \"Cation efflux system CzcA/CusA/SilA/NccA/HelA/CnrA * Arsenical pump ATPase, ArsA/GET3\",\n", - " \"bio_property\": \"heavy metal resistance * detoxification\",\n", - " \"env_property\": \"high metal concentration * toxicity\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Both features are involved in the efflux and resistance mechanisms against toxic heavy metals, indicating an environment with high metal concentrations.\"\n", - " },\n", - " \"3\": {\n", - " \"feature_id\": \"GO:0031460\",\n", - " \"feature_label\": \"glycine betaine transport\",\n", - " \"bio_property\": \"osmoprotection * stress response\",\n", + " \"feature_id\": \"GO:0031460 * IPR004681\",\n", + " \"feature_label\": \"glycine betaine transport * TRAP transporter large membrane protein DctM\",\n", + " \"bio_property\": \"osmoprotection * transporter activity\",\n", " \"env_property\": \"marine * high salinity\",\n", " \"confidence\": \"high\",\n", - " \"explanation\": \"Glycine betaine is a known osmoprotectant in high osmolarity environments such as those with high salinity.\"\n", - " },\n", - " \"4\": {\n", - " \"feature_id\": \"GO:0008743 * IPR014234\",\n", - " \"feature_label\": \"L-threonine 3-dehydrogenase activity * N-acetylmuramoyl-L-alanine amidase CwlD\",\n", - " \"bio_property\": \"enzyme activity * cell wall metabolism\",\n", - " \"env_property\": \"nutrient flux * cell wall turnover\",\n", - " \"confidence\": \"medium\",\n", - " \"explanation\": \"L-threonine 3-dehydrogenase is involved in amino acid metabolism and the CwlD amidase in bacterial cell wall turnover, both of which relate to dynamic nutrient flux and cell wall recycling in the ecosystem.\"\n", - " },\n", - " \"5\": {\n", - " \"feature_id\": \"IPR011868 * sk__Bacteria;k__;p__Candidatus_Gottesmanbacteria\",\n", - " \"feature_label\": \"Molybdate ABC transporter, ATP-binding protein * Candidatus Gottesmanbacteria\",\n", - " \"bio_property\": \"molybdate transport * specialized metabolism\",\n", - " \"env_property\": \"trace element concentration * microbial diversity\",\n", - " \"confidence\": \"medium\",\n", - " \"explanation\": \"The presence of a molybdate transporter suggests a necessity for trace element acquisition, while Candidatus Gottesmanbacteria indicates specialized microbial taxa adapted to unique biochemical conditions.\"\n", - " }\n", - " }\n", - "}\n", - "\n", - "\n", - "### Key Points in Relationships\n", - "- **High sulfate and anaerobic conditions** likely contribute to the presence of dissimilatory sulfite reductase and cytochrome systems supporting sulfate reduction processes.\n", - "- **High metal concentrations** necessitate the bioavailability and active transport of cations, leading to the presence of ATPase/plasma membrane cation efflux proteins.\n", - "- **High salinity environments** explain the necessity for osmoprotectants like glycine betaine transport.\n", - "- **Nutrient flux and cell wall turnover** processes are indicated by metabolism-related enzymes, showing dynamic bioreactor conditions.\n", - "- **Trace elements and microbial diversity** contribute to supporting specialized bacterial populations and their transport systems.\n", - "\n", - "By focusing on these different features and environmental properties, we can effectively characterize the biogeochemical and ecological functionalities of the Engineered:Bioreactor ecosystem. The confidence levels are based on established associations between these features and their typical environments, ensuring the relevancy and reliability of the reported findings.\n", - "[]\n", - "[{'ecosystem': 'Engineered:Bioremediation:Terephthalate:Wastewater', 'feature_id': 'GO:0004114 * IPR004501', 'feature_label': \"3',5'-cyclic-nucleotide phosphodiesterase activity * Phosphotransferase system, EIIC component, type 3\", 'bio_property': 'signal transduction*sugar transport', 'env_property': 'high organic load*nutrient dense', 'confidence': 'high', 'explanation': 'Systems involved in signal transduction and sugar transport are crucial for microbial responses to high organic load environments.'}, {'ecosystem': 'Engineered:Bioremediation:Terephthalate:Wastewater', 'feature_id': 'GO:0008901 * IPR010960', 'feature_label': 'ferredoxin hydrogenase activity * Flavocytochrome c', 'bio_property': 'electron transport chain*anaerobic respiration', 'env_property': 'oxygen-limited*high organic load', 'confidence': 'high', 'explanation': 'Ferredoxin hydrogenase and Flavocytochrome c are indicative of anaerobic conditions often found in high organic load environments, enhancing the electron transport chain.'}, {'ecosystem': 'Engineered:Bioremediation:Terephthalate:Wastewater', 'feature_id': 'GO:0019512 * IPR004300', 'feature_label': 'lactose catabolic process via tagatose-6-phosphate * Glycoside hydrolase family 57, N-terminal domain', 'bio_property': 'lactose metabolism*carbohydrate degradation', 'env_property': 'high organic load*carbohydrate-rich conditions', 'confidence': 'high', 'explanation': 'These features are involved in carbohydrate metabolism, crucial for environments rich in organic carbon sources such as those present in terephthalate wastewater.'}, {'ecosystem': 'Engineered:Bioremediation:Terephthalate:Wastewater', 'feature_id': 'GO:0004037 * IPR017813', 'feature_label': 'allantoicase activity * Mycothiol acetyltransferase', 'bio_property': 'amino acid metabolism*detoxification', 'env_property': 'nutrient dense*potentially toxin-rich', 'confidence': 'medium', 'explanation': 'Enzymes involved in amino acid metabolism and detoxification are likely to be relevant in environments that are nutrient-dense and may contain toxic compounds.'}, {'ecosystem': 'Engineered:Bioremediation:Terephthalate:Wastewater', 'feature_id': 'IPR014580 * IPR014984', 'feature_label': 'Uncharacterised conserved protein UCP033199 * HopJ type III effector protein', 'bio_property': 'unknown function*pathogenicity', 'env_property': 'diverse microbial community*complex interactions', 'confidence': 'medium', 'explanation': 'Presence of pathogenicity-related proteins indicates the environment might support a complex microbial community, including potential microbial interactions.'}, {'ecosystem': 'Engineered:Bioremediation:Terephthalate:Wastewater', 'feature_id': 'IPR000957 * GO:0043462', 'feature_label': 'Sulphate/thiosulphate-binding, conserved site * regulation of ATP-dependent activity', 'bio_property': 'sulphur metabolism*energy regulation', 'env_property': 'sulphate-rich*variable energy availability', 'confidence': 'medium', 'explanation': 'Features relating to sulphur metabolism and energy regulation suggest adaptation to environments that have high levels of sulphate and variable energy sources.'}, {'ecosystem': 'Engineered:Bioremediation:Terephthalate:Wastewater', 'feature_id': 'sk__Bacteria;k__;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides * sk__Bacteria;k__;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella', 'feature_label': 'Bacteroides * Collinsella', 'bio_property': 'complex carbohydrate breakdown*secondary metabolism', 'env_property': 'high fiber*complex organic matter', 'confidence': 'high', 'explanation': 'Bacteroides and Collinsella are known for their roles in breaking down complex carbohydrates, indicating adaptation to high fiber and complex organic matter environments.'}]\n", - "[{'ecosystem': 'Engineered:Built environment', 'feature_id': 'IPR009413', 'feature_label': 'Hemolysin, aegerolysin type', 'bio_property': 'cell lysis*pathogenicity', 'env_property': 'humid*high dust load', 'confidence': 'high', 'explanation': 'Hemolysins like aegerolysin type are often associated with environments rich in organic material, where they can easily access hemolytic substrates. In the built environment, these conditions are typically found in dusty, humid areas which provide the needed substrates and conditions for microbial growth.'}, {'ecosystem': 'Engineered:Built environment', 'feature_id': 'IPR010960', 'feature_label': 'Flavocytochrome c', 'bio_property': 'electron transport*oxidative stress response', 'env_property': 'industrial*pollutant-rich', 'confidence': 'high', 'explanation': 'Flavocytochromes are involved in electron transport chains and are crucial for oxidative stress response. In built environments, particularly in industrial settings with pollutants, organisms with such features may prevail due to their enhanced ability to manage oxidative stress caused by pollutants.'}, {'ecosystem': 'Engineered:Built environment', 'feature_id': 'IPR021822', 'feature_label': 'Protein of unknown function DUF3405', 'bio_property': 'potential regulatory function*protein-protein interaction', 'env_property': 'varies', 'confidence': 'medium', 'explanation': 'Though the exact function is unknown, proteins with DUF3405 domains may be involved in regulatory processes and protein-protein interactions. These properties tend to be universal and can adapt to a variety of environmental conditions.'}, {'ecosystem': 'Engineered:Built environment', 'feature_id': 'IPR022190', 'feature_label': 'Protein of unknown function DUF3716', 'bio_property': 'potential stress response*structural component', 'env_property': 'high foot traffic*biofilm formation', 'confidence': 'medium', 'explanation': 'Proteins with DUF3716 might play roles in structural integrity or stress response within microbial communities. In high-traffic areas where human interaction is frequent, biofilm formation is a common adaptive response, suggesting DUF3716 proteins may contribute to biofilm resilience.'}, {'ecosystem': 'Engineered:Built environment', 'feature_id': 'sk__Eukaryota;k__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Eurotiales;f__Aspergillaceae', 'feature_label': 'Eurotiales (fungal order including Aspergillus)', 'bio_property': 'decomposition*secondary metabolite production', 'env_property': 'indoor air*material degradation', 'confidence': 'high', 'explanation': 'Members of the Aspergillaceae family, such as Aspergillus, are known for their ability to decompose organic matter and produce numerous secondary metabolites. These fungi commonly thrive in indoor environments where they can contribute to material degradation.'}]\n", - "JSON decode error for result: Expecting value: line 1 column 1 (char 0)\n", - "Content that caused the error: Here's the requested analysis based on the provided features and environmental context:\n", - "\n", - "\n", - "{\n", - " \"Engineered:Food production\": {\n", - " \"1\": {\n", - " \"feature_id\": \"IPR007210 * GO:0031460\",\n", - " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport\",\n", - " \"bio_property\": \"osmoprotection * stress response\",\n", - " \"env_property\": \"marine * high salinity\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Glycine betaine is a known osmoprotectant in high osmolarity environments.\"\n", + " \"explanation\": \"Glycine betaine is transported through membrane proteins like DctM which aids in osmoprotection under high salinity conditions typical of marine environments.\"\n", " },\n", " \"2\": {\n", - " \"feature_id\": \"GO:0004638 * IPR022380\",\n", - " \"feature_label\": \"phosphoribosylaminoimidazole carboxylase activity * Glutamyl-Q tRNA(Asp) synthetase\",\n", - " \"bio_property\": \"nucleotide biosynthesis * translation accuracy\",\n", - " \"env_property\": \"nutrient-rich * chemically regulated\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Phosphoribosylaminoimidazole carboxylase is crucial for purine biosynthesis, which is essential in nutrient-rich environments where rapid cell division occurs. Glutamyl-Q tRNA(Asp) synthetase maintains fidelity in protein synthesis under such conditions.\"\n", - " },\n", - " \"3\": {\n", - " \"feature_id\": \"IPR002914 * IPR000477\",\n", - " \"feature_label\": \"Pollen allergen Poa p IX/Phl p VI * Reverse transcriptase domain\",\n", - " \"bio_property\": \"immune response * retrotransposition\",\n", - " \"env_property\": \"biologically diverse * viral presence\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Allergens like Poa p IX can elicit immune responses, indicating a complex biological system. Reverse transcriptase suggests viral elements often found in such environments.\"\n", - " },\n", - " \"4\": {\n", - " \"feature_id\": \"IPR002631 * IPR004264\",\n", - " \"feature_label\": \"Plasmid replication protein * Transposase, Tnp1/En/Spm-like\",\n", - " \"bio_property\": \"genetic mobility * DNA replication\",\n", - " \"env_property\": \"antibiotic-rich * high genetic variability\",\n", - " \"confidence\": \"medium\",\n", - " \"explanation\": \"Plasmid replication proteins and transposases facilitate genetic exchange and mobility. Such features are typical in environments where antibiotic resistance and genetic adaptability are crucial.\"\n", - " },\n", - " \"5\": {\n", - " \"feature_id\": \"IPR004501 * IPR024309\",\n", - " \"feature_label\": \"Phosphotransferase system, EIIC component, type 3 * Nuclear Testis protein, N-terminal\",\n", - " \"bio_property\": \"sugar transport * transcription regulation\",\n", - " \"env_property\": \"nutrient fluctuation * regulatory complexity\",\n", + " \"feature_id\": \"IPR003563 * GO:0004638\",\n", + " \"feature_label\": \"Oxidized purine nucleoside triphosphate * phosphoribosylaminoimidazole carboxylase activity\",\n", + " \"bio_property\": \"nucleotide metabolism * DNA repair\",\n", + " \"env_property\": \"marine * UV exposure\",\n", " \"confidence\": \"medium\",\n", - " \"explanation\": \"Phosphotransferase systems are involved in sugar uptake, critical in fluctuating nutrient environments. Nuclear testis proteins often regulate gene expression, crucial in environments requiring intricate cellular coordination.\"\n", - " },\n", - " \"6\": {\n", - " \"feature_id\": \"GO:0004984 * IPR018216\",\n", - " \"feature_label\": \"olfactory receptor activity * Cathelicidin, conserved site\",\n", - " \"bio_property\": \"sensory perception * antimicrobial activity\",\n", - " \"env_property\": \"microbial interaction * complex signaling\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Olfactory receptors and antimicrobial peptides like cathelicidins indicate complex microbial interactions and signaling typical in highly regulated, biologically active environments.\"\n", - " }\n", - " }\n", - "}\n", - "\n", - "\n", - "### Key Points:\n", - "1. **Feature Groupings**: Grouped features by combining where they complement each other biologically, as this often reflects shared environmental adaptations or requirements.\n", - "2. **Environmental Context**: Focused on properties like nutrient availability, salinity, biological diversity, and genetic variability which are crucial in engineered food production environments.\n", - "3. **Confidence Levels**: Assigned based on the strength of known biological-environmental relationships and consistency with the environment's expectations.\n", - "[]\n", - "JSON decode error for result: Expecting value: line 1 column 1 (char 0)\n", - "Content that caused the error: Here is a JSON output structure based on the relationships between microbial metagenomic features and environmental properties of the Engineered:Food production:Dairy products ecosystem. The JSON will prioritize reporting relationships involving groups of multiple features:\n", - "\n", - "\n", - "{\n", - " \"Engineered:Food production:Dairy products\": {\n", - " \"1\": {\n", - " \"feature_id\": \"GO:0001510 * GO:0017148 * IPR006848\",\n", - " \"feature_label\": \"RNA methylation * negative regulation of translation * Transcription regulator, putative, lactococcus phage-type\",\n", - " \"bio_property\": \"gene expression regulation * transcriptional control\",\n", - " \"env_property\": \"nutrient-rich * temperature-controlled\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"In dairy product ecosystems, regulating gene expression and transcription is crucial for the adaptation to nutrient-rich, temperature-controlled environments often found in fermentation processes.\"\n", - " },\n", - " \"2\": {\n", - " \"feature_id\": \"GO:0008740 * IPR011735 * IPR028955\",\n", - " \"feature_label\": \"L-rhamnose isomerase activity * WlaTC/HtrL glycosyltransferase * Immunity protein 57\",\n", - " \"bio_property\": \"carbohydrate metabolism * immune response\",\n", - " \"env_property\": \"sugar-rich * varied microbial interactions\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Carbohydrate metabolism and immune response are important in dairy production where sugar content is high, and there are complex microbial interactions, including preservation against pathogens.\"\n", + " \"explanation\": \"Marine environments typically have high UV exposure, which can lead to DNA damage. Enzymes involved in DNA repair and nucleotide metabolism help to mitigate this damage.\"\n", " },\n", " \"3\": {\n", - " \"feature_id\": \"IPR001360 * IPR023870\",\n", - " \"feature_label\": \"Glycoside hydrolase family 1 * Poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA\",\n", - " \"bio_property\": \"polysaccharide breakdown * biofilm formation\",\n", - " \"env_property\": \"lactose presence * biofilm-prone surfaces\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"In dairy products, glycoside hydrolases facilitate the breakdown of lactose while biofilm formation is significant for microbial stability and interaction on dairy processing surfaces.\"\n", - " },\n", - " \"4\": {\n", - " \"feature_id\": \"IPR004501 * IPR008300\",\n", - " \"feature_label\": \"Phosphotransferase system, EIIC component, type 3 * Phosphate propanoyltransferase\",\n", - " \"bio_property\": \"phosphate and sugar transport * phosphorylation\",\n", - " \"env_property\": \"nutrient uptake * fermentation by-products\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Phosphate and sugar transport systems are essential for microbial growth and energy utilization in the fermentation processes of dairy product production, leading to significant nutrient uptake and by-products.\"\n", - " },\n", - " \"5\": {\n", - " \"feature_id\": \"IPR010133 * IPR007464 * IPR017559\",\n", - " \"feature_label\": \"Bacteriocin-type signal sequence * Bacteriocin, class IId * Alkyl hydroperoxide reductase subunit C\",\n", - " \"bio_property\": \"antibacterial activity * oxidative stress response\",\n", - " \"env_property\": \"microbial competition * aeration\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Antibacterial activity and oxidative stress response play crucial roles in dairy ecosystems where microbial competition and varying aeration conditions influence microbial community dynamics.\"\n", - " }\n", - " }\n", - "}\n", - "\n", - "\n", - "Each entry in the JSON provides detailed and high-confidence relationships between the specific features and environmental properties relevant to the dairy product production ecosystem. The key biological properties such as gene regulation, carbohydrate metabolism, and antibacterial activity are tied with environmental properties like nutrient-rich conditions, sugar presence, and microbial competition in fermentation settings. This nuanced understanding supports the production processes by highlighting the microbial functionalities and their environmental dependencies.\n", - "[]\n", - "JSON decode error for result: Extra data: line 55 column 1 (char 3734)\n", - "Content that caused the error: {\n", - " \"Engineered:Food production:Fermented beverages\": {\n", - " \"1\": {\n", - " \"feature_id\": \"GO:0004122 * IPR004642\",\n", - " \"feature_label\": \"Cystathionine beta-synthase activity * Serine dehydratase, alpha subunit\",\n", - " \"bio_property\": \"amino acid metabolism * sulfur compound biosynthesis\",\n", - " \"env_property\": \"nutrient-rich * acidic conditions\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Fermented beverages often contain sulfur-containing amino acids, and enzymes involved in their metabolism are active in nutrient-rich environments with varying pH levels, including acidic conditions.\"\n", - " },\n", - " \"2\": {\n", - " \"feature_id\": \"GO:0042176 * IPR000938\",\n", - " \"feature_label\": \"Regulation of protein catabolic process * CAP Gly-rich domain\",\n", - " \"bio_property\": \"protein degradation * stress response\",\n", - " \"env_property\": \"dynamic conditions * varying pH\",\n", + " \"feature_id\": \"IPR007037 * GO:0018551\",\n", + " \"feature_label\": \"Siderophore-interacting protein, C-terminal domain * dissimilatory sulfite reductase activity\",\n", + " \"bio_property\": \"iron acquisition * sulfur metabolism\",\n", + " \"env_property\": \"marine * anoxic zones\",\n", " \"confidence\": \"medium\",\n", - " \"explanation\": \"The regulation of protein catabolic processes is crucial in environments with dynamic conditions such as those found during fermentation where there are fluctuations in pH and other stress factors.\"\n", - " },\n", - " \"3\": {\n", - " \"feature_id\": \"IPR004868 * GO:0031460\",\n", - " \"feature_label\": \"DNA-directed DNA polymerase, family B, mitochondria/virus * Glycine betaine transport\",\n", - " \"bio_property\": \"DNA replication * osmoprotection\",\n", - " \"env_property\": \"high temperature * high salinity\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"DNA-directed polymerase activities are important in high-temperature environments where specialized replication mechanisms are needed. Glycine betaine transport is crucial for osmoprotection in high-salinity conditions, often encountered together in fermentation setups.\"\n", + " \"explanation\": \"Sulfite reductase and siderophore-interacting proteins are crucial for iron and sulfur metabolism in anoxic zones often found in marine environments.\"\n", " },\n", " \"4\": {\n", - " \"feature_id\": \"IPR006541 * IPR019895\",\n", - " \"feature_label\": \"Bacteriocin-associated integral membrane protein * Putative bacteriocin export ABC transporter, lactococcin 972 group\",\n", - " \"bio_property\": \"bacteriocin production * antimicrobial activity\",\n", - " \"env_property\": \"competitive microbial community * nutrient-rich\",\n", + " \"feature_id\": \"IPR011802 * GO:0018551\",\n", + " \"feature_label\": \"Adenylylsulphate reductase, beta subunit * dissimilatory sulfite reductase activity\",\n", + " \"bio_property\": \"sulfur metabolism\",\n", + " \"env_property\": \"marine * anoxic zones\",\n", " \"confidence\": \"high\",\n", - " \"explanation\": \"Bacteriocins play a key role in microbial competition and self-preservation within nutrient-rich communities typical of fermented environments, helping dominant strains outcompete others.\"\n", + " \"explanation\": \"Both adenylylsulfate reductase and dissimilatory sulfite reductase are involved in sulfur metabolism, which is particularly important in anoxic marine zones.\"\n", " },\n", " \"5\": {\n", - " \"feature_id\": \"IPR004501 * IPR007165\",\n", - " \"feature_label\": \"Phosphotransferase system, EIIC component, type 3 * Mycobacterial 4 TMS phage holin, superfamily IV\",\n", - " \"bio_property\": \"sugar transport * phage attack resistance\",\n", - " \"env_property\": \"carbon-rich * high microbial density\",\n", - " \"confidence\": \"medium\",\n", - " \"explanation\": \"Phosphotransferase systems are involved in sugar uptake within carbon-rich environments. Holins provide resistance to phage attacks, which can be frequent in high-density microbial communities such as those in fermentation.\"\n", - " },\n", - " \"6\": {\n", - " \"feature_id\": \"IPR014242 * IPR024405\",\n", - " \"feature_label\": \"Spore cortex biosynthesis protein, YabQ * Prophage protein BhlA/UviB\",\n", - " \"bio_property\": \"sporulation * prophage immunity\",\n", - " \"env_property\": \"fluctuating nutrients * potential phage presence\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Sporulation is a survival strategy in fluctuating nutrient environments. Prophage immunity elements help protect against phage infections that could arise during fermentation disruptions.\"\n", - " }\n", - " }\n", - "}\n", - "\n", - "\n", - "This JSON output is structured to provide clear and concise relationships between observed metagenomic features and environmental properties in the context of the Engineered:Food production:Fermented beverages ecosystem. Each entry contains detailed explanations to justify the association.\n", - "[]\n", - "[{'ecosystem': 'Engineered:Solid waste:Composting', 'feature_id': 'GO:0004122 * IPR002723', 'feature_label': 'cystathionine beta-synthase activity * N(4)-bis(aminopropyl)spermidine synthase, C-terminal', 'bio_property': 'sulfur metabolism*polyamine biosynthesis', 'env_property': 'nutrient recycling*high organic matter', 'confidence': 'high', 'explanation': 'Cystathionine beta-synthase is involved in sulfur amino acid metabolism, critical for nutrient recycling in compost. Polyamines play roles in cellular growth and death, prevalent in high organic matter conditions.'}, {'ecosystem': 'Engineered:Solid waste:Composting', 'feature_id': 'GO:0016999 * IPR008557', 'feature_label': 'antibiotic metabolic process * Alkaline phosphatase PhoX', 'bio_property': 'antibiotic biosynthesis*phosphorus metabolism', 'env_property': 'antibiotic presence*fluctuating pH', 'confidence': 'high', 'explanation': 'The antibiotic metabolic process is important for microbial competition in composting environments. Alkaline phosphatase is crucial in phosphorus cycling, especially in environments with variable pH.'}, {'ecosystem': 'Engineered:Solid waste:Composting', 'feature_id': 'IPR014242 * IPR014931 * IPR014580', 'feature_label': 'Spore cortex biosynthesis protein, YabQ * Protein of unknown function DUF1805 * Uncharacterised conserved protein UCP033199', 'bio_property': 'spore formation*stress response proteins', 'env_property': 'high temperature*variable moisture levels', 'confidence': 'medium', 'explanation': 'Spore formation is a key survival strategy in composting environments due to the fluctuating and often extreme conditions such as high temperature and variable moisture levels.'}, {'ecosystem': 'Engineered:Solid waste:Composting', 'feature_id': 'IPR022343 * IPR022380', 'feature_label': 'GCR1-cAMP receptor * Glutamyl-Q tRNA(Asp) synthetase', 'bio_property': 'signal transduction*tRNA modification', 'env_property': 'variable substrate availability', 'confidence': 'high', 'explanation': 'Signal transduction mechanisms and tRNA modifications are essential in adapting to nutrient availability fluctuations typical in composting environments.'}, {'ecosystem': 'Engineered:Solid waste:Composting', 'feature_id': 'sk__Bacteria;k__;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides', 'feature_label': 'Bacteroides', 'bio_property': 'degradation of complex organic material', 'env_property': 'high organic material load', 'confidence': 'high', 'explanation': 'Bacteroides are well-known for their ability to degrade complex polysaccharides and proteins, which is essential in the composting process of solid waste with high organic content.'}]\n", - "[{'ecosystem': 'Engineered:Wastewater', 'feature_id': 'GO:0018551 * IPR007343', 'feature_label': 'dissimilatory sulfite reductase activity * zinc metallopeptidase putative', 'bio_property': 'sulfate reduction*cellular metal ion homeostasis', 'env_property': 'anaerobic*high metal ion content', 'confidence': 'high', 'explanation': 'Dissimilatory sulfite reductase is crucial for sulfate reduction in anaerobic environments. Zinc metallopeptidases often play a role in managing metal ion concentrations in cells.'}, {'ecosystem': 'Engineered:Wastewater', 'feature_id': 'GO:0008901 * IPR001360', 'feature_label': 'ferredoxin hydrogenase activity * Glycoside hydrolase family 1', 'bio_property': 'energy production*carbohydrate metabolism', 'env_property': 'nutrient-rich*presence of organic material', 'confidence': 'high', 'explanation': 'Ferredoxin hydrogenases are involved in energy production, while glycoside hydrolases assist in breaking down complex carbohydrates, both essential in nutrient-rich environments rich in organic material.'}, {'ecosystem': 'Engineered:Wastewater', 'feature_id': 'GO:0019068 * IPR005021', 'feature_label': 'virion assembly * Terminase large subunit-like', 'bio_property': 'viral replication*DNA packaging', 'env_property': 'microbial diverse*high microbial load', 'confidence': 'high', 'explanation': 'Virion assembly and the terminase large subunit are vital components in the life cycle of viruses, suggesting a significant presence of viral populations in a highly diverse microbial environment.'}, {'ecosystem': 'Engineered:Wastewater', 'feature_id': 'GO:0019512 * IPR006879', 'feature_label': 'lactose catabolic process via tagatose-6-phosphate * Carbohydrate deacetylase YdjC-like', 'bio_property': 'lactose metabolism*polysaccharide degradation', 'env_property': 'high organic carbon*diverse substrate availability', 'confidence': 'high', 'explanation': 'Lactose catabolism and carbohydrate deacetylation are crucial for breaking down complex sugars and polysaccharides, indicating a high availability of diverse organic substrates in the environment.'}, {'ecosystem': 'Engineered:Wastewater', 'feature_id': 'GO:0015858 * IPR014984', 'feature_label': 'nucleoside transport * HopJ type III effector protein', 'bio_property': 'nucleotide transport*host-pathogen interaction', 'env_property': 'high microbial competition*pathogen presence', 'confidence': 'medium', 'explanation': 'Nucleoside transport and type III effector proteins are associated with high microbial competition and interactions, typical in environments with pathogenic and resistant microbial strains.'}, {'ecosystem': 'Engineered:Wastewater', 'feature_id': 'IPR022458 * IPR035576', 'feature_label': 'Conjugative coupling factor TraG/TraD * Type VI secretion system TssC', 'bio_property': 'horizontal gene transfer*competitive advantage', 'env_property': 'high microbial diversity*presence of pathogenic bacteria', 'confidence': 'high', 'explanation': 'Conjugative coupling factors and Type VI secretion systems facilitate gene transfer and microbial warfare, indicating a highly diverse microbial ecosystem with competitive and pathogenic interactions.'}, {'ecosystem': 'Engineered:Wastewater', 'feature_id': 'GO:0080009 * IPR032191', 'feature_label': 'mRNA methylation * CCR4-NOT transcription complex subunit 1, CAF1-binding domain', 'bio_property': 'gene regulation*mRNA stability', 'env_property': 'high microbial activity*rapid environmental change', 'confidence': 'medium', 'explanation': 'mRNA methylation and CCR4-NOT complex involvement are crucial for gene regulation and adaptation, which are essential in dynamic environments with rapid changes.'}, {'ecosystem': 'Engineered:Wastewater', 'feature_id': 'IPR000494 * IPR021725', 'feature_label': 'Receptor L-domain * Pathogenicity locus', 'bio_property': 'signal transduction*virulence', 'env_property': 'pathogen-prevalent*high selective pressure', 'confidence': 'high', 'explanation': 'Receptor L-domain and pathogenicity loci are critical for signal transduction and virulence in bacterial pathogens, indicative of environments with high selective pressure and prevalent pathogens.'}]\n", - "[{'ecosystem': 'Engineered:Wastewater:Activated Sludge', 'feature_id': 'GO:0015444 * IPR010706', 'feature_label': 'P-type magnesium transporter activity * Fatty acid cis-trans isomerase', 'bio_property': 'magnesium transport*fatty acid isomerization', 'env_property': 'metal ion rich*nutrient dense', 'confidence': 'high', 'explanation': 'The activity of a magnesium transporter can be vital for microorganisms in environments rich in metal ions, while fatty acid isomerization is significant for adapting membrane fluidity in nutrient-dense conditions.'}, {'ecosystem': 'Engineered:Wastewater:Activated Sludge', 'feature_id': 'GO:0018551 * IPR004462', 'feature_label': 'dissimilatory sulfite reductase activity * Desulfoferrodoxin, N-terminal domain', 'bio_property': 'sulfur metabolism*iron-sulfur cluster binding', 'env_property': 'sulfurous*anaerobic', 'confidence': 'high', 'explanation': 'Dissimilatory sulfite reductase is crucial for sulfur reduction in sulfur-rich environments, and desulfoferrodoxin is involved in iron-sulfur metabolism, often occurring under anaerobic conditions.'}, {'ecosystem': 'Engineered:Wastewater:Activated Sludge', 'feature_id': 'GO:0008901 * IPR019235', 'feature_label': 'ferredoxin hydrogenase activity * Protein of unknown function DUF2178, transmembrane', 'bio_property': 'hydrogen metabolism*transmembrane transport', 'env_property': 'redox active*variable osmolarity', 'confidence': 'medium', 'explanation': 'Ferredoxin hydrogenases play a role in electron transfer and hydrogen metabolism, while the transmembrane protein might facilitate ion or molecule transport in redox-active and fluctuating osmolarity environments.'}, {'ecosystem': 'Engineered:Wastewater:Activated Sludge', 'feature_id': 'IPR001360 * IPR007117', 'feature_label': 'Glycoside hydrolase family 1 * Expansin, cellulose-binding-like domain', 'bio_property': 'carbohydrate degradation*plant cell wall modification', 'env_property': 'organic matter rich*structured', 'confidence': 'high', 'explanation': 'Glycoside hydrolases and expansins are involved in breaking down complex carbohydrates and modifying plant cell walls, respectively, indicating a role in environments abundant with organic matter and structured matrices.'}, {'ecosystem': 'Engineered:Wastewater:Activated Sludge', 'feature_id': 'GO:0019068 * IPR008016', 'feature_label': 'virion assembly * Portal protein Gp10', 'bio_property': 'viral replication*structural viral component', 'env_property': 'biologically diverse*microbial dense', 'confidence': 'medium', 'explanation': 'Virion assembly and portal proteins are essential for the formation of viral particles, reflecting a high diversity of biological entities and a dense microbial population susceptible to viral infection.'}, {'ecosystem': 'Engineered:Wastewater:Activated Sludge', 'feature_id': 'IPR035576 * IPR033762', 'feature_label': 'Type VI secretion system TssC * MCM OB domain', 'bio_property': 'protein secretion*DNA replication licensing', 'env_property': 'competitive*high cell density', 'confidence': 'high', 'explanation': 'The Type VI secretion system and MCM OB domain indicate mechanisms for competitive interactions and efficient DNA replication, essential in environments with high cellular density and competitive inter-microbial interactions.'}, {'ecosystem': 'Engineered:Wastewater:Activated Sludge', 'feature_id': 'GO:0006928 * IPR032830', 'feature_label': 'obsolete movement of cell or subcellular component * Helicase XPB/Ssl2, N-terminal domain', 'bio_property': 'DNA repair*cellular motility', 'env_property': 'stressful*fluctuating chemical conditions', 'confidence': 'medium', 'explanation': 'The obsolete movement of cellular components and helicase activity are pivotal for DNA repair and motility under stress conditions, which are typical of environments with fluctuating chemical characteristics.'}]\n", - "JSON decode error for result: Expecting value: line 1 column 1 (char 0)\n", - "Content that caused the error: Below is the requested JSON output structure, reflecting the relationships between microbial metagenomic features and environmental properties in the Engineered:Wastewater:Water and sludge ecosystem.\n", - "\n", - "\n", - "{\n", - " \"Engineered:Wastewater:Water and sludge\": {\n", - " \"1\": {\n", - " \"feature_id\": \"GO:0019512 * GO:0033920 * IPR010945\",\n", - " \"feature_label\": \"lactose catabolic process via tagatose-6-phosphate * 6-phospho-beta-galactosidase activity * Malate dehydrogenase, type 2\",\n", - " \"bio_property\": \"lactose metabolism * carbohydrate degradation * energy production\",\n", - " \"env_property\": \"high organic load * rich in nutrients\",\n", + " \"feature_id\": \"IPR008557 * IPR010036\",\n", + " \"feature_label\": \"Alkaline phosphatase PhoX * Magnesium-dependent phosphatase-1, eukaryotic/archaeal-type\",\n", + " \"bio_property\": \"phosphatase activity * nutrient cycling\",\n", + " \"env_property\": \"marine * phosphorous limitation\",\n", " \"confidence\": \"high\",\n", - " \"explanation\": \"The presence of lactose catabolic pathways and relevant enzymes indicates an adaption to environments rich in organic matter and nutrients typically found in wastewater.\"\n", - " },\n", - " \"2\": {\n", - " \"feature_id\": \"GO:0045151 * IPR011868\",\n", - " \"feature_label\": \"acetoin biosynthetic process * Molybdate ABC transporter, ATP-binding protein\",\n", - " \"bio_property\": \"secondary metabolite production * trace element transport\",\n", - " \"env_property\": \"variable redox conditions * metal-rich\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Acetoin production and molybdate transport are adaptive traits relevant to variable redox conditions and the presence of trace metals often found in wastewater environments.\"\n", - " },\n", - " \"3\": {\n", - " \"feature_id\": \"IPR017821 * IPR018470 * IPR017559\",\n", - " \"feature_label\": \"Succinate CoA transferase * Periplasmic metal-binding protein Tp34-type * Alkyl hydroperoxide reductase subunit C\",\n", - " \"bio_property\": \"energy production * metal binding and transport * oxidative stress response\",\n", - " \"env_property\": \"anaerobic zones * presence of heavy metals * oxidative stress conditions\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"These proteins are indicative of microbial metabolic versatility in adapting to anaerobic conditions, binding and managing heavy metals, and responding to oxidative stress in wastewater environments.\"\n", - " },\n", - " \"4\": {\n", - " \"feature_id\": \"GO:0019068 * IPR010517 * IPR010789\",\n", - " \"feature_label\": \"virion assembly * Phage tail tube protein, Siphoviridae * Terminase small subunit, Skunalikevirus-type\",\n", - " \"bio_property\": \"viral replication and assembly\",\n", - " \"env_property\": \"microbial infections * high microbial diversity\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"The presence of phage-related proteins and virion assembly processes suggest active viral replication, contributing to microbial control dynamics and diversity in the wastewater environment.\"\n", - " },\n", - " \"5\": {\n", - " \"feature_id\": \"GO:0004521 * GO:0017148\",\n", - " \"feature_label\": \"RNA endonuclease activity * negative regulation of translation\",\n", - " \"bio_property\": \"RNA processing * gene expression regulation\",\n", - " \"env_property\": \"stress conditions * nutrient competition\",\n", - " \"confidence\": \"medium\",\n", - " \"explanation\": \"Regulation of RNA and translation suggests adaptive mechanisms to environmental stress and nutrient competition, frequent conditions in wastewater ecosystems.\"\n", + " \"explanation\": \"Phosphatases like PhoX and magnesium-dependent phosphatase play roles in nutrient cycling in marine environments, which are often limited by phosphorus.\"\n", " },\n", " \"6\": {\n", - " \"feature_id\": \"IPR014984 * IPR011119\",\n", - " \"feature_label\": \"HopJ type III effector protein * Uncharacterised domain, helicase/relaxase, putative\",\n", - " \"bio_property\": \"host interaction * DNA modification\",\n", - " \"env_property\": \"high microbial interaction * presence of host organisms\",\n", + " \"feature_id\": \"IPR014931 * IPR017813\",\n", + " \"feature_label\": \"Protein of unknown function DUF1805 * Mycothiol acetyltransferase\",\n", + " \"bio_property\": \"detoxification * unknown\",\n", + " \"env_property\": \"marine * pollution\",\n", " \"confidence\": \"medium\",\n", - " \"explanation\": \"These proteins are typically associated with microbial interactions and possibly pathogenic relationships, suggesting a complex microbial ecosystem with host interactions in wastewater.\"\n", + " \"explanation\": \"The presence of mycothiol acetyltransferase suggests a role in detoxification which may be necessary in marine environments affected by pollution.\"\n", " },\n", " \"7\": {\n", - " \"feature_id\": \"- sk__Bacteria;k__;p__Verrucomicrobia;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia\",\n", - " \"feature_label\": \"Verrucomicrobiae; Akkermansia\",\n", - " \"bio_property\": \"gut symbiotic relationships * mucus degradation\",\n", - " \"env_property\": \"organic matter decomposition * anaerobic conditions\",\n", - " \"confidence\": \"medium\",\n", - " \"explanation\": \"The presence of Akkermansia, typically associated with mucus degradation, indicates their role in organic matter decomposition under anaerobic conditions prevalent in sludge.\"\n", - " }\n", - " }\n", - "}\n", - "\n", - "\n", - "This structured approach reflects the connections between the metagenomic features and the environmental properties of the specific engineered wastewater ecosystem. Each set of features highlights specific biological activities relevant to adapting to the varied and complex wastewater environment.\n", - "[]\n", - "[{'ecosystem': 'Environmental:Aquatic:Estuary', 'feature_id': 'IPR011802', 'feature_label': 'Adenylylsulphate reductase, beta subunit', 'bio_property': 'sulfate reduction pathway*energy metabolism', 'env_property': 'sulfate-rich*anaerobic conditions', 'confidence': 'high', 'explanation': 'Adenylylsulphate reductase is integral to the sulfate reduction pathway, which is crucial in sulfate-rich, anaerobic estuary environments.'}, {'ecosystem': 'Environmental:Aquatic:Estuary', 'feature_id': 'IPR011946', 'feature_label': 'Integrase, integron-type', 'bio_property': 'genetic recombination*horizontal gene transfer', 'env_property': 'high microbial density*variable environmental conditions', 'confidence': 'medium', 'explanation': 'Integron-type integrases facilitate genetic recombination and horizontal gene transfer, often observed in environments with high microbial interaction and variable conditions.'}, {'ecosystem': 'Environmental:Aquatic:Estuary', 'feature_id': 'IPR014984', 'feature_label': 'HopJ type III effector protein', 'bio_property': 'pathogenesis*host-pathogen interaction', 'env_property': 'biotic interactions*nutrient flux', 'confidence': 'medium', 'explanation': 'The HopJ type III effector protein is involved in bacterial pathogenesis, indicating an environment with significant biotic interactions and nutrient flux.'}, {'ecosystem': 'Environmental:Aquatic:Estuary', 'feature_id': 'GO:0046797', 'feature_label': 'viral procapsid maturation', 'bio_property': 'virus assembly*viral replication', 'env_property': 'high viral abundance*nutrient cycling', 'confidence': 'medium', 'explanation': 'Procapsid maturation is a pivotal step in viral replication, reflecting high viral activity and turnover within nutrient cycles in estuaries.'}, {'ecosystem': 'Environmental:Aquatic:Estuary', 'feature_id': 'IPR028282', 'feature_label': 'WASH complex subunit 7, central domain', 'bio_property': 'actin cytoskeleton organization*endosomal trafficking', 'env_property': 'dynamic sediment composition*pollutant presence', 'confidence': 'medium', 'explanation': 'WASH complex is involved in actin cytoskeleton remodeling and might relate to the dynamic sediment and pollutant interactions prevalent in estuarine environments.'}, {'ecosystem': 'Environmental:Aquatic:Estuary', 'feature_id': 'sk__Bacteria;k__;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Candidatus_Pelagibacter;s__Candidatus_Pelagibacter_ubique', 'feature_label': 'Pelagibacter ubique', 'bio_property': 'oligotrophy*marine microbial loop', 'env_property': 'nutrient-poor*oligotrophic conditions', 'confidence': 'high', 'explanation': 'Pelagibacter ubique is a model organism for oligotrophy, thriving in nutrient-poor, oligotrophic conditions often found in clear estuarine waters.'}]\n", - "[{'ecosystem': 'Environmental:Aquatic:Estuary:Sediment', 'feature_id': 'GO:0005471', 'feature_label': 'ATP:ADP antiporter activity', 'bio_property': 'cellular energy transport*metabolic regulation', 'env_property': 'dynamic environment*variable nutrient availability', 'confidence': 'high', 'explanation': 'ATP:ADP antiporters are crucial for maintaining energy homeostasis in environments with fluctuating nutrient levels.'}, {'ecosystem': 'Environmental:Aquatic:Estuary:Sediment', 'feature_id': 'IPR007343', 'feature_label': 'Uncharacterised protein family, zinc metallopeptidase putative', 'bio_property': 'proteolysis*metal ion binding', 'env_property': 'metal-rich sediments', 'confidence': 'medium', 'explanation': 'Zinc metallopeptidases participate in protein degradation and are typically found in metal-rich environments where metal ions serve as cofactors.'}, {'ecosystem': 'Environmental:Aquatic:Estuary:Sediment', 'feature_id': 'IPR010518', 'feature_label': 'Flagellar regulatory FleQ', 'bio_property': 'motility regulation*signal transduction', 'env_property': 'turbid water*variable oxygen levels', 'confidence': 'high', 'explanation': 'FleQ regulates flagellar synthesis, which is essential for motility in turbid, oxygen-variable estuary sediments.'}, {'ecosystem': 'Environmental:Aquatic:Estuary:Sediment', 'feature_id': 'IPR014984', 'feature_label': 'HopJ type III effector protein', 'bio_property': 'pathogenesis*host interaction', 'env_property': 'biotic interactions*high microbial diversity', 'confidence': 'medium', 'explanation': 'Type III effector proteins, such as HopJ, are commonly associated with microbial pathogenesis and interactions within highly diverse microbial communities.'}, {'ecosystem': 'Environmental:Aquatic:Estuary:Sediment', 'feature_id': 'IPR021249', 'feature_label': 'Protein of unknown function DUF2788', 'bio_property': 'unknown function', 'env_property': 'unknown', 'confidence': 'unknown', 'explanation': 'The protein function is currently unknown, preventing reliable association with specific environmental properties.'}]\n", - "[{'ecosystem': 'Environmental:Aquatic:Freshwater:Lake', 'feature_id': 'IPR026395', 'feature_label': 'CshA domain', 'bio_property': 'cold shock response*RNA chaperone activity', 'env_property': 'low temperature', 'confidence': 'high', 'explanation': 'The CshA domain is associated with cold shock proteins which help organisms survive and function under low-temperature conditions by preventing the formation of secondary RNA structures.'}, {'ecosystem': 'Environmental:Aquatic:Freshwater:Lake', 'feature_id': 'sk__Bacteria;k__;p__Actinobacteria;c__Actinobacteria;o__Micrococcales;f__Microbacteriaceae;g__Candidatus_Limnoluna', 'feature_label': 'Actinobacteria in genus Candidatus Limnoluna', 'bio_property': 'organic matter degradation*nutrient cycling', 'env_property': 'nutrient-rich', 'confidence': 'medium', 'explanation': 'Actinobacteria, particularly those in the genus Candidatus Limnoluna, are known for their role in breaking down complex organic molecules and cycling nutrients in freshwater ecosystems, indicating the presence of nutrient-rich conditions.'}]\n", - "JSON decode error for result: Expecting value: line 1 column 1 (char 0)\n", - "Content that caused the error: Sure, given the specified features and their descriptions, here is an analysis of their relationships with the environmental properties of the Environmental:Aquatic:Freshwater:Lotic:Sediment ecosystem.\n", - "\n", - "**Feature Analysis and Relationships:**\n", - "\n", - "1. **Feature Identifier(s):** IPR004813\n", - " - **Feature Description(s):** Oligopeptide transporter, OPT superfamily\n", - " - **Bio_property:** Nutrient uptake * Peptide transport\n", - " - **Env_property:** Nutrient cycling * Organic matter decomposition\n", - " - **Confidence Level:** High\n", - " - **Brief Explanation:** The oligopeptide transporter (OPT) superfamily plays a crucial role in the absorption and transport of small peptides, which are significant for nutrient cycling and the decomposition of organic matter in sediment environments. These functions are essential for sustaining the microbial community and overall ecosystem health.\n", - "\n", - "2. **Feature Identifier(s):** IPR012657\n", - " - **Feature Description(s):** 23S rRNA-intervening sequence protein\n", - " - **Bio_property:** Ribosome function * Protein synthesis\n", - " - **Env_property:** High microbial activity * Rich in microbial biomass\n", - " - **Confidence Level:** Medium\n", - " - **Brief Explanation:** The presence of 23S rRNA-intervening sequence proteins indicates active ribosomal function and protein synthesis, which are indicative of high microbial activity and biomass in sedimentary environments. This relationship suggests a rich and diverse microbial community that can adapt to various environmental conditions.\n", - "\n", - "3. **Feature Identifier(s):** IPR022380\n", - " - **Feature Description(s):** Glutamyl-Q tRNA(Asp) synthetase\n", - " - **Bio_property:** Protein translation fidelity * Specialized aminoacyl-tRNA synthesis\n", - " - **Env_property:** Low nutrient availability * Stress adaptation\n", - " - **Confidence Level:** High\n", - " - **Brief Explanation:** Glutamyl-Q tRNA(Asp) synthetase is crucial for maintaining protein translation fidelity under various stress conditions, frequently observed in environments with low nutrient availability. This feature reflects the ability of microbial communities to adapt to and thrive in challenging environments by ensuring accurate protein synthesis under stress.\n", - "\n", - "\n", - "{\n", - " \"Environmental:Aquatic:Freshwater:Lotic:Sediment\": {\n", - " \"1\": {\n", - " \"feature_id\": \"IPR004813\",\n", - " \"feature_label\": \"Oligopeptide transporter, OPT superfamily\",\n", - " \"bio_property\": \"Nutrient uptake * Peptide transport\",\n", - " \"env_property\": \"Nutrient cycling * Organic matter decomposition\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"The OPT superfamily plays a key role in nutrient uptake and peptide transport, crucial for nutrient cycling and organic matter decomposition in sediment.\"\n", - " },\n", - " \"2\": {\n", - " \"feature_id\": \"IPR012657\",\n", - " \"feature_label\": \"23S rRNA-intervening sequence protein\",\n", - " \"bio_property\": \"Ribosome function * Protein synthesis\",\n", - " \"env_property\": \"High microbial activity * Rich in microbial biomass\",\n", - " \"confidence\": \"medium\",\n", - " \"explanation\": \"The presence of 23S rRNA-intervening sequence proteins suggests high ribosomal function and protein synthesis, indicative of high microbial activity and biomass.\"\n", - " },\n", - " \"3\": {\n", - " \"feature_id\": \"IPR022380\",\n", - " \"feature_label\": \"Glutamyl-Q tRNA(Asp) synthetase\",\n", - " \"bio_property\": \"Protein translation fidelity * Specialized aminoacyl-tRNA synthesis\",\n", - " \"env_property\": \"Low nutrient availability * Stress adaptation\",\n", + " \"feature_id\": \"IPR011868 * sk__Bacteria;k__;p__Chloroflexi;c__Thermoflexia;o__Thermoflexales;f__Thermoflexaceae;g__Thermoflexus\",\n", + " \"feature_label\": \"Molybdate ABC transporter, ATP-binding protein * Chloroflexi (Thermoflexia)\",\n", + " \"bio_property\": \"heavy metal transport * thermophilic adaptation\",\n", + " \"env_property\": \"marine * hydrothermal vents\",\n", " \"confidence\": \"high\",\n", - " \"explanation\": \"Glutamyl-Q tRNA(Asp) synthetase is essential for maintaining protein translation fidelity, reflecting microbial adaptation to low nutrient availability and stress.\"\n", + " \"explanation\": \"Molybdate transporters and thermophilic Chloroflexi are often found in hydrothermal vents, which are rich in heavy metals and temperature variations.\"\n", " }\n", " }\n", "}\n", "\n", "\n", - "This JSON output provides an organized and detailed analysis of each feature, explaining the relationship between microbial metagenomic features and the environmental properties of the lotic sediment ecosystem, with high and medium confidence levels.\n", + "These results identify relationships between observed microscopic features and the environmental characteristics of marine ecosystems, supported by high or medium confidence level explanations based on known biological and environmental properties.\n", "[]\n", - "[{'ecosystem': 'Environmental:Aquatic:Lentic:Brackish', 'feature_id': 'IPR007210 * GO:0031460', 'feature_label': 'Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport', 'bio_property': 'osmoprotection*stress response', 'env_property': 'marine*high salinity', 'confidence': 'high', 'explanation': 'Glycine betaine is a known osmoprotectant in high osmolarity environments.'}, {'ecosystem': 'Environmental:Aquatic:Lentic:Brackish', 'feature_id': 'GO:0043093 * IPR011735', 'feature_label': 'FtsZ-dependent cytokinesis * WlaTC/HtrL glycosyltransferase', 'bio_property': 'cell division*cell wall synthesis', 'env_property': 'versatile nutrient sources*variable carbon availability', 'confidence': 'medium', 'explanation': 'WlaTC/HtrL glycosyltransferase is involved in cell wall synthesis, which is crucial for cell division especially in variable carbon availability conditions.'}, {'ecosystem': 'Environmental:Aquatic:Lentic:Brackish', 'feature_id': 'IPR009677 * IPR020484 * IPR021239 * IPR025123', 'feature_label': 'Protein of unknown function DUF1266 * Protein of unknown function DUF5503 * Protein of unknown function DUF2625 * Domain of unknown function DUF4049', 'bio_property': 'unknown*potentially regulatory or structural proteins', 'env_property': 'dynamic environmental conditions', 'confidence': 'medium', 'explanation': 'Domains of unknown function often indicate adaptive proteins, which can play a crucial role in responding to dynamic environmental conditions.'}, {'ecosystem': 'Environmental:Aquatic:Lentic:Brackish', 'feature_id': 'IPR028955 * IPR031834', 'feature_label': 'Immunity protein 57 * Antitoxin RnlB/LsoB', 'bio_property': 'bacterial immunity*toxin neutralization', 'env_property': 'microbial competition*high bacterial diversity', 'confidence': 'high', 'explanation': 'Immunity proteins and antitoxins are critical for survival in environments with high microbial competition, preventing self-toxicity and neutralizing toxins from other bacteria.'}, {'ecosystem': 'Environmental:Aquatic:Lentic:Brackish', 'feature_id': 'IPR000036', 'feature_label': 'Peptidase A26, omptin', 'bio_property': 'protein degradation*virulence', 'env_property': 'high bacterial load', 'confidence': 'high', 'explanation': 'Omptins are known for their role in protein degradation and virulence, which can be advantageous in environments with high bacterial loads and competition.'}, {'ecosystem': 'Environmental:Aquatic:Lentic:Brackish', 'feature_id': 'IPR005126', 'feature_label': 'NapC/NirT cytochrome c, N-terminal', 'bio_property': 'electron transport*nitrate reduction', 'env_property': 'variable redox conditions*rich organic matter', 'confidence': 'high', 'explanation': 'NapC/NirT cytochrome c are involved in electron transport and nitrate reduction, which are essential processes in environments with variable redox conditions and rich organic matter.'}, {'ecosystem': 'Environmental:Aquatic:Lentic:Brackish', 'feature_id': 'IPR023870', 'feature_label': 'Poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA', 'bio_property': 'biofilm formation*cell adhesion', 'env_property': 'sediment stability*nutrient trapping', 'confidence': 'high', 'explanation': 'Biofilm formation and cell adhesion facilitated by PgaA can contribute to sediment stability and efficient nutrient trapping in brackish environments.'}]\n", - "[{'ecosystem': 'Environmental:Aquatic:Marine', 'feature_id': 'GO:0031460 * IPR007210', 'feature_label': 'glycine betaine transport * Glycine betaine/proline betaine transport system ATP-binding protein ProV-like', 'bio_property': 'osmoprotection*stress response', 'env_property': 'marine*high salinity', 'confidence': 'high', 'explanation': 'Glycine betaine is a known osmoprotectant used by organisms to maintain osmotic balance in high salinity environments typically encountered in marine settings.'}, {'ecosystem': 'Environmental:Aquatic:Marine', 'feature_id': 'GO:0004037 * GO:0008743 * IPR010036', 'feature_label': 'allantoicase activity * L-threonine 3-dehydrogenase activity * Magnesium-dependent phosphatase-1, eukaryotic/archaeal type', 'bio_property': 'nitrogen metabolism*amino acid metabolism', 'env_property': 'marine*nitrogen cycling', 'confidence': 'high', 'explanation': 'Allantoicase and L-threonine 3-dehydrogenase are enzymes involved in nitrogen metabolism and amino acid pathways which are crucial for nutrient cycling in marine environments. The magnesium-dependent phosphatase-1 is also involved in these metabolic processes.'}, {'ecosystem': 'Environmental:Aquatic:Marine', 'feature_id': 'GO:0018551 * IPR011802 * IPR007037', 'feature_label': 'dissimilatory sulfite reductase activity * Adenylylsulphate reductase, beta subunit * Siderophore-interacting protein, C-terminal domain', 'bio_property': 'sulfur metabolism*iron acquisition', 'env_property': 'marine*sulfate-rich*iron-limited', 'confidence': 'high', 'explanation': 'Dissimilatory sulfite reductase and adenylylsulphate reductase are key enzymes in sulfur metabolism, transforming sulfate to sulfide in sulfate-rich marine environments. Siderophore-interacting proteins are involved in iron acquisition, critical in iron-limited marine settings.'}, {'ecosystem': 'Environmental:Aquatic:Marine', 'feature_id': 'IPR016300 * IPR011868', 'feature_label': 'Arsenical pump ATPase, ArsA/GET3 * Molybdate ABC transporter, ATP-binding protein', 'bio_property': 'heavy metal resistance*detoxification', 'env_property': 'marine*heavy metal presence*pollutant presence', 'confidence': 'high', 'explanation': 'The arsenical pump ATPase and molybdate ABC transporter are linked to heavy metal resistance and detoxification, processes essential in marine ecosystems where pollutants and heavy metals are often present.'}, {'ecosystem': 'Environmental:Aquatic:Marine', 'feature_id': 'GO:0004638 * IPR006322', 'feature_label': 'phosphoribosylaminoimidazole carboxylase activity * Glutathione reductase, eukaryote/bacterial', 'bio_property': 'purine biosynthesis*oxidative stress response', 'env_property': 'marine*oxidative environments', 'confidence': 'medium', 'explanation': 'Phosphoribosylaminoimidazole carboxylase is part of purine biosynthesis, which is fundamental for cellular functions. Glutathione reductase plays a crucial role in maintaining redox balance, which is vital in marine environments with varying oxidative stresses.'}]\n", "JSON decode error for result: Expecting value: line 1 column 1 (char 0)\n", - "Content that caused the error: Here is the JSON output structured to include detailed and reliable information about the relationships between the observed features and the environmental properties of the Environmental:Aquatic:Marine:Hydrothermal vents ecosystem.\n", + "Content that caused the error: Here is the JSON output structure based on the observed features in the Environmental:Aquatic:Marine:Hydrothermal vents ecosystem.\n", "\n", "\n", "{\n", @@ -6998,675 +6715,378 @@ " \"1\": {\n", " \"feature_id\": \"GO:0018551\",\n", " \"feature_label\": \"dissimilatory sulfite reductase activity\",\n", - " \"bio_property\": \"sulfur metabolism * energy acquisition\",\n", - " \"env_property\": \"high temperature * high pressure * high sulfur concentration * reduced oxygen levels\",\n", + " \"bio_property\": \"sulfur metabolism\",\n", + " \"env_property\": \"high sulfur content\",\n", " \"confidence\": \"high\",\n", - " \"explanation\": \"Dissimilatory sulfite reductase activity is critical for sulfur metabolizing organisms found in sulfur-rich hydrothermal vent environments.\"\n", + " \"explanation\": \"Dissimilatory sulfite reductase is an enzyme involved in the reduction of sulfite to sulfide, which is crucial in environments with high sulfur content such as hydrothermal vents.\"\n", " },\n", " \"2\": {\n", " \"feature_id\": \"IPR002723\",\n", " \"feature_label\": \"N(4)-bis(aminopropyl)spermidine synthase, C-terminal\",\n", - " \"bio_property\": \"polyamine synthesis * stress response\",\n", - " \"env_property\": \"extreme conditions * variable temperature * nutrient variability\",\n", + " \"bio_property\": \"polyamine biosynthesis\",\n", + " \"env_property\": \"extreme conditions\",\n", " \"confidence\": \"medium\",\n", - " \"explanation\": \"Polyamines like spermidine contribute to cellular stability and stress resistance, essential in fluctuating and extreme hydrothermal vent environments.\"\n", + " \"explanation\": \"Polyamines help stabilize DNA and proteins under extreme conditions, an adaptation seen in organisms living in harsh environments like hydrothermal vents.\"\n", " },\n", " \"3\": {\n", " \"feature_id\": \"IPR007445\",\n", " \"feature_label\": \"Type IV pilus inner membrane component PilO\",\n", - " \"bio_property\": \"motility * adhesion * biofilm formation\",\n", - " \"env_property\": \"high pressure * variable substrate * thermal gradients\",\n", + " \"bio_property\": \"surface attachment, motility\",\n", + " \"env_property\": \"high temperature, high pressure\",\n", " \"confidence\": \"high\",\n", - " \"explanation\": \"Type IV pili are involved in adherence to surfaces and motility, which are essential for colonization and survival in the diverse and variable substrates of hydrothermal vents.\"\n", + " \"explanation\": \"Type IV pili are involved in surface attachment and motility which are essential for microbial colonization in the harsh conditions of hydrothermal vents characterized by high temperatures and pressures.\"\n", " },\n", " \"4\": {\n", " \"feature_id\": \"sk__Bacteria;k__;p__Aquificae;c__Aquificae;o__Desulfurobacteriales;f__Desulfurobacteriaceae;g__Desulfurobacterium\",\n", - " \"feature_label\": \"Desulfurobacterium genus\",\n", - " \"bio_property\": \"thermophily * sulfur reduction * chemolithoautotrophy\",\n", - " \"env_property\": \"high temperature * high sulfur concentration * reduced oxygen levels\",\n", + " \"feature_label\": \"Desulfurobacterium (Bacteria; Aquificae; Desulfurobacteriales)\",\n", + " \"bio_property\": \"sulfur reduction\",\n", + " \"env_property\": \"anaerobic, high sulfur\",\n", " \"confidence\": \"high\",\n", - " \"explanation\": \"Members of the Desulfurobacterium genus thrive in high-temperature environments and utilize sulfur compounds as electron acceptors, common in hydrothermal vents.\"\n", + " \"explanation\": \"Desulfurobacterium is known for its sulfur-reducing capabilities, making it well-suited for anaerobic environments rich in sulfur, such as hydrothermal vents.\"\n", " },\n", " \"5\": {\n", " \"feature_id\": \"sk__Eukaryota;k__Metazoa;p__Annelida;c__Polychaeta;o__Terebellida\",\n", - " \"feature_label\": \"Terebellida order\",\n", - " \"bio_property\": \"filter feeding * burrowing * symbiotic relationships\",\n", - " \"env_property\": \"particulate matter availability * substrate variability * chemical gradients\",\n", + " \"feature_label\": \"Polychaeta (e.g., Annelida; Polychaeta; Terebellida)\",\n", + " \"bio_property\": \"adaptation to hypoxic conditions\",\n", + " \"env_property\": \"hypoxic, high pressure\",\n", " \"confidence\": \"medium\",\n", - " \"explanation\": \"Polychaetes, particularly those in the Terebellida order, are adapted to the deposit of particulate matter and establish symbiotic relationships with microorganisms in hydrothermal vent environments.\"\n", + " \"explanation\": \"Members of Polychaeta, such as Terebellida, are adapted to hypoxic conditions, which are typical of deep-sea hydrothermal vent ecosystems.\"\n", " }\n", " }\n", "}\n", "\n", "\n", - "### Relationships Explained\n", + "### Explanation:\n", + "- **GO:0018551 - dissimilatory sulfite reductase activity**: Relates to sulfur metabolism in high sulfur content environments, typical of hydrothermal vents.\n", + " \n", + "- **IPR002723 - N(4)-bis(aminopropyl)spermidine synthase, C-terminal**: Associated with polyamine biosynthesis which stabilizes cells under extreme environmental conditions.\n", + " \n", + "- **IPR007445 - Type IV pilus inner membrane component PilO**: Facilitates microbial surface attachment and motility in high-temperature and high-pressure environments of hydrothermal vents.\n", + " \n", + "- **sk__Bacteria;k__;p__Aquificae;c__Aquificae;o__Desulfurobacteriales;f__Desulfurobacteriaceae;g__Desulfurobacterium**: Desulfurising bacteria that thrive in anaerobic, sulfur-rich environments like hydrothermal vents.\n", + " \n", + "- **sk__Eukaryota;k__Metazoa;p__Annelida;c__Polychaeta;o__Terebellida**: Annelida adapted to hypoxic and high-pressure conditions, as found in hydrothermal vent ecosystems.\n", "\n", - "**Dissimilatory sulfite reductase activity (GO:0018551):**\n", - "- **Biological Properties:** Sulfur metabolism and energy acquisition.\n", - "- **Environmental Properties:** High temperature, high pressure, high sulfur concentration, and reduced oxygen levels.\n", - "- **Explanation:** Hydrothermal vents are rich in sulfur compounds. Organisms leveraging dissimilatory sulfite reductase activity can reduce sulfur compounds to derive energy, helping them thrive in the vent ecosystem.\n", - "\n", - "**N(4)-bis(aminopropyl)spermidine synthase, C-terminal (IPR002723):**\n", - "- **Biological Properties:** Polyamine synthesis, stress response.\n", - "- **Environmental Properties:** Extreme conditions, variable temperature, nutrient variability.\n", - "- **Explanation:** Hydrothermal vent ecosystems experience extreme and fluctuating conditions. Polyamines like spermidine stabilize cellular structures and are involved in stress responses, aiding microbial survival.\n", - "\n", - "**Type IV pilus inner membrane component PilO (IPR007445):**\n", - "- **Biological Properties:** Motility, adhesion, biofilm formation.\n", - "- **Environmental Properties:** High pressure, variable substrate, thermal gradients.\n", - "- **Explanation:** Type IV pili are crucial for bacterial motility and adhesion, facilitating colonization and biofilm formation on diverse surfaces in high-pressure, thermally varied hydrothermal vent environments.\n", - "\n", - "**Desulfurobacterium genus (sk__Bacteria;k__;p__Aquificae;c__Aquificae;o__Desulfurobacteriales;f__Desulfurobacteriaceae;g__Desulfurobacterium):**\n", - "- **Biological Properties:** Thermophily, sulfur reduction, chemolithoautotrophy.\n", - "- **Environmental Properties:** High temperature, high sulfur concentration, reduced oxygen levels.\n", - "- **Explanation:** Desulfurobacterium species are adapted to high-temperature and sulfur-rich environments of hydrothermal vents, utilizing sulfur compounds for energy in oxygen-poor conditions.\n", - "\n", - "**Terebellida order (sk__Eukaryota;k__Metazoa;p__Annelida;c__Polychaeta;o__Terebellida):**\n", - "- **Biological Properties:** Filter feeding, burrowing, symbiotic relationships.\n", - "- **Environmental Properties:** Particulate matter availability, substrate variability, chemical gradients.\n", - "- **Explanation:** Polychaetes of the Terebellida order utilize available particulate matter for nutrition and have adapted to the varied substrates and chemical environments found in hydrothermal vents. They may also engage in symbiotic relationships with vent microorganisms.\n", + "This comprehensive analysis uses identifiers and contextual knowledge to explain the interplay between microbial and environmental properties, ensuring reliable inferences.\n", "[]\n", - "[{'ecosystem': 'Environmental:Aquatic:Marine:Intertidal zone:Coral reef', 'feature_id': 'GO:0004114 * IPR001320', 'feature_label': \"3',5'-cyclic-nucleotide phosphodiesterase activity * Ionotropic glutamate receptor, C-terminal\", 'bio_property': 'signal transduction*ion transport', 'env_property': 'variable light*varying nutrient availability', 'confidence': 'high', 'explanation': 'Signal transduction and ion transport are critical for organisms in environments with fluctuating light and nutrient conditions, common in coral reefs.'}, {'ecosystem': 'Environmental:Aquatic:Marine:Intertidal zone:Coral reef', 'feature_id': 'IPR000263 * IPR003514', 'feature_label': 'Geminivirus AR1/BR1 coat protein * Microviridae F protein', 'bio_property': 'viral replication*host-pathogen interactions', 'env_property': 'high biodiversity*varying pathogen load', 'confidence': 'medium', 'explanation': 'The presence of viral proteins suggests a high level of viral-host interactions, which are influenced by the high biodiversity and pathogen load in coral reefs.'}, {'ecosystem': 'Environmental:Aquatic:Marine:Intertidal zone:Coral reef', 'feature_id': 'IPR033762 * sk__Eukaryota;k__;p__;c__Dinophyceae;o__Suessiales;f__Symbiodiniaceae;g__Symbiodinium', 'feature_label': 'MCM OB domain * Dinoflagellates (Symbiodinium)', 'bio_property': 'DNA replication*symbiosis', 'env_property': 'high solar radiation*variable nutrient levels', 'confidence': 'high', 'explanation': 'Dinoflagellates like Symbiodinium are symbionts in coral reefs, contributing to their energy needs through photosynthesis. DNA replication is crucial for their rapid growth in response to high solar radiation.'}]\n", - "JSON decode error for result: Expecting value: line 1 column 1 (char 0)\n", - "Content that caused the error: Sure, let's organize and summarize the observed features and infer their relationships with the environmental properties of the specific ecosystem. Below is a JSON structure containing several examples of features and their relationships to the Environmental:Aquatic:Marine:Intertidal zone:Estuary ecosystem:\n", - "\n", - "\n", - "{\n", - " \"Environmental:Aquatic:Marine:Intertidal zone:Estuary\": {\n", + "JSON decode error for result: Extra data: line 31 column 1 (char 2220)\n", + "Content that caused the error: {\n", + " \"Environmental:Aquatic:Marine:Intertidal zone:Coral reef\": {\n", " \"1\": {\n", - " \"feature_id\": \"IPR004763 * IPR021552\",\n", - " \"feature_label\": \"Cation efflux system CzcA/CusA/SilA/NccA/HelA/CnrA * Putative, 10TM heavy-metal exporter\",\n", - " \"bio_property\": \"metal ion transport * detoxification\",\n", - " \"env_property\": \"high metal concentrations * pollution\",\n", + " \"feature_id\": \"GO:0004114 * IPR000263\",\n", + " \"feature_label\": \"3',5'-cyclic-nucleotide phosphodiesterase activity * Geminivirus AR1/BR1 coat protein\",\n", + " \"bio_property\": \"signal transduction * viral infection\",\n", + " \"env_property\": \"high nutrient cycling * presence of viral pathogens\",\n", " \"confidence\": \"high\",\n", - " \"explanation\": \"These features are related to the transport and removal of heavy metals, suggesting an adaptation to environments with high metal concentrations and possible pollution.\"\n", + " \"explanation\": \"3',5'-cyclic-nucleotide phosphodiesterase activity is involved in breaking down cAMP which is crucial in signal transduction and nutrient cycling. Geminivirus AR1/BR1 coat proteins indicate the presence of viruses, which can infect both algae and corals, affecting the overall health of the reef ecosystem.\"\n", " },\n", " \"2\": {\n", - " \"feature_id\": \"IPR017559\",\n", - " \"feature_label\": \"Alkyl hydroperoxide reductase subunit C\",\n", - " \"bio_property\": \"oxidative stress response * detoxification\",\n", - " \"env_property\": \"high oxygen levels * oxidative stress\",\n", + " \"feature_id\": \"IPR001320 * IPR033762\",\n", + " \"feature_label\": \"Ionotropic glutamate receptor, C-terminal * MCM OB domain\",\n", + " \"bio_property\": \"neuronal signaling * DNA replication\",\n", + " \"env_property\": \"complex habitat structure * high biodiversity\",\n", " \"confidence\": \"high\",\n", - " \"explanation\": \"Alkyl hydroperoxide reductase is involved in the reduction of peroxides, indicating an adaptation to environments with oxidative stress.\"\n", + " \"explanation\": \"Ionotropic glutamate receptors are implicated in neuronal signaling, crucial in higher organisms' interaction within the habitat. MCM OB domain is found in proteins involved in DNA replication, indicating high cellular activity which correlates with the complex and biodiverse nature of coral reefs.\"\n", " },\n", " \"3\": {\n", - " \"feature_id\": \"GO:0046797\",\n", - " \"feature_label\": \"viral procapsid maturation\",\n", - " \"bio_property\": \"viral infection * capsid assembly\",\n", - " \"env_property\": \"presence of viral pathogens * microbial interactions\",\n", - " \"confidence\": \"medium\",\n", - " \"explanation\": \"The presence of viral procapsid maturation involves viral infection processes, suggesting an environment with active viral-microbial interactions.\"\n", - " },\n", - " \"4\": {\n", - " \"feature_id\": \"IPR001360\",\n", - " \"feature_label\": \"Glycoside hydrolase family 1\",\n", - " \"bio_property\": \"carbohydrate metabolism * degradation of polysaccharides\",\n", - " \"env_property\": \"high organic matter * nutrient cycling\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Glycoside hydrolase enzymes break down complex sugars, indicating the presence of organic matter and active nutrient cycling within the ecosystem.\"\n", - " },\n", - " \"5\": {\n", - " \"feature_id\": \"sk__Bacteria;k__;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Candidatus_Pelagibacter;s__Candidatus_Pelagibacter_ubique\",\n", - " \"feature_label\": \"Candidatus Pelagibacter ubique\",\n", - " \"bio_property\": \"photoheterotrophy * organic carbon utilization\",\n", - " \"env_property\": \"nutrient-poor * stable marine environment\",\n", + " \"feature_id\": \"IPR003514 * sk__Eukaryota;k__;p__;c__Dinophyceae;o__Suessiales;f__Symbiodiniaceae;g__Symbiodinium\",\n", + " \"feature_label\": \"Microviridae F protein * Symbiodinium genus\",\n", + " \"bio_property\": \"viral assembly * symbiosis\",\n", + " \"env_property\": \"presence of viruses * mutualistic relationships * high sunlight exposure\",\n", " \"confidence\": \"high\",\n", - " \"explanation\": \"Candidatus Pelagibacter ubique is known for their ability to utilize dissolved organic carbon in nutrient-poor marine environments, indicative of specific stable estuarine conditions.\"\n", - " },\n", - " \"6\": {\n", - " \"feature_id\": \"IPR017813\",\n", - " \"feature_label\": \"Mycothiol acetyltransferase\",\n", - " \"bio_property\": \"mycothiol biosynthesis * redox regulation\",\n", - " \"env_property\": \"variable nutrient conditions * fluctuating redox states\",\n", - " \"confidence\": \"medium\",\n", - " \"explanation\": \"Presence of mycothiol biosynthesis suggests adaptation to varying nutrient and redox conditions in the estuarine ecosystem.\"\n", + " \"explanation\": \"Microviridae F protein is a critical component of viral assembly, suggesting the presence of viruses in coral reefs. Symbiodinium (a genus of dinoflagellates) is involved in mutualistic relationships with coral, essential for nutrient exchange and high productivity in sunlight-rich environments.\"\n", " }\n", " }\n", "}\n", "\n", "\n", - "**Key Points:**\n", + "### Explanation:\n", + "1. **Feature: GO:0004114 (3',5'-cyclic-nucleotide phosphodiesterase activity) and IPR000263 (Geminivirus AR1/BR1 coat protein)**\n", + " - **Bio_property**: The involvement of 3',5'-cyclic-nucleotide phosphodiesterase in signal transduction highlights nutrient cycling processes. The Geminivirus AR1/BR1 coat protein indicates viral infection pathways.\n", + " - **Env_property**: The Coral reefs are high in nutrient cycling due to constant balance between organisms. The presence of viral pathogens often impacts the health and balance of the ecosystem.\n", + " - **Explanation**: These features highlight the dynamic nutrient cycles and the impact of viral presence on coral reef ecosystems.\n", + "\n", + "2. **Feature: IPR001320 (Ionotropic glutamate receptor, C-terminal) and IPR033762 (MCM OB domain)**\n", + " - **Bio_property**: Ionotropic glutamate receptors are essential for neuronal signaling, an indicator of complex organismal interactions. MCM OB domain's role in DNA replication suggests high cellular proliferation.\n", + " - **Env_property**: Coral reefs are known for their complex habitat structure and high biodiversity.\n", + " - **Explanation**: These features represent the intricate ecological interactions and cellular activities that define coral reef environments.\n", "\n", - "1. **Metal ion transport and detoxification**: Presence of heavy metal transport systems is highly correlated with environments featuring high metal concentrations.\n", - "2. **Oxidative stress response**: Enzymes involved in reducing oxidative stress indicate adaptation to areas with high oxygen levels.\n", - "3. **Viral processes**: Activities related to viral capsid formation suggest environmental interactions involving viruses.\n", - "4. **Carbohydrate metabolism**: Glycoside hydrolases point to a high organic matter content and active nutrient cycling within the ecosystem.\n", - "5. **Specific microbial taxa**: Special adaptations like those seen in \"Candidatus Pelagibacter ubique\" include utilization of organic carbon in nutrient-poor conditions.\n", - "6. **Redox regulation**: Enzymes like mycothiol acetyltransferase indicate adaptation to fluctuating redox conditions.\n", + "3. **Feature: IPR003514 (Microviridae F protein) and sk__Eukaryota;k__;p__;c__Dinophyceae;o__Suessiales;f__Symbiodiniaceae;g__Symbiodinium**\n", + " - **Bio_property**: The Microviridae F protein indicates viral assembly processes. Symbiodinium genus suggests symbiosis, critical for reef health.\n", + " - **Env_property**: The presence of viruses, mutualistic symbiotic relationships, and high levels of sunlight exposure are characteristic of coral reef environments.\n", + " - **Explanation**: These features indicate the presence of viruses and essential symbiotic relationships that contribute to the productivity and resilience of coral reefs.\n", "\n", - "Each of these inferences serves to illuminate how specific molecular and biological functions of microbes are directly influenced by their environmental properties in the described estuarine ecosystem.\n", + "By examining these relationships, we gain a more comprehensive understanding of the interplay between microbial features and environmental properties in coral reef ecosystems.\n", "[]\n", + "[{'ecosystem': 'Environmental:Aquatic:Marine:Intertidal zone:Estuary', 'feature_id': 'GO:0046797 * IPR017559', 'feature_label': 'Viral procapsid maturation * Alkyl hydroperoxide reductase subunit C', 'bio_property': 'viral lifecycle*oxidative stress response', 'env_property': 'variable salinity*high UV exposure', 'confidence': 'high', 'explanation': 'Viral procapsid maturation is essential in viral lifecycles occurring in estuaries, which often have fluctuating salinity. Alkyl hydroperoxide reductase is involved in reducing oxidative stress, an important response to high UV exposure typical of intertidal zones.'}, {'ecosystem': 'Environmental:Aquatic:Marine:Intertidal zone:Estuary', 'feature_id': 'IPR001360 * IPR004763 * IPR017813', 'feature_label': 'Glycoside hydrolase family 1 * Cation efflux system CzcA/CusA/SilA/NccA/HelA/CnrA * Mycothiol acetyltransferase', 'bio_property': 'carbohydrate metabolism*heavy metal resistance*mycothiol biosynthesis', 'env_property': 'organic matter enrichment*heavy metal contamination', 'confidence': 'high', 'explanation': 'Glycoside hydrolases participate in the breakdown of complex carbohydrates, prevalent in estuaries due to organic matter enrichment. The cation efflux system is crucial for heavy metal resistance, often necessary in estuaries with varying levels of pollutant contamination. Mycothiol biosynthesis is another adaptive response to oxidative and chemically stressful conditions.'}, {'ecosystem': 'Environmental:Aquatic:Marine:Intertidal zone:Estuary', 'feature_id': 'IPR002723 * IPR017813', 'feature_label': 'N(4)-bis(aminopropyl)spermidine synthase, C-terminal * Mycothiol acetyltransferase', 'bio_property': 'polyamine biosynthesis*mycothiol biosynthesis', 'env_property': 'high bacterial activity', 'confidence': 'medium', 'explanation': 'Both polyamine biosynthesis and mycothiol biosynthesis are indicative of high microbial activity and stress adaptation, common in nutrient-rich and bacteria-dense environments like estuarine intertidal zones.'}, {'ecosystem': 'Environmental:Aquatic:Marine:Intertidal zone:Estuary', 'feature_id': 'IPR014580 * IPR014931', 'feature_label': 'Uncharacterised conserved protein UCP033199 * Protein of unknown function DUF1805', 'bio_property': 'unknown specific function but likely involved in stress response or general metabolic activity', 'env_property': 'varied environmental conditions', 'confidence': 'medium', 'explanation': 'The presence of uncharacterized proteins often correlates with organisms adapted to varied and fluctuating conditions, such as those in estuarine environments.'}, {'ecosystem': 'Environmental:Aquatic:Marine:Intertidal zone:Estuary', 'feature_id': 'sk__Bacteria;k__;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Candidatus_Pelagibacter;s__Candidatus_Pelagibacter_ubique * IPR026395', 'feature_label': 'Candidatus Pelagibacter ubique * CshA domain', 'bio_property': 'high competitive fitness*cold-shock adaptation', 'env_property': 'seasonal temperature fluctuations', 'confidence': 'high', 'explanation': 'Candidatus Pelagibacter ubique is known for its competitive fitness in nutrient-limited environments, aligned with the dynamic nutrient deposition found in estuaries. The CshA domain is associated with cold-shock adaptation, relevant to the temperature variability in intertidal zones.'}]\n", + "[{'ecosystem': 'Environmental:Aquatic:Marine:Oceanic', 'feature_id': 'GO:0031460 * IPR007210', 'feature_label': 'glycine betaine transport * Glycine betaine/proline betaine transport system ATP-binding protein ProV-like', 'bio_property': 'osmoprotection*stress response', 'env_property': 'marine*high salinity', 'confidence': 'high', 'explanation': 'Glycine betaine is a known osmoprotectant that helps microorganisms survive in high osmolarity environments such as marine ecosystems.'}, {'ecosystem': 'Environmental:Aquatic:Marine:Oceanic', 'feature_id': 'IPR001208 * IPR032830', 'feature_label': 'MCM domain * Helicase XPB/Ssl2, N-terminal domain', 'bio_property': 'DNA replication*DNA repair', 'env_property': 'marine*high UV exposure', 'confidence': 'high', 'explanation': 'Marine environments often have high UV exposure, which can damage DNA. MCM domains and helicase XPB/Ssl2 are involved in DNA repair and replication mechanisms that would be essential in such conditions.'}, {'ecosystem': 'Environmental:Aquatic:Marine:Oceanic', 'feature_id': 'IPR010518 * IPR001320', 'feature_label': 'Flagellar regulatory FleQ * Ionotropic glutamate receptor, C-terminal', 'bio_property': 'motility*signal transduction', 'env_property': 'marine*nutrient gradient', 'confidence': 'medium', 'explanation': 'Motility and chemotaxis signal transduction are vital for navigating nutrient gradients in marine environments. Flagellar regulatory proteins and ionotropic receptors play crucial roles in these processes.'}, {'ecosystem': 'Environmental:Aquatic:Marine:Oceanic', 'feature_id': 'IPR014984 * IPR011946', 'feature_label': 'HopJ type III effector protein * Integrase, integron-type', 'bio_property': 'pathogenicity*horizontal gene transfer', 'env_property': 'marine*microbial interaction', 'confidence': 'medium', 'explanation': 'Marine ecosystems often involve complex microbial interactions. Pathogenicity-related proteins and integrases facilitate these interactions via horizontal gene transfer, enhancing adaptive capabilities.'}, {'ecosystem': 'Environmental:Aquatic:Marine:Oceanic', 'feature_id': 'IPR028282 * sk__Bacteria;k__;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Candidatus_Pelagibacter;s__Candidatus_Pelagibacter_ubique', 'feature_label': 'WASH complex subunit 7, central domain * Candidatus Pelagibacter ubique', 'bio_property': 'actin cytoskeleton organization*oligotrophy', 'env_property': 'marine*nutrient poor', 'confidence': 'high', 'explanation': 'Candidatus Pelagibacter ubique is known for its oligotrophic lifestyle, thriving in nutrient-poor conditions typical of many marine environments. The WASH complex involvement in actin cytoskeleton organization aids in cellular maintenance and adaptation in such nutrient-limited environments.'}]\n", + "[{'ecosystem': 'Environmental:Aquatic:Marine:Sediment', 'feature_id': 'GO:0046797', 'feature_label': 'viral procapsid maturation', 'bio_property': 'viral replication*capsid formation', 'env_property': 'sediment*viral prevalence*nutrient cycling', 'confidence': 'high', 'explanation': 'The presence of genes involved in viral procapsid maturation in marine sediment ecosystems suggests significant viral activity. Viruses are crucial players in nutrient cycling as they lyse microbial cells, releasing nutrients back into the environment.'}, {'ecosystem': 'Environmental:Aquatic:Marine:Sediment', 'feature_id': 'sk__Eukaryota;k__Metazoa;p__Arthropoda;c__Ostracoda;o__Halocyprida', 'feature_label': 'sk__Eukaryota;k__Metazoa;p__Arthropoda;c__Ostracoda;o__Halocyprida', 'bio_property': 'biodiversity*detritus processing', 'env_property': 'sediment*benthic zone*organic matter richness', 'confidence': 'high', 'explanation': 'Ostracods are known for their role in breaking down organic matter in sediment. Their presence indicates a sediment environment rich in organic material, which they help decompose and recycle, maintaining sediment health.'}]\n", "JSON decode error for result: Expecting value: line 1 column 1 (char 0)\n", - "Content that caused the error: Here is the detailed JSON output with the required results:\n", + "Content that caused the error: Sure, let's identify and explain the relationships between the observed microbial metagenomic features and the specific environmental properties of the \"Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond\" ecosystem.\n", + "\n", + "Here's the structured JSON format with the observation results:\n", "\n", "\n", "{\n", - " \"Environmental:Aquatic:Marine:Oceanic\": {\n", + " \"Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond\": {\n", " \"1\": {\n", - " \"feature_id\": \"GO:0031460 * IPR007210\",\n", - " \"feature_label\": \"glycine betaine transport * Glycine betaine/proline betaine transport system ATP-binding protein ProV-like\",\n", - " \"bio_property\": \"osmoprotection * stress response\",\n", - " \"env_property\": \"marine * high salinity\",\n", + " \"feature_id\": \"GO:0004638\",\n", + " \"feature_label\": \"phosphoribosylaminoimidazole carboxylase activity\",\n", + " \"bio_property\": \"purine metabolism\",\n", + " \"env_property\": \"high salinity * high pH\",\n", " \"confidence\": \"high\",\n", - " \"explanation\": \"Glycine betaine is a known osmoprotectant in high osmolarity environments, and its transport is vital for organism survival in marine environments with high salinity.\"\n", + " \"explanation\": \"Phosphoribosylaminoimidazole carboxylase is involved in purine biosynthesis, which is crucial for the synthesis of nucleotides. In extreme conditions like high salinity and pH, the adaptation of nucleotide synthesis pathways can be a critical survival mechanism for organisms.\"\n", " },\n", " \"2\": {\n", - " \"feature_id\": \"IPR010518 * IPR032830\",\n", - " \"feature_label\": \"Flagellar regulatory FleQ * Helicase XPB/Ssl2, N-terminal domain\",\n", - " \"bio_property\": \"motility * DNA repair\",\n", - " \"env_property\": \"high nutrient turnover * moderate UV exposure\",\n", - " \"confidence\": \"medium\",\n", - " \"explanation\": \"The flagellar regulatory protein and helicase are associated with motility and genomic integrity, respectively. Both properties are essential in environments with high nutrient turnover where movement is necessary and moderate UV exposure likely causing DNA damage requires efficient repair mechanisms.\"\n", + " \"feature_id\": \"IPR006093\",\n", + " \"feature_label\": \"Oxygen oxidoreductase covalent FAD-binding site\",\n", + " \"bio_property\": \"oxidative stress response * flavoproteins\",\n", + " \"env_property\": \"high salinity * high pH * oxidative stress\",\n", + " \"confidence\": \"high\",\n", + " \"explanation\": \"The oxygen oxidoreductase enzymes, which contain covalent FAD-binding sites, are vital for cellular responses to oxidative stress. These enzymes help protect cells from oxidative damage, which could be prevalent in salt crystallizer ponds due to high salinity and alkalinity conditions that could generate reactive oxygen species.\"\n", " },\n", " \"3\": {\n", - " \"feature_id\": \"GO:0004114 * IPR025479\",\n", - " \"feature_label\": \"3',5'-cyclic-nucleotide phosphodiesterase activity * Domain of unknown function DUF4329\",\n", - " \"bio_property\": \"signal transduction * unknown\",\n", - " \"env_property\": \"variable extracellular signals * high environmental diversity\",\n", - " \"confidence\": \"medium\",\n", - " \"explanation\": \"The 3',5'-cyclic-nucleotide phosphodiesterase activity suggests involvement in signal transduction processes, which is crucial in an environment with variable extracellular signals and high diversity. The associated domain of unknown function (DUF4329) might indicate a yet unidentified role in adapting to such an environment.\"\n", - " },\n", - " \"4\": {\n", - " \"feature_id\": \"IPR000938 * GO:0006928\",\n", - " \"feature_label\": \"CAP Gly-rich domain * obsolete movement of cell or subcellular component\",\n", - " \"bio_property\": \"stress response * cell motility\",\n", - " \"env_property\": \"dynamic water currents * mechanical stress\",\n", - " \"confidence\": \"medium\",\n", - " \"explanation\": \"The CAP Gly-rich domain is associated with stress response, which could be due to mechanical stress from dynamic water currents, implying these features contribute to cellular adaptations that allow movement or resilience in such conditions.\"\n", - " },\n", - " \"5\": {\n", - " \"feature_id\": \"sk__Bacteria;k__;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Candidatus_Pelagibacter;s__Candidatus_Pelagibacter_ubique\",\n", - " \"feature_label\": \"Candidatus Pelagibacter ubique\",\n", - " \"bio_property\": \"oligotrophy * carbon cycling\",\n", - " \"env_property\": \"low nutrient * open ocean\",\n", + " \"feature_id\": \"IPR011946\",\n", + " \"feature_label\": \"Integrase, integron-type\",\n", + " \"bio_property\": \"horizontal gene transfer\",\n", + " \"env_property\": \"high salinity * high pH * genetic diversity\",\n", " \"confidence\": \"high\",\n", - " \"explanation\": \"Candidatus Pelagibacter ubique is known for its oligotrophic lifestyle, adapted to low nutrient conditions prevalent in the open ocean, playing a significant role in carbon cycling.\"\n", + " \"explanation\": \"Integrases, particularly the integron-type, are enzymes that facilitate horizontal gene transfer, allowing bacteria to acquire new genes, including those providing resistance to harsh environmental conditions such as high salinity and high pH. This mechanism significantly contributes to genetic diversity and adaptability in extreme environments.\"\n", " }\n", " }\n", "}\n", "\n", "\n", - "In this JSON output, we are reporting on relationships between specific feature identifiers, their biological properties, and relevant environmental properties in the marine ecosystem. The confidence level varies based on how well-established the connections are in scientific literature, with detailed explanations provided for each feature subset.\n", - "[]\n", - "JSON decode error for result: Extra data: line 23 column 1 (char 1239)\n", - "Content that caused the error: {\n", - " \"Environmental:Aquatic:Marine:Sediment\": {\n", - " \"1\": {\n", - " \"feature_id\": \"GO:0046797\",\n", - " \"feature_label\": \"viral procapsid maturation\",\n", - " \"bio_property\": \"viral life cycle * structural biology\",\n", - " \"env_property\": \"marine * high particle suspension\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Marine sediments can be high in particulate matter, providing habitats for various viruses that infect marine organisms. Viral procapsid maturation is a crucial step in the viral life cycle, suggesting that viral activity is prevalent in this environment.\"\n", - " },\n", - " \"2\": {\n", - " \"feature_id\": \"sk__Eukaryota;k__Metazoa;p__Arthropoda;c__Ostracoda;o__Halocyprida\",\n", - " \"feature_label\": \"Eukaryota * Metazoa * Arthropoda * Ostracoda * Halocyprida\",\n", - " \"bio_property\": \"biotic complexity * ecological interactions\",\n", - " \"env_property\": \"marine * anoxic layers\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Halocyprida (a type of Ostracoda) are small crustaceans often found in anoxic layers of marine sediments where they play a key role in the benthic food web, interacting with diverse microorganisms.\"\n", - " }\n", - " }\n", - "}\n", + "In these results:\n", + "1. **Feature GO:0004638 (phosphoribosylaminoimidazole carboxylase activity)** is primarily involved in purine metabolism, which is essential for nucleotide synthesis. The adaptation of these metabolic pathways is crucial in environments with high salinity and high pH, providing a means for organisms to survive and proliferate in such harsh conditions.\n", + "\n", + "2. **Feature IPR006093 (Oxygen oxidoreductase covalent FAD-binding site)** is linked with the oxidative stress response. Flavoproteins play key roles in managing oxidative stress, especially in environments that pose extreme oxidative challenges, such as salt crystallizer ponds with high salinity and pH levels.\n", "\n", + "3. **Feature IPR011946 (Integrase, integron-type)** facilitates horizontal gene transfer, which enhances genetic diversity and evolution, critical for survival in extreme environmental conditions like high salinity and high pH. This genetic adaptability can provide essential functions enabling microbes to thrive in such challenging ecosystems.\n", "\n", - "### Notes:\n", - "1. Only observed features with high confidence and relevant associations are included.\n", - "2. The relationship between the microbiology features and the environment properties focuses on specific environmental situations such as high particle suspension and anoxic layers, which are characteristic of marine sediments.\n", - "3. The explanations are concise, carefully linking biological properties to specific environmental conditions.\n", + "These explanations firmly link the metagenomic features to specific biophysical adaptations required to endure the harsh conditions of the salt crystallizer pond ecosystem.\n", "[]\n", - "[{'ecosystem': 'Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond', 'feature_id': 'IPR006093 * GO:0034614', 'feature_label': 'Oxygen oxidoreductase covalent FAD-binding site * cellular response to oxidative stress', 'bio_property': 'oxidative stress resistance*energy generation', 'env_property': 'high salinity*high sunlight exposure', 'confidence': 'high', 'explanation': 'Oxidative enzymes with FAD-binding sites are crucial for detoxifying reactive oxygen species (ROS) prevalent in high saline environments exposed to intense sunlight.'}, {'ecosystem': 'Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond', 'feature_id': 'IPR011946 * GO:0006310', 'feature_label': 'Integrase, integron-type * DNA integration', 'bio_property': 'genomic rearrangement*horizontal gene transfer', 'env_property': 'variable nutrient conditions', 'confidence': 'medium', 'explanation': 'Integron-type integrases facilitate the capture and rearrangement of gene cassettes, helping microorganisms adapt to the fluctuating nutrient availability in salt crystallizer ponds.'}, {'ecosystem': 'Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond', 'feature_id': 'GO:0004638 * IPR004831', 'feature_label': 'Phosphoribosylaminoimidazole carboxylase activity * PurM-like domain', 'bio_property': 'nucleotide biosynthesis*metabolic adaptation', 'env_property': 'nutrient poor*high pH', 'confidence': 'high', 'explanation': 'Phosphoribosylaminoimidazole carboxylase is pivotal in purine biosynthesis, a pathway critical for nucleotide metabolism, which is especially crucial in nutrient-poor and high pH conditions of saline-alkaline environments.'}]\n", - "[{'ecosystem': 'Environmental:Terrestrial:Soil', 'feature_id': 'GO:0008918 * IPR011735', 'feature_label': 'lipopolysaccharide 3-alpha-galactosyltransferase activity * WlaTC/HtrL glycosyltransferase', 'bio_property': 'lipopolysaccharide biosynthesis*glycosylation', 'env_property': 'microbial diversity*nutrient cycles', 'confidence': 'high', 'explanation': 'Lipopolysaccharides are key components of the outer membrane of Gram-negative bacteria, influencing microbial diversity and playing roles in nutrient cycling in soil ecosystems.'}, {'ecosystem': 'Environmental:Terrestrial:Soil', 'feature_id': 'IPR000522 * IPR031834', 'feature_label': 'ABC transporter, permease protein, BtuC-like * Antitoxin RnlB/LsoB', 'bio_property': 'nutrient uptake*toxin-antitoxin systems', 'env_property': 'nutrient availability*competition', 'confidence': 'high', 'explanation': 'ABC transporters facilitate the uptake of essential nutrients in nutrient-limited soil environments, while toxin-antitoxin systems play roles in microbial competition and survival.'}, {'ecosystem': 'Environmental:Terrestrial:Soil', 'feature_id': 'IPR000036 * IPR028955', 'feature_label': 'Peptidase A26, omptin * Immunity protein 57', 'bio_property': 'proteolysis*immune evasion', 'env_property': 'microbial interactions*pathogen resistance', 'confidence': 'medium', 'explanation': 'Peptidase activity contributes to protein turnover and microbial interactions in the soil, while immunity proteins can be linked to microbial defense mechanisms against pathogens.'}, {'ecosystem': 'Environmental:Terrestrial:Soil', 'feature_id': 'IPR006949 * IPR007210', 'feature_label': 'Baseplate protein J-like * Glycine betaine/proline betaine transport system ATP-binding protein ProV-like', 'bio_property': 'phage structure*osmoprotection', 'env_property': 'soil moisture*microbial population dynamics', 'confidence': 'medium', 'explanation': 'Baseplate proteins are components of bacteriophages influencing microbial population dynamics, and osmoprotection systems help bacteria survive in varying soil moisture conditions.'}, {'ecosystem': 'Environmental:Terrestrial:Soil', 'feature_id': 'IPR003791 * IPR025123', 'feature_label': 'Protein of unknown function UPF0178 * Domain of unknown function DUF4049', 'bio_property': 'functional novelty', 'env_property': 'unknown', 'confidence': 'low', 'explanation': 'Proteins of unknown function may represent novel enzymatic or structural adaptations specific to soil environments, but further characterization is needed.'}, {'ecosystem': 'Environmental:Terrestrial:Soil', 'feature_id': 'IPR010856 * IPR020497', 'feature_label': 'Gig2-like * Domain of unknown function DUF5440', 'bio_property': 'unknown', 'env_property': 'unknown', 'confidence': 'unknown', 'explanation': 'Insufficient data to establish a relationship.'}, {'ecosystem': 'Environmental:Terrestrial:Soil', 'feature_id': 'IPR020484 * IPR021239', 'feature_label': 'Protein of unknown function DUF5503 * Protein of unknown function DUF2625', 'bio_property': 'unknown', 'env_property': 'unknown', 'confidence': 'unknown', 'explanation': 'Insufficient data to establish a relationship.'}]\n", - "[{'ecosystem': 'Host-associated:Birds', 'feature_id': 'IPR007037 * IPR007925 * GO:0000502', 'feature_label': 'Siderophore-interacting protein, C-terminal domain * Relaxosome protein TraM * proteasome complex', 'bio_property': 'iron transport*conjugative transfer*protein degradation', 'env_property': 'microbiota-rich*nutrient variable', 'confidence': 'high', 'explanation': 'Siderophores are critical in iron transport, essential in nutrient-variable environments. Relaxosome proteins facilitate DNA conjugation, prevalent in mixed microbial populations. Proteasomes are involved in protein regulation and degradation, important in dense microbiota where protein turnover is high.'}, {'ecosystem': 'Host-associated:Birds', 'feature_id': 'IPR004759 * GO:0015307', 'feature_label': 'Glutamate:g-aminobutyrate antiporter * obsolete drug:proton antiporter activity', 'bio_property': 'amino acid transport*membrane transport', 'env_property': 'gut-associated*variable pH', 'confidence': 'medium', 'explanation': 'Antiporters, such as the Glutamate:g-aminobutyrate antiporter, are vital in amino acid transport and pH balance within the gut, which hosts a variable pH environment.'}, {'ecosystem': 'Host-associated:Birds', 'feature_id': 'IPR007210 * GO:0031460', 'feature_label': 'Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport', 'bio_property': 'osmoprotection*stress response', 'env_property': 'marine*high salinity', 'confidence': 'high', 'explanation': 'Glycine betaine is a known osmoprotectant, providing resistance to high salinity environments typically observed in marine settings.'}, {'ecosystem': 'Host-associated:Birds', 'feature_id': 'IPR002723 * IPR019895 * GO:0008861', 'feature_label': 'N(4)-bis(aminopropyl)spermidine synthase, C-terminal * Putative bacteriocin export ABC transporter, lactococcin 972 group * formate C-acetyltransferase activity', 'bio_property': 'polyamine biosynthesis*bacteriocin transport*metabolic enzyme', 'env_property': 'competing microbial community*nutrient recycling', 'confidence': 'medium', 'explanation': 'Polyamine biosynthesis and bacteriocin transport are important in densely packed microbial communities, facilitating competitive interactions. Formate C-acetyltransferases are involved in metabolic pathways crucial for nutrient recycling.'}, {'ecosystem': 'Host-associated:Birds', 'feature_id': 'sk__Bacteria * sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales', 'feature_label': 'Bacteria * Firmicutes; Clostridia; Clostridiales', 'bio_property': 'phylogeny*population structure', 'env_property': 'high microbial diversity*anaerobic', 'confidence': 'high', 'explanation': 'Firmicutes, particularly Clostridiales, are common in high-diversity, anaerobic environments like bird guts, impacting digestion and health.'}]\n", - "[{'ecosystem': 'Host-associated:Human', 'feature_id': 'GO:0004984 * GO:0016032', 'feature_label': 'olfactory receptor activity * viral process', 'bio_property': 'chemosensation*infection', 'env_property': 'high host interaction', 'confidence': 'high', 'explanation': 'Olfactory receptors are crucial in sensing the environment, while viral processes are indicative of host-pathogen interactions.'}, {'ecosystem': 'Host-associated:Human', 'feature_id': 'GO:0019512 * GO:0033920 * IPR004300 * IPR013148', 'feature_label': 'lactose catabolic process via tagatose-6-phosphate * 6-phospho-beta-galactosidase activity * Glycoside hydrolase family 57, N-terminal domain * Glycosyl hydrolase family 32, N-terminal', 'bio_property': 'carbohydrate metabolism', 'env_property': 'nutrient availability and utilization', 'confidence': 'high', 'explanation': 'These features are linked to carbohydrate metabolism, specifically in the breakdown and utilization of lactose, which reflects the nutrient profile directly available in the human gastrointestinal tract.'}, {'ecosystem': 'Host-associated:Human', 'feature_id': 'GO:0004352 * IPR010945 * IPR017821', 'feature_label': 'glutamate dehydrogenase (NAD+) activity * Malate dehydrogenase, type 2 * Succinate CoA transferase', 'bio_property': 'energy metabolism', 'env_property': 'metabolically active', 'confidence': 'high', 'explanation': 'These enzymes play a critical role in energy metabolism by participating in the Krebs cycle and amino acid metabolism, indicative of a metabolically active environment within the human host.'}, {'ecosystem': 'Host-associated:Human', 'feature_id': 'IPR006322 * IPR015304 * IPR018470', 'feature_label': 'Glutathione reductase, eukaryote/bacterial * ZinT domain * Periplasmic metal-binding protein Tp34-type', 'bio_property': 'oxidative stress response*metal ion regulation', 'env_property': 'metal ion fluctuations', 'confidence': 'high', 'explanation': 'These features are involved in maintaining cellular redox balance and regulating metal ions, reflecting the host environment where metal homeostasis and oxidative stress are significant concerns.'}, {'ecosystem': 'Host-associated:Human', 'feature_id': 'IPR004868 * IPR008016 * IPR012969', 'feature_label': 'DNA-directed DNA polymerase, family B, mitochondria/virus * Portal protein Gp10 * Fibrinogen binding protein', 'bio_property': 'genetic replication and host interaction', 'env_property': 'infection and immune response', 'confidence': 'high', 'explanation': 'These features relate to viral DNA replication and interaction with host proteins, indicating an environment where host-pathogen interactions and immune responses are prevalent.'}, {'ecosystem': 'Host-associated:Human', 'feature_id': 'GO:0019068 * IPR007119 * IPR021505', 'feature_label': 'virion assembly * Phage minor structural protein, N-terminal domain * Bacteriophage B3, Orf6', 'bio_property': 'bacteriophage activity', 'env_property': 'bacteriophage presence', 'confidence': 'high', 'explanation': 'These features are linked to bacteriophage activities, reflecting an environment where phage-bacteria interactions are occurring, which is common in the human microbiome.'}, {'ecosystem': 'Host-associated:Human', 'feature_id': 'IPR008981 * IPR010024 * IPR028049', 'feature_label': 'F-MuLV receptor-binding * Conserved hypothetical protein CHP1671 * NTF2 fold immunity protein', 'bio_property': 'host-pathogen interactions', 'env_property': 'variable immune pressure', 'confidence': 'high', 'explanation': 'These protein domains are associated with pathogen recognition and immune responses, indicating an environment where host immune response plays a significant role.'}]\n", + "[{'ecosystem': 'Environmental:Terrestrial:Soil', 'feature_id': 'GO:0008918 * IPR011735', 'feature_label': 'lipopolysaccharide 3-alpha-galactosyltransferase activity * WlaTC/HtrL glycosyltransferase', 'bio_property': 'cell wall synthesis*lipopolysaccharide biosynthesis', 'env_property': 'nutrient-rich*microbial diversity', 'confidence': 'high', 'explanation': 'Lipopolysaccharide biosynthesis is crucial for microbial cell wall formation, which is especially important in nutrient-rich environments with high microbial competition and diversity.'}, {'ecosystem': 'Environmental:Terrestrial:Soil', 'feature_id': 'IPR000036 * IPR025123', 'feature_label': 'Peptidase A26, omptin * Domain of unknown function DUF4049', 'bio_property': 'proteolysis*defensive enzymatic activity', 'env_property': 'organic matter decomposition*nutrient cycling', 'confidence': 'medium', 'explanation': 'Peptidases such as omptin are involved in the breakdown of proteins, aiding in the decomposition of organic matter and subsequent nutrient cycling within the soil.'}, {'ecosystem': 'Environmental:Terrestrial:Soil', 'feature_id': 'IPR000522 * IPR021239', 'feature_label': 'ABC transporter, permease protein, BtuC-like * Protein of unknown function DUF2625', 'bio_property': 'transportation of molecules*transmembrane movement', 'env_property': 'complex soil matrix*nutrient availability', 'confidence': 'high', 'explanation': 'ABC transporters are crucial for moving various molecules across cellular membranes, a vital function in the complex soil matrix where access to nutrients can vary significantly.'}, {'ecosystem': 'Environmental:Terrestrial:Soil', 'feature_id': 'IPR010856 * IPR028955', 'feature_label': 'Gig2-like * Immunity protein 57', 'bio_property': 'immune response*pathogen defense', 'env_property': 'competitive microbial habitats*pathogen presence', 'confidence': 'medium', 'explanation': 'Proteins involved in the immune response are important in soil environments that are competitive and host to various pathogens, aiding in microbe survival and dominance.'}, {'ecosystem': 'Environmental:Terrestrial:Soil', 'feature_id': 'IPR031834 * IPR003791', 'feature_label': 'Antitoxin RnlB/LsoB * Protein of unknown function UPF0178', 'bio_property': 'toxin-antitoxin systems*stress response', 'env_property': 'microbial interaction networks*environmental stress', 'confidence': 'medium', 'explanation': 'Antitoxin proteins are involved in stress responses and managing toxin exposure from other microbes or environmental sources, crucial in microbial-rich soil environments.'}]\n", + "[{'ecosystem': 'Host-associated:Birds', 'feature_id': 'GO:0000502 * GO:0008772 * IPR007925 * IPR009677', 'feature_label': 'proteasome complex * isocitrate dehydrogenase (NADP+) kinase activity * Relaxosome protein TraM * Protein of unknown function DUF1266', 'bio_property': 'protein degradation*metabolism regulation*protein interaction', 'env_property': 'host immunity*nutrient cycling', 'confidence': 'high', 'explanation': 'The proteasome complex is involved in protein degradation, key for cellular maintenance and host immunity. Isocitrate dehydrogenase kinase activity affects metabolism regulation. Relaxosome protein TraM and DUF1266 (unknown function) suggest interactions important for horizontal gene transfer, which may aid in adaptability to host environments.'}, {'ecosystem': 'Host-associated:Birds', 'feature_id': 'IPR004759 * IPR007037 * IPR007920 * IPR035286 * sk__Bacteria;k__;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales', 'feature_label': 'Glutamate:g-aminobutyrate antiporter * Siderophore-interacting protein, C-terminal domain * Protein of unknown function UPF0223 * Protein of unknown function DUF5361 * Bacteroidetes', 'bio_property': 'amino acid transport*iron acquisition*protein function', 'env_property': 'gut microbiota*nutrient uptake*low oxygen environment', 'confidence': 'high', 'explanation': 'Bacteroidetes are prevalent in the gut microbiota of birds, contributing to nutrient uptake and low oxygen environments. Glutamate:g-aminobutyrate antiporter is involved in amino acid transport critical in nutrient-rich environments. Siderophore-interacting proteins aid in iron acquisition required for growth in the gut.'}, {'ecosystem': 'Host-associated:Birds', 'feature_id': 'IPR019895 * IPR007037 * IPR031010 * sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae', 'feature_label': 'Putative bacteriocin export ABC transporter, lactococcin 972 group * Siderophore-interacting protein, C-terminal domain * Radical SAM mobile pair protein A * Firmicutes; Ruminococcaceae', 'bio_property': 'bacteriocin export*iron acquisition*radical SAM reactions', 'env_property': 'gut microbiota*antibacterial activity', 'confidence': 'high', 'explanation': 'Firmicutes, like Ruminococcaceae, are gut-associated. Bacteriocin export mechanisms suggest a role in inter-bacterial interactions and competitive inhibition. Iron acquisition remains crucial in these environments, while radical SAM enzymes are involved in diverse biosynthetic processes.'}]\n", + "[{'ecosystem': 'Host-associated:Human', 'feature_id': 'GO:0016032 * GO:0019068 * IPR007119 * IPR008016 * IPR010960 * IPR011868', 'feature_label': 'viral process * virion assembly * Phage minor structural protein, N-terminal domain * Portal protein Gp10 * Flavocytochrome c * Molybdate ABC transporter, ATP-binding protein', 'bio_property': 'viral infection and replication*phage formation*virion structural integrity*metabolic adaptation', 'env_property': 'high infection pressure*diverse microbial interactions*variable nutrient availability', 'confidence': 'high', 'explanation': 'Several features related to viral processes indicate a high infection pressure environment that requires significant microbial adaptation mechanisms, which align with human host-associated ecosystems where various viruses co-exist and interact with the host and microbial flora.'}, {'ecosystem': 'Host-associated:Human', 'feature_id': 'GO:0004352 * GO:0004638 * GO:0019512 * GO:0033920 * IPR004300 * IPR013148 * IPR035364 * IPR005126 * IPR017821 * IPR006322', 'feature_label': 'glutamate dehydrogenase (NAD+) activity * phosphoribosylaminoimidazole carboxylase activity * lactose catabolic process via tagatose-6-phosphate * 6-phospho-beta-galactosidase activity * Glycoside hydrolase family 57, N-terminal domain * Glycosyl hydrolase family 32, N-terminal * Glycosyl hydrolase 101, beta-sandwich domain * NapC/NirT cytochrome c, N-terminal * Succinate CoA transferase * Glutathione reductase, eukaryote/bacterial', 'bio_property': 'carbohydrate metabolism*energy production*nitrogen metabolism*antioxidant activity', 'env_property': 'nutrient availability*redox dynamics*gastrointestinal tract conditions', 'confidence': 'high', 'explanation': 'The features are rich in enzymes involved in carbohydrate metabolism and energy production, reflecting the nutrient-dense and metabolically active environment of the human gastrointestinal tract, which supports complex microbial and host metabolic interactions.'}, {'ecosystem': 'Host-associated:Human', 'feature_id': 'GO:0004521 * IPR002631 * IPR004868 * IPR012706 * IPR026345 * IPR028049', 'feature_label': 'RNA endonuclease activity * Plasmid replication protein * DNA-directed DNA polymerase, family B, mitochondria/virus * Rib/alpha/Esp surface antigen * Adhesin isopeptide-forming adherence domain * NTF2 fold immunity protein', 'bio_property': 'nucleic acid metabolism*genetic material replication and repair*immune evasion*surface adhesion', 'env_property': 'intestinal mucosal surfaces*homeostatic and inflammatory conditions*microbial competition', 'confidence': 'high', 'explanation': \"These features indicate nucleic acid processing and interaction with the host's immune system, highlighting the dynamic and competitive environment of intestinal mucosal surfaces, where microbes adapt and compete for adhesion and immune evasion.\"}, {'ecosystem': 'Host-associated:Human', 'feature_id': 'IPR004764 * IPR019895 * IPR005126 * IPR004868 * IPR010945 * IPR010960', 'feature_label': 'Hydrophobe/amphiphile efflux-1 HAE1 * Putative bacteriocin export ABC transporter, lactococcin 972 group * NapC/NirT cytochrome c, N-terminal * DNA-directed DNA polymerase, family B, mitochondria/virus * Malate dehydrogenase, type 2 * Flavocytochrome c', 'bio_property': 'antibiotic resistance*metabolite transport*energy production', 'env_property': 'antibiotic exposure*microbial community interactions*variable redox potential', 'confidence': 'high', 'explanation': 'The presence of efflux and transport-related proteins, combined with enzymes involved in energy generation, suggests an environment where antibiotic pressure and complex metabolic interactions are prevalent, consistent with the human host-associated ecosystem.'}]\n", + "[{'ecosystem': 'Host-associated:Human:Digestive system', 'feature_id': 'GO:0015858 * GO:0022857 * IPR000522', 'feature_label': 'nucleoside transport * transmembrane transporter activity * ABC transporter, permease protein, BtuC-like', 'bio_property': 'nutrient uptake*transmembrane transport', 'env_property': 'nutrient-rich', 'confidence': 'high', 'explanation': 'The extensive presence of transporters, including nucleoside and other ABC transporters, is indicative of nutrient assimilation processes critical in a nutrient-rich environment like the human digestive system.'}, {'ecosystem': 'Host-associated:Human:Digestive system', 'feature_id': 'GO:0019068 * GO:0046797 * IPR004975 * IPR008016', 'feature_label': 'virion assembly * viral procapsid maturation * Poxvirus VLTF2, trans-activator * Portal protein Gp10', 'bio_property': 'viral replication*virion formation', 'env_property': 'host-associated', 'confidence': 'high', 'explanation': 'Viral-related proteins and activities suggest active viral replication within the digestive system, which is a known host-associated environment where viruses interact with host cells for their life cycles.'}, {'ecosystem': 'Host-associated:Human:Digestive system', 'feature_id': 'GO:0019512 * IPR004501', 'feature_label': 'lactose catabolic process via tagatose-6-phosphate * Phosphotransferase system, EIIC component, type 3', 'bio_property': 'carbohydrate metabolism', 'env_property': 'nutrient-rich*varied diet', 'confidence': 'high', 'explanation': 'The presence of genes involved in lactose catabolism and the phosphotransferase system suggests adaptation to a varied, carbohydrate-rich diet in the human digestive system.'}, {'ecosystem': 'Host-associated:Human:Digestive system', 'feature_id': 'GO:0004352 * IPR010945', 'feature_label': 'glutamate dehydrogenase (NAD+) activity * Malate dehydrogenase, type 2', 'bio_property': 'amino acid metabolism*intermediary metabolism', 'env_property': 'nutrient-rich*metabolically active', 'confidence': 'high', 'explanation': 'The activities related to amino acid and intermediary metabolism are essential for handling the diverse range of nutrients available in the human gut.'}, {'ecosystem': 'Host-associated:Human:Digestive system', 'feature_id': 'IPR005126 * IPR008016', 'feature_label': 'NapC/NirT cytochrome c, N-terminal * Portal protein Gp10', 'bio_property': 'electron transport*viral replication', 'env_property': 'anaerobic*host-associated', 'confidence': 'medium', 'explanation': 'Electron transport is crucial for energy production in anaerobic conditions, typical of parts of the digestive system. Concurrently, viral proteins indicate ongoing viral activity, relevant in host-associated environments.'}, {'ecosystem': 'Host-associated:Human:Digestive system', 'feature_id': 'IPR012672 * IPR035576 * IPR035177', 'feature_label': 'Type III secretion system YscX * Type VI secretion system TssC * Type VI secretion system TssN', 'bio_property': 'secretion of effector proteins*bacterial competition', 'env_property': 'microbiome interaction*host-associated', 'confidence': 'high', 'explanation': 'The presence of secretion systems indicates complex microbial interactions and competition within the microbiome, typical in the densely populated human digestive tract.'}, {'ecosystem': 'Host-associated:Human:Digestive system', 'feature_id': 'sk__Bacteria;k__;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella * sk__Bacteria;k__;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides', 'feature_label': 'Collinsella * Bacteroides', 'bio_property': 'fiber degradation*niche adaptation', 'env_property': 'high fiber diet', 'confidence': 'high', 'explanation': 'Collinsella and Bacteroides are known to be involved in polysaccharide metabolism, fitting well in an environment where plant-derived fibers are abundant, such as in human digestive systems with a high-fiber diet.'}]\n", + "[{'ecosystem': 'Host-associated:Human:Digestive system:Large intestine', 'feature_id': 'GO:0019317 * IPR004300 * sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae', 'feature_label': 'fucose catabolic process * Glycoside hydrolase family 57, N-terminal domain * Lachnospiraceae family', 'bio_property': 'fucose metabolism*carbohydrate processing*specific microbiota', 'env_property': 'nutrient-rich*low oxygen*moderate pH', 'confidence': 'high', 'explanation': 'Fucose is found in the mucus of the gut lining, providing a substrate that supports specific carbohydrate processing abilities. Lachnospiraceae family bacteria are known to be prevalent in the human gut and capable of utilizing such oligosaccharides.'}, {'ecosystem': 'Host-associated:Human:Digestive system:Large intestine', 'feature_id': 'IPR017559 * IPR012770 * sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae', 'feature_label': 'Alkyl hydroperoxide reductase subunit C * Trehalose operon transcriptional repressor * Ruminococcaceae family', 'bio_property': 'antioxidant activity*carbohydrate metabolism regulation', 'env_property': 'low oxygen*intermediate moisture', 'confidence': 'high', 'explanation': 'Alkyl hydroperoxide reductase offers protection against oxidative stress, which is essential in low-oxygen environments like the large intestine. The Trehalose operon is involved in carbohydrate metabolism, crucial for the digestibility of dietary fibers, a primary function of the Ruminococcaceae family in the gut.'}, {'ecosystem': 'Host-associated:Human:Digestive system:Large intestine', 'feature_id': 'GO:0015858 * IPR009677 * IPR006541 * sk__Bacteria;k__;p__Firmicutes;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium', 'feature_label': 'nucleoside transport * DUF1266 * Bacteriocin-associated integral membrane protein * Phascolarctobacterium genus', 'bio_property': 'nucleoside uptake*bacteriocin production*specific microbiota', 'env_property': 'nutrient recycling*competitive environment', 'confidence': 'medium', 'explanation': 'Phascolarctobacterium species participate in the recycling of nucleosides and nucleotides, which are key for microbial community balance and competition within the gut. Bacteriocin production helps these microorganisms prevail in such a competitive ecosystem.'}, {'ecosystem': 'Host-associated:Human:Digestive system:Large intestine', 'feature_id': 'GO:0008918 * IPR014234 * IPR006391 * sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Subdoligranulum', 'feature_label': 'lipopolysaccharide 3-alpha-galactosyltransferase activity * N-acetylmuramoyl-L-alanine amidase CwlD * P-type ATPase, B chain, subfamily IA * Subdoligranulum genus', 'bio_property': 'lipopolysaccharide modification*cell wall remodeling*ion transport', 'env_property': 'microbial community stability*nutrient-rich', 'confidence': 'high', 'explanation': 'The presence of enzymes involved in lipopolysaccharide modification, cell wall remodeling, and ion transport suggests a role for Subdoligranulum in maintaining cell integrity and microbial community stability in the nutrient-rich environment of the large intestine.'}, {'ecosystem': 'Host-associated:Human:Digestive system:Large intestine', 'feature_id': 'IPR008016 * IPR010960 * IPR017821 * sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales', 'feature_label': 'Portal protein Gp10 * Flavocytochrome c * Succinate CoA transferase', 'bio_property': 'virus-like particle assembly*electron transfer*succinate metabolism', 'env_property': 'variable nutrient levels*controlled competition', 'confidence': 'medium', 'explanation': 'These features suggest the presence of complex microbial interactions, including virus-like particle assembly (Gp10), efficient electron transfer (Flavocytochrome c), and succinate metabolism. Such functionalities are critical in a dynamic gut environment with varying nutrient levels.'}]\n", "JSON decode error for result: Expecting value: line 1 column 1 (char 0)\n", - "Content that caused the error: Sure, let's analyze the given features and align them with the environmental properties of the human digestive system. I'll generate the JSON output as requested, focusing on features with well-supported relationships.\n", + "Content that caused the error: Given the context and requirements of the task, the following JSON object outlines the relationships between microbial metagenomic features and environmental properties in the Host-associated:Human:Digestive system:Large intestine:Fecal ecosystem.\n", "\n", "\n", "{\n", - " \"Host-associated:Human:Digestive system\": {\n", + " \"Host-associated:Human:Digestive system:Large intestine:Fecal\": {\n", " \"1\": {\n", - " \"feature_id\": \"GO:0004122 * IPR004642\",\n", - " \"feature_label\": \"cystathionine beta-synthase activity * Serine dehydratase, alpha subunit\",\n", - " \"bio_property\": \"sulfur amino acid metabolism * amino acid metabolism\",\n", - " \"env_property\": \"nutrient-rich * variable pH\",\n", + " \"feature_id\": \"GO:0019317 * GO:0019512 * GO:0033920\",\n", + " \"feature_label\": \"fucose catabolic process * lactose catabolic process via tagatose-6-phosphate * 6-phospho-beta-galactosidase activity\",\n", + " \"bio_property\": \"carbohydrate metabolism * energy production\",\n", + " \"env_property\": \"nutrient-rich * complex carbohydrate substrate\",\n", " \"confidence\": \"high\",\n", - " \"explanation\": \"Enzymes involved in amino acid metabolism are essential for the breakdown and assimilation of dietary proteins, which are abundant in the human digestive system.\"\n", + " \"explanation\": \"The large intestine is rich in complex carbohydrates from dietary fibers. These features are involved in the breakdown of these compounds, aiding in energy production and nutrient absorption.\"\n", " },\n", " \"2\": {\n", - " \"feature_id\": \"GO:0015858 * GO:0022857 * IPR000522\",\n", - " \"feature_label\": \"nucleoside transport * transmembrane transporter activity * ABC transporter, permease protein, BtuC-like\",\n", - " \"bio_property\": \"nutrient uptake * membrane transport\",\n", - " \"env_property\": \"nutrient-rich * variable pH\",\n", + " \"feature_id\": \"GO:0015858 * IPR004501\",\n", + " \"feature_label\": \"nucleoside transport * Phosphotransferase system, EIIC component, type 3\",\n", + " \"bio_property\": \"nucleotide metabolism * transport system\",\n", + " \"env_property\": \"dynamic nutrient availability * competitive microbial environment\",\n", " \"confidence\": \"high\",\n", - " \"explanation\": \"The digestive system is nutrient-rich, requiring efficient transport systems for uptake of nucleosides and other nutrients. Transport proteins facilitate these processes.\"\n", + " \"explanation\": \"Efficient transport and utilization of nucleosides are crucial in an environment with varying nutrient availability. The phosphotransferase system indicates structured nutrient uptake pathways to manage competition.\"\n", " },\n", " \"3\": {\n", - " \"feature_id\": \"GO:0019512 * IPR010945\",\n", - " \"feature_label\": \"lactose catabolic process via tagatose-6-phosphate * Malate dehydrogenase, type 2\",\n", - " \"bio_property\": \"carbohydrate metabolism * energy production\",\n", - " \"env_property\": \"nutrient-rich * microbial fermentation\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Lactose metabolism and fermentation are crucial in the gut where lactose from dairy intake is broken down by gut bacteria. Malate dehydrogenase is involved in the TCA cycle, essential for energy production.\"\n", - " },\n", - " \"4\": {\n", - " \"feature_id\": \"IPR003514 * IPR004975 * IPR008016\",\n", - " \"feature_label\": \"Microviridae F protein * Poxvirus VLTF2, trans-activator * Portal protein Gp10\",\n", - " \"bio_property\": \"viral replication * viral assembly\",\n", - " \"env_property\": \"high microbial diversity * phage-rich environments\",\n", - " \"confidence\": \"medium\",\n", - " \"explanation\": \"The human gut harbors a diverse range of microbes including bacteriophages and viruses that can infect bacteria. These proteins are involved in viral replication and assembly processes.\"\n", - " },\n", - " \"5\": {\n", - " \"feature_id\": \"GO:0046797 * IPR021505\",\n", - " \"feature_label\": \"viral procapsid maturation * Bacteriophage B3, Orf6\",\n", - " \"bio_property\": \"viral life cycle * bacteriophage development\",\n", - " \"env_property\": \"high microbial diversity * phage-rich environments\",\n", + " \"feature_id\": \"IPR007920 * IPR010360 * IPR024264\",\n", + " \"feature_label\": \"Protein of unknown function UPF0223 * Protein of unknown function DUF956 * Domain of unknown function DUF3786\",\n", + " \"bio_property\": \"potential regulatory roles * hypothetical framework\",\n", + " \"env_property\": \"unknown specific, assumed complex microbial community interactions\",\n", " \"confidence\": \"medium\",\n", - " \"explanation\": \"Phages play a critical role in microbial dynamics within the gut. Proteins related to the phage life cycle, such as those involved in procapsid maturation, are important in this context.\"\n", + " \"explanation\": \"While the exact functions are unknown, these proteins may play a role in regulatory processes or interactions within the complex microbial community of the large intestine.\"\n", " },\n", - " \"6\": {\n", - " \"feature_id\": \"IPR012672 * IPR012673 * IPR035576\",\n", - " \"feature_label\": \"Type III secretion system YscX * Type III secretion system chaperone SycN * Type VI secretion system TssC\",\n", - " \"bio_property\": \"host-pathogen interaction * secretion system\",\n", - " \"env_property\": \"high microbial competition * host immune environment\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Secretion systems are used by gut bacteria to inject effector proteins into host cells or other bacteria, playing a key role in microbial competition and interactions with the host.\"\n", - " },\n", - " \"7\": {\n", - " \"feature_id\": \"IPR014154 * IPR017813\",\n", - " \"feature_label\": \"Global transcriptional regulator CodY * Mycothiol acetyltransferase\",\n", - " \"bio_property\": \"regulation of gene expression * stress response\",\n", - " \"env_property\": \"nutrient-rich * variable pH\",\n", + " \"4\": {\n", + " \"feature_id\": \"IPR003563 * IPR009229\",\n", + " \"feature_label\": \"Oxidized purine nucleoside triphosphate * Staphylococcal AgrD\",\n", + " \"bio_property\": \"DNA repair * quorum sensing\",\n", + " \"env_property\": \"high microbial density * oxidative stress\",\n", " \"confidence\": \"high\",\n", - " \"explanation\": \"Regulatory proteins like CodY and mycothiol-related enzymes are crucial for bacteria to adapt to changing nutrient conditions and stress in the gut.\"\n", + " \"explanation\": \"In a dense microbial environment like the gut, DNA damage repair mechanisms are essential to maintain genomic integrity. Quorum sensing (e.g., AgrD) facilitates microbial communication in high-density settings.\"\n", " },\n", - " \"8\": {\n", - " \"feature_id\": \"sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae\",\n", - " \"feature_label\": \"Lachnospiraceae family\",\n", - " \"bio_property\": \"butyrate production * fiber degradation\",\n", - " \"env_property\": \"anaerobic * carbohydrate-rich\",\n", + " \"5\": {\n", + " \"feature_id\": \"sk__Bacteria;k__;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella * sk__Bacteria;k__;p__Firmicutes;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium * sk__Bacteria;k__;p__Verrucomicrobia;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia\",\n", + " \"feature_label\": \"Collinsella * Phascolarctobacterium * Akkermansia\",\n", + " \"bio_property\": \"microbiota composition * host interaction\",\n", + " \"env_property\": \"anaerobic conditions * presence of mucus layer * dietary fibers\",\n", " \"confidence\": \"high\",\n", - " \"explanation\": \"Members of the Lachnospiraceae family are known for their ability to produce butyrate, a beneficial short-chain fatty acid, through fermentation of dietary fibers.\"\n", + " \"explanation\": \"These genera are known colonizers of the gut, thriving in anaerobic conditions and utilizing dietary fibers and mucus for growth. They play significant roles in host digestion and health.\"\n", " }\n", " }\n", "}\n", "\n", "\n", - "This JSON output includes high-confidence relationships between microbial metagenomic features and environmental properties relevant to the human digestive system. It prioritizes multiple feature subsets where possible and ensures thorough, reliable annotations.\n", - "[]\n", - "JSON decode error for result: Expecting value: line 1 column 1 (char 0)\n", - "Content that caused the error: Sure, let's delve into the relationships between the observed microbial metagenomic features and the environmental properties of the Host-associated:Human:Digestive system:Large intestine ecosystem. \n", + "**Explanation of Results:**\n", "\n", - "I'll provide a thorough and reliable analysis for each feature or feature subset:\n", + "1. **Carbohydrate Metabolism:** Features associated with fucose and lactose catabolism are crucial in the nutrient-rich environment of the large intestine that contains dietary fibers. These microbial activities are highly relevant for energy production and nutrient absorption.\n", "\n", + "2. **Nucleotide Metabolism and Transport:** Features related to nucleoside transport and the phosphotransferase system demonstrate the importance of nutrient uptake and utilization in a competitive microbial setting, highlighting the need for structured nutrient acquisition strategies.\n", "\n", - "{\n", - " \"Host-associated:Human:Digestive system:Large intestine\": {\n", - " \"1\": {\n", - " \"feature_id\": \"GO:0001510\",\n", - " \"feature_label\": \"RNA methylation\",\n", - " \"bio_property\": \"gene expression regulation * RNA stability\",\n", - " \"env_property\": \"nutritionally rich * low redox potential\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"RNA methylation in the gut helps in regulating gene expression and maintaining RNA stability, which is crucial for host-microbe interactions in a nutritionally rich environment with low oxidative stress.\"\n", - " },\n", - " \"2\": {\n", - " \"feature_id\": \"GO:0019317 * IPR004300\",\n", - " \"feature_label\": \"Fucose catabolic process * Glycoside hydrolase family 57, N-terminal domain\",\n", - " \"bio_property\": \"fucose utilization * carbohydrate metabolism\",\n", - " \"env_property\": \"high fiber diet * complex carbohydrate availability\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Fucose catabolism and glycoside hydrolase are involved in breaking down complex carbohydrates in the large intestine, where a high fiber diet provides diverse polysaccharides.\"\n", - " },\n", - " \"3\": {\n", - " \"feature_id\": \"IPR005126\",\n", - " \"feature_label\": \"NapC/NirT cytochrome c, N-terminal\",\n", - " \"bio_property\": \"electron transport * oxidative stress response\",\n", - " \"env_property\": \"anaerobic conditions * low oxygen\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"NapC/NirT cytochrome c is crucial for electron transport under anaerobic conditions found in the large intestine, aiding in maintaining redox balance.\"\n", - " },\n", - " \"4\": {\n", - " \"feature_id\": \"IPR017559 * IPR017821\",\n", - " \"feature_label\": \"Alkyl hydroperoxide reductase subunit C * Succinate CoA transferase\",\n", - " \"bio_property\": \"detoxification * energy production\",\n", - " \"env_property\": \"high oxidative stress * nutrient metabolism\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"These enzymes help in detoxifying reactive oxygen species and in energy production processes, addressing the high oxidative stress and diverse metabolic needs in the gut.\"\n", - " },\n", - " \"5\": {\n", - " \"feature_id\": \"IPR012770\",\n", - " \"feature_label\": \"Trehalose operon transcriptional repressor\",\n", - " \"bio_property\": \"osmoprotection * sugar metabolism regulation\",\n", - " \"env_property\": \"osmotic stress * variable sugar availability\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Trehalose operon regulation provides osmoprotection and adapts sugar metabolism in response to varying osmotic conditions and sugar availability in the large intestine.\"\n", - " },\n", - " \"6\": {\n", - " \"feature_id\": \"IPR001101\",\n", - " \"feature_label\": \"Plectin repeat\",\n", - " \"bio_property\": \"structural stability * cytoskeletal interactions\",\n", - " \"env_property\": \"mechanical stress * host cell interaction\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Plectin repeats provide structural stability and facilitate cytoskeletal interactions, which are essential in the large intestine for withstanding mechanical stress and maintaining host-microbe interactions.\"\n", - " },\n", - " \"7\": {\n", - " \"feature_id\": \"IPR023972\",\n", - " \"feature_label\": \"Conserved hypothetical protein CHP04069, acyl carrier-related\",\n", - " \"bio_property\": \"lipid metabolism * protein-protein interaction\",\n", - " \"env_property\": \"lipid-rich diet * microbial community interactions\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"This conserved protein related to acyl carriers is involved in lipid metabolism and protein interactions, important for managing a lipid-rich diet and microbial interactions in the large intestine.\"\n", - " },\n", - " \"8\": {\n", - " \"feature_id\": \"IPR006541 * IPR008016\",\n", - " \"feature_label\": \"Bacteriocin-associated integral membrane protein * Portal protein Gp10\",\n", - " \"bio_property\": \"antimicrobial activity * viral infection\",\n", - " \"env_property\": \"microbial competition * pathogen presence\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Bacteriocin-associated proteins provide antimicrobial functions, and portal proteins are involved in viral infections. Both play roles in maintaining microbial competition and managing pathogen presence in the gut.\"\n", - " },\n", - " \"9\": {\n", - " \"feature_id\": \"sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnospira\",\n", - " \"feature_label\": \"Lachnospira species\",\n", - " \"bio_property\": \"butyrate production * fiber degradation\",\n", - " \"env_property\": \"high fiber diet * butyrate-rich environment\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Lachnospira species are known for their ability to degrade fiber and produce butyrate, which is prevalent in a high fiber diet and contributes to a butyrate-rich environment in the large intestine.\"\n", - " },\n", - " \"10\": {\n", - " \"feature_id\": \"sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Subdoligranulum\",\n", - " \"feature_label\": \"Subdoligranulum species\",\n", - " \"bio_property\": \"short-chain fatty acid production * polysaccharide degradation\",\n", - " \"env_property\": \"dietary polysaccharides * short-chain fatty acid availability\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Subdoligranulum species are involved in degrading dietary polysaccharides and producing short-chain fatty acids, which are abundant in the large intestine due to diet.\"\n", - " }\n", - " }\n", - "}\n", + "3. **Hypothetical Functions:** Protein domains of unknown function are grouped to suggest potential regulatory or interaction roles within the complex microbial ecosystem, although these associations come with a medium confidence level due to the lack of specific functional information.\n", + "\n", + "4. **DNA Repair and Quorum Sensing:** Features for oxidized purine nucleoside triphosphate (DNA repair) and Staphylococcal AgrD (quorum sensing) underscore the significance of maintaining genomic integrity and microbial communication in high-density environments like the large intestine.\n", "\n", + "5. **Microbiota Composition:** The presence of specific bacterial genera (Collinsella, Phascolarctobacterium, Akkermansia) is closely tied to the anaerobic conditions and the availability of dietary fibers and mucus in the large intestine, validating their role in the gut ecosystem and host interactions.\n", "\n", - "This structured JSON outlines the relationship between microbial features and the environmental context within the large intestine with clear biological properties, environmental properties, and high-confidence explanations for each feature.\n", + "These relationships provide insight into how microbial genomic features correspond to the environmental characteristics and functionalities within the large intestine.\n", "[]\n", - "[{'ecosystem': 'Host-associated:Human:Digestive system:Large intestine:Fecal', 'feature_id': 'GO:0015858 * IPR004501', 'feature_label': 'nucleoside transport * Phosphotransferase system, EIIC component, type 3', 'bio_property': 'nucleoside transport across membranes*carbohydrate transport system', 'env_property': 'nutrient-rich*low pH', 'confidence': 'high', 'explanation': 'Nucleoside transport and phosphotransferase systems are critical in nutrient absorption and carbohydrate metabolism, which is essential in the nutrient-rich, low-pH environment of the large intestine.'}, {'ecosystem': 'Host-associated:Human:Digestive system:Large intestine:Fecal', 'feature_id': 'GO:0019512 * GO:0033920', 'feature_label': 'lactose catabolic process via tagatose-6-phosphate * 6-phospho-beta-galactosidase activity', 'bio_property': 'lactose metabolism*carbohydrate breakdown', 'env_property': 'high lactose diet*anaerobic conditions', 'confidence': 'high', 'explanation': 'Lactose catabolic pathways are particularly relevant in environments where a high lactose diet is present, and the activity of these enzymes supports carbohydrate breakdown under anaerobic conditions typical of the large intestine.'}, {'ecosystem': 'Host-associated:Human:Digestive system:Large intestine:Fecal', 'feature_id': 'GO:0019317 * IPR026366', 'feature_label': 'fucose catabolic process * Putative selenium metabolism protein, YedE family', 'bio_property': 'fucose metabolism*selenium utilization', 'env_property': 'complex carbohydrate diet*presence of trace elements', 'confidence': 'high', 'explanation': 'The fucose catabolic process and selenium metabolism are crucial for breaking down complex carbohydrates and utilizing trace elements that are often found in complex diets, characteristic of the large intestine environment.'}, {'ecosystem': 'Host-associated:Human:Digestive system:Large intestine:Fecal', 'feature_id': 'GO:0008743 * IPR019646', 'feature_label': \"L-threonine 3-dehydrogenase activity * Aminoglycoside-2''-adenylyltransferase\", 'bio_property': 'amino acid catabolism*antibiotic resistance', 'env_property': 'protein-rich diet*exposure to antibiotic residues', 'confidence': 'high', 'explanation': 'L-threonine dehydrogenase plays a role in amino acid catabolism which is essential in a protein-rich diet, while aminoglycoside transferases confer antibiotic resistance, important in environments where antibiotic residues might be present.'}, {'ecosystem': 'Host-associated:Human:Digestive system:Large intestine:Fecal', 'feature_id': 'IPR016041 * IPR024264', 'feature_label': 'CO dehydrogenase/acetyl-CoA synthase delta subunit, TIM barrel * Domain of unknown function DUF3786', 'bio_property': 'carbon utilization*unknown function possibly related to carbon metabolism', 'env_property': 'presence of short-chain fatty acids (SCFAs)*fermentative conditions', 'confidence': 'high', 'explanation': 'CO dehydrogenase/acetyl-CoA synthase is key for carbon utilization under fermentative conditions producing SCFAs in the gut, and DUF3786 may play an associated unknown role in these processes.'}, {'ecosystem': 'Host-associated:Human:Digestive system:Large intestine:Fecal', 'feature_id': 'sk__Bacteria;k__;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella * sk__Bacteria;k__;p__Firmicutes;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium', 'feature_label': 'Collinsella * Phascolarctobacterium', 'bio_property': 'gut microbiota composition*SCFA production', 'env_property': 'fiber-rich diet*low oxygen availability', 'confidence': 'high', 'explanation': 'Both Collinsella and Phascolarctobacterium are integral components of gut microbiota associated with the production of short-chain fatty acids (SCFAs) under low oxygen conditions typical in a fiber-rich diet.'}]\n", - "JSON decode error for result: Extra data: line 71 column 1 (char 4889)\n", + "JSON decode error for result: Extra data: line 46 column 1 (char 3428)\n", "Content that caused the error: {\n", " \"Host-associated:Human:Digestive system:Large intestine:Sigmoid colon\": {\n", " \"1\": {\n", - " \"feature_id\": \"GO:0031460 * IPR024735\",\n", - " \"feature_label\": \"glycine betaine transport * Conjugative transposon protein TcpC\",\n", - " \"bio_property\": \"osmoprotection * genetic exchange\",\n", - " \"env_property\": \"high osmolarity\",\n", + " \"feature_id\": \"GO:0015858 * IPR006322 * IPR011868\",\n", + " \"feature_label\": \"nucleoside transport * Glutathione reductase, eukaryote/bacterial * Molybdate ABC transporter, ATP-binding protein\",\n", + " \"bio_property\": \"transport processes * redox balance * nutrient acquisition\",\n", + " \"env_property\": \"nutrient-rich environment * low pH\",\n", " \"confidence\": \"high\",\n", - " \"explanation\": \"Glycine betaine acts as an osmoprotectant in high osmolarity environments often found in the gut. Conjugative transposons facilitate horizontal gene transfer, which may include genes for osmoprotection.\"\n", + " \"explanation\": \"Nucleoside transport and nutrient acquisition are critical for microbial survival in the nutrient-rich sigmoid colon. The glutathione reductase and molybdate transporter help manage oxidative stress and nutrient acquisition in this low pH environment.\"\n", " },\n", " \"2\": {\n", - " \"feature_id\": \"GO:0015858 * IPR012727\",\n", - " \"feature_label\": \"nucleoside transport * Glycine oxidase ThiO\",\n", - " \"bio_property\": \"nucleotide metabolism * oxidative stress resistance\",\n", - " \"env_property\": \"low pH * anaerobic\",\n", + " \"feature_id\": \"GO:0019512 * GO:0033920 * IPR001360\",\n", + " \"feature_label\": \"lactose catabolic process via tagatose-6-phosphate * 6-phospho-beta-galactosidase activity * Glycoside hydrolase family 1\",\n", + " \"bio_property\": \"carbohydrate metabolism * energy generation\",\n", + " \"env_property\": \"presence of complex carbohydrates\",\n", " \"confidence\": \"high\",\n", - " \"explanation\": \"Nucleoside transport is crucial for nucleotide salvage in the metabolically demanding gut environment. Glycine oxidase is involved in oxidative stress resistance, crucial for survival in the low pH, anaerobic condition of the gut.\"\n", + " \"explanation\": \"These features are involved in the breakdown and metabolism of lactose and other carbohydrates prevalent in the diet. This highlights how the microbial community adapts to carbohydrate-rich conditions in the sigmoid colon.\"\n", " },\n", " \"3\": {\n", - " \"feature_id\": \"GO:0043093 * IPR004759\",\n", - " \"feature_label\": \"FtsZ-dependent cytokinesis * Glutamate:g-aminobutyrate antiporter\",\n", - " \"bio_property\": \"bacterial cell division * neurotransmitter regulation\",\n", - " \"env_property\": \"rich in neurotransmitters * nutrient variability\",\n", + " \"feature_id\": \"GO:0043093 * IPR004763 * IPR026345\",\n", + " \"feature_label\": \"FtsZ-dependent cytokinesis * Cation efflux system CzcA/CusA/SilA/NccA/HelA/CnrA * Adhesin isopeptide-forming adherence domain\",\n", + " \"bio_property\": \"cell division * ion transport * adherence\",\n", + " \"env_property\": \"high microbial density\",\n", " \"confidence\": \"high\",\n", - " \"explanation\": \"FtsZ-dependent cytokinesis indicates active cell division, supported by the nutrient-rich environment of the gut. The Glutamate:g-aminobutyrate antiporter is involved in neurotransmitter regulation, relevant in an environment rich in these compounds.\"\n", + " \"explanation\": \"Features related to cell division, ion transport, and adherence reflect adaptation to a densely populated environment where microbes need to efficiently divide, manage ionic stress, and attach to surfaces.\"\n", " },\n", " \"4\": {\n", - " \"feature_id\": \"GO:0019512 * IPR006322\",\n", - " \"feature_label\": \"lactose catabolic process via tagatose-6-phosphate * Glutathione reductase, eukaryote/bacterial\",\n", - " \"bio_property\": \"carbohydrate metabolism * antioxidant defense\",\n", - " \"env_property\": \"high lactose content * oxidative stress\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"The large intestine processes high levels of lactose, requiring specific catabolic pathways. Glutathione reductase provides protection against oxidative stress, which is prevalent in metabolically active environments.\"\n", - " },\n", - " \"5\": {\n", - " \"feature_id\": \"IPR004763 * sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales\",\n", - " \"feature_label\": \"Cation efflux system CzcA/CusA/SilA/NccA/HelA/CnrA * Clostridiales\",\n", - " \"bio_property\": \"metal resistance * anaerobic metabolism\",\n", - " \"env_property\": \"metal exposure * anaerobic\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"The cation efflux system is crucial for resisting toxic metals in the gut. Clostridiales' ability to thrive in anaerobic conditions complements the low oxygen environment of the large intestine.\"\n", - " },\n", - " \"6\": {\n", - " \"feature_id\": \"GO:0000502 * IPR035391\",\n", - " \"feature_label\": \"proteasome complex * Arylsulfotransferase, N-terminal domain\",\n", - " \"bio_property\": \"protein degradation * detoxification\",\n", - " \"env_property\": \"immune response * high sulfate levels\",\n", + " \"feature_id\": \"IPR004764 * IPR005694 * IPR018721\",\n", + " \"feature_label\": \"Hydrophobe/amphiphile efflux-1 HAE1 * Efflux pump membrane protein * Protein of unknown function DUF2252\",\n", + " \"bio_property\": \"efflux systems * resistance mechanisms\",\n", + " \"env_property\": \"antibiotic presence * toxic compound presence\",\n", " \"confidence\": \"medium\",\n", - " \"explanation\": \"Proteasomes are involved in degrading damaged proteins, supporting immune homeostasis. Arylsulfotransferase aids in detoxification of sulfate compounds, relevant in environments with high sulfate levels.\"\n", - " },\n", - " \"7\": {\n", - " \"feature_id\": \"GO:0004638 * IPR015304\",\n", - " \"feature_label\": \"phosphoribosylaminoimidazole carboxylase activity * ZinT domain\",\n", - " \"bio_property\": \"purine biosynthesis * zinc homeostasis\",\n", - " \"env_property\": \"nutrient-rich * presence of heavy metals\",\n", - " \"confidence\": \"medium\",\n", - " \"explanation\": \"Phosphoribosylaminoimidazole carboxylase is important for purine biosynthesis in nutrient-rich conditions. The ZinT domain helps in zinc homeostasis, crucial for metal presence in the gut.\"\n", - " },\n", - " \"8\": {\n", - " \"feature_id\": \"GO:0019512 * IPR007516\",\n", - " \"feature_label\": \"lactose catabolic process via tagatose-6-phosphate * Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal\",\n", - " \"bio_property\": \"carbohydrate metabolism * redox metabolism\",\n", - " \"env_property\": \"high lactose content * anaerobic\",\n", - " \"confidence\": \"medium\",\n", - " \"explanation\": \"Lactose metabolism is vital in the gut. Coenzyme F420 hydrogenase/dehydrogenase is involved in redox reactions, which are essential in the reducing environment of the large intestine.\"\n", - " }\n", - " }\n", - "}\n", - "\n", - "\n", - "This output structure provides detailed and reliable associations between observed microbiological features in the sigmoid colon environment and its corresponding biological and environmental properties with clearly defined confidence levels.\n", - "[]\n", - "[{'ecosystem': 'Host-associated:Human:Digestive system:Oral', 'feature_id': 'IPR001077 * GO:0008171', 'feature_label': 'O-methyltransferase domain * O-methyltransferase activity', 'bio_property': 'methanol biosynthesis*secondary metabolite biosynthesis', 'env_property': 'variable pH*varied nutrient availability', 'confidence': 'high', 'explanation': 'O-methyltransferases are involved in the biosynthesis of various secondary metabolites and can affect the microbial ecology by altering organic compound profiles responsive to nutrient variability and pH changes in the oral cavity.'}, {'ecosystem': 'Host-associated:Human:Digestive system:Oral', 'feature_id': 'IPR008013 * GO:0070323', 'feature_label': 'GATA-type transcription activator, N-terminal * DNA-binding transcription factor activity', 'bio_property': 'gene expression regulation*cellular differentiation', 'env_property': 'anaerobic pockets*host-microbe interface', 'confidence': 'high', 'explanation': 'GATA-type transcription factors regulate transcription in response to oxygen gradients within biofilms and anaerobic microenvironments in the oral ecosystem, crucial for microbial survival at the host interface.'}, {'ecosystem': 'Host-associated:Human:Digestive system:Oral', 'feature_id': 'IPR019108 * GO:0006123', 'feature_label': 'Cytochrome c oxidase caa3-type, assembly factor CtaG-related * cytochrome-c oxidase activity', 'bio_property': 'electron transport chain*aerobic respiration', 'env_property': 'fluctuating oxygen levels*host-derived nutrients', 'confidence': 'high', 'explanation': 'Cytochrome c oxidase is integral to the electron transport chain and aerobic respiration, allowing microbes to adapt to fluctuating oxygen levels and varying availability of nutrients derived from the host.'}, {'ecosystem': 'Host-associated:Human:Digestive system:Oral', 'feature_id': 'IPR026395 * GO:0031460', 'feature_label': 'CshA domain * RNA helicase activity', 'bio_property': 'RNA processing*translation regulation', 'env_property': 'thermal gradients*salivary fluid dynamics', 'confidence': 'medium', 'explanation': 'RNA helicases like CshA play a role in RNA metabolism and protein synthesis, allowing microbes to modulate gene expression in response to thermal changes and varying salivary fluid conditions.'}, {'ecosystem': 'Host-associated:Human:Digestive system:Oral', 'feature_id': 'IPR030985 * sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Eubacteriaceae;g__Eubacterium;s__Eubacterium_sp._oral_clone_FX028', 'feature_label': 'Putative peptide maturation system protein * Eubacterium_sp._oral_clone_FX028', 'bio_property': 'peptide modification*proteolysis', 'env_property': 'nutrient gradients*interspecies interactions', 'confidence': 'medium', 'explanation': 'Peptide maturation systems and proteolysis are crucial for microbial interactions and nutrient acquisition, influencing microbial community dynamics within the complex nutrient gradients of the oral cavity.'}, {'ecosystem': 'Host-associated:Human:Digestive system:Oral', 'feature_id': 'sk__Archaea;k__;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter;s__Methanobrevibacter_oralis * IPR021447', 'feature_label': 'Methanobrevibacter_oralis * Protein of unknown function DUF3097', 'bio_property': 'methanogenesis*unknown protein function', 'env_property': 'anaerobic niches*biofilm formation', 'confidence': 'medium', 'explanation': 'Methanobrevibacter oralis is a key archaeon in anaerobic niches associated with methanogenesis, contributing to oral microbial ecology. The function of DUF3097 is unknown, but it may play a role in biofilm dynamics or methanogenic pathways.'}, {'ecosystem': 'Host-associated:Human:Digestive system:Oral', 'feature_id': 'IPR032576 * GO:0006397', 'feature_label': 'Domain of unknown function DUF4921 * mRNA processing', 'bio_property': 'mRNA modification*genetic regulation', 'env_property': 'biotic stress*nutrient variability', 'confidence': 'medium', 'explanation': 'Although the exact role of DUF4921 is unclear, its association with mRNA processing suggests it may help microbes respond to biotic stresses and environmental nutrient fluctuations in the oral cavity.'}]\n", - "[{'ecosystem': 'Host-associated:Human:Digestive system:Oral:Saliva', 'feature_id': 'GO:0004352 * GO:0033920 * IPR004868 * IPR012706', 'feature_label': 'glutamate dehydrogenase (NAD+) activity * 6-phospho-beta-galactosidase activity * DNA-directed DNA polymerase, family B, mitochondria/virus * Rib/alpha/Esp surface antigen', 'bio_property': 'amino acid metabolism*lactose degradation*DNA replication and repair*surface adherence', 'env_property': 'moist*nutrient-rich', 'confidence': 'high', 'explanation': 'The saliva environment is rich in nutrients, supporting diverse metabolic activities including amino acid metabolism and lactose degradation. DNA repair and replication are essential for maintaining integrity in a complex microbial community, and surface antigens assist in microbial adhesion to oral tissues.'}, {'ecosystem': 'Host-associated:Human:Digestive system:Oral:Saliva', 'feature_id': 'IPR004300 * IPR010960 * IPR015304', 'feature_label': 'Glycoside hydrolase family 57, N-terminal domain * Flavocytochrome c * ZinT domain', 'bio_property': 'carbohydrate metabolism*electron transport*metal ion binding', 'env_property': 'fluctuating oxygen levels*variable metal ion concentrations', 'confidence': 'high', 'explanation': 'Glycoside hydrolases facilitate carbohydrate breakdown in the nutrient-rich oral environment. Flavocytochrome c is involved in electron transport processes under fluctuating oxygen levels. ZinT domain proteins help in metal ion homeostasis, adapting to variable concentrations.'}, {'ecosystem': 'Host-associated:Human:Digestive system:Oral:Saliva', 'feature_id': 'IPR008016 * IPR021505 * IPR022458', 'feature_label': 'Portal protein Gp10 * Bacteriophage B3, Orf6 * Conjugative coupling factor TraG/TraD', 'bio_property': 'viral infection and propagation*conjugative transfer', 'env_property': 'high microbial diversity', 'confidence': 'high', 'explanation': 'The high microbial diversity in saliva supports viral replication and horizontal gene transfer, facilitated by bacteriophages and conjugative elements. These processes contribute to genetic variability and adaptation of the oral microbiome.'}, {'ecosystem': 'Host-associated:Human:Digestive system:Oral:Saliva', 'feature_id': 'IPR007210 * GO:0031460', 'feature_label': 'Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport', 'bio_property': 'osmoprotection*stress response', 'env_property': \"saliva's variable osmolarity\", 'confidence': 'high', 'explanation': 'Glycine betaine functions as an osmoprotectant in environments with variable osmolarity, as found in the oral cavity. This provides microbial protection against osmotic stress.'}, {'ecosystem': 'Host-associated:Human:Digestive system:Oral:Saliva', 'feature_id': 'IPR011119 * IPR028962 * IPR031012', 'feature_label': 'Uncharacterised domain, helicase/relaxase, putative * Immunity protein 10 * Radical SAM mobile pair protein B', 'bio_property': 'genome stability*bacteriophage immunity*radical-mediated enzymatic activity', 'env_property': 'dynamic microbial interactions', 'confidence': 'medium', 'explanation': 'The dynamic microbial interactions within the oral cavity necessitate mechanisms for genome stability and bacteriophage immunity. Radical SAM proteins contribute to various enzymatic reactions critical for microbial survival.'}]\n", - "JSON decode error for result: Expecting value: line 1 column 1 (char 0)\n", - "Content that caused the error: Below are the identified relationships between the microbial metagenomic features in the Host-associated:Human:Skin ecosystem and environmental properties. The relationships are focused on groups of features when possible and are presented with high confidence:\n", - "\n", - "\n", - "{\n", - " \"Host-associated:Human:Skin\": {\n", - " \"1\": {\n", - " \"feature_id\": \"IPR010706 * GO:0004037\",\n", - " \"feature_label\": \"Fatty acid cis-trans isomerase * allantoicase activity\",\n", - " \"bio_property\": \"membrane adaptation * nitrogen metabolism\",\n", - " \"env_property\": \"desiccation * nutrient variability\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Fatty acid cis-trans isomerase is involved in altering membrane fluidity under stress conditions like desiccation. Allantoicase participates in nitrogen metabolism, which can be crucial in environments with variable nutrient availability.\"\n", - " },\n", - " \"2\": {\n", - " \"feature_id\": \"IPR017821 * IPR010945\",\n", - " \"feature_label\": \"Succinate CoA transferase * Malate dehydrogenase, type 2\",\n", - " \"bio_property\": \"metabolic versatility * energy metabolism\",\n", - " \"env_property\": \"nutrient variability * fluctuating moisture\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Both succinate CoA transferase and malate dehydrogenase type 2 are involved in metabolic processes that allow microbes to adapt to varying nutrient compositions and moisture levels in the skin environment.\"\n", - " },\n", - " \"3\": {\n", - " \"feature_id\": \"IPR000938 * IPR014984\",\n", - " \"feature_label\": \"CAP Gly-rich domain * HopJ type III effector protein\",\n", - " \"bio_property\": \"transcriptional regulation * host interaction\",\n", - " \"env_property\": \"host immune evasion * inflammatory conditions\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"The CAP Gly-rich domain is involved in transcriptional regulation, including stress responses, while HopJ effectors are known for manipulating host immune responses, relevant to managing inflammation and immune evasion on the skin surface.\"\n", - " },\n", - " \"4\": {\n", - " \"feature_id\": \"IPR017523 * IPR032576\",\n", - " \"feature_label\": \"Conserved hypothetical protein CHP03089 * Domain of unknown function DUF4921\",\n", - " \"bio_property\": \"structural integrity * unknown function (potential stress response)\",\n", - " \"env_property\": \"physical abrasion * microenvironmental stress\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Conserved hypothetical proteins often play roles in maintaining cellular or structural integrity under various stressors, and domains of unknown function like DUF4921, often are later found to contribute to stress response mechanisms, helping microbes withstand skin surface conditions.\"\n", + " \"explanation\": \"Efflux systems are essential for dealing with toxic compounds and antibiotics that may be present in the large intestine, contributing to microbial resistance mechanisms in the gut environment.\"\n", " },\n", " \"5\": {\n", - " \"feature_id\": \"IPR012706 * IPR026359\",\n", - " \"feature_label\": \"Rib/alpha/Esp surface antigen * SasC/Mrp/FmtB intercellular aggregation domain\",\n", - " \"bio_property\": \"surface adhesion * biofilm formation\",\n", - " \"env_property\": \"biotic interactions * stable microbial communities\",\n", + " \"feature_id\": \"sk__Bacteria * sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales * sk__Bacteria;k__;p__Actinobacteria;c__Coriobacteriia;o__Eggerthellales\",\n", + " \"feature_label\": \"Bacteria * Firmicutes * Actinobacteria\",\n", + " \"bio_property\": \"microbial diversity * community structure\",\n", + " \"env_property\": \"anoxic conditions * presence of complex organic matter\",\n", " \"confidence\": \"high\",\n", - " \"explanation\": \"Rib/alpha/Esp surface antigens and aggregation domains are known to facilitate surface adhesion and biofilm formation, essential for maintaining stable microbial communities on the skin by mediating interactions between microbial populations and with the host cells.\"\n", + " \"explanation\": \"The presence of diverse bacterial groups such as Firmicutes and Actinobacteria indicates a complex, anoxic environment rich in organic matter that supports a diverse microbial community.\"\n", " }\n", " }\n", "}\n", "\n", - "\n", - "### Summary:\n", - "- The listed features demonstrate significant relationships between microbial genetic expressions and adaptations necessary for surviving and thriving in the unique environment of human skin, correlating with various environmental stresses and nutrient dynamics.\n", - "- The confidence levels for associations between features and environmental properties are all high, ensuring reliable data for understanding these relationships.\n", - "\n", - "This dataset provides insight into the resilience and adaptability of skin-associated microbial communities, emphasizing the biological properties aligning with specific environmental conditions.\n", + "This JSON output elucidates the relationships between various microbial metagenomic features and environmental properties in the sigmoid colon. Each feature or subset of features is thoroughly examined to provide a reliable association, with a focus on multiple features sharing biological properties, thereby enhancing the confidence of inferred relationships.\n", "[]\n", - "[{'ecosystem': 'Host-associated:Human:Skin:Naris', 'feature_id': 'GO:0019317 * GO:0019512 * GO:0033920', 'feature_label': 'fucose catabolic process * lactose catabolic process via tagatose-6-phosphate * 6-phospho-beta-galactosidase activity', 'bio_property': 'catabolism of sugars*carbohydrate metabolism', 'env_property': 'nutrient-rich*chemically complex', 'confidence': 'high', 'explanation': 'The presence of genes involved in the catabolism of fucose, lactose, and other carbohydrates indicates the ability of the microbial community to utilize a variety of sugars, which is consistent with an environment rich in diverse chemical substrates such as the human skin where various complex carbohydrates are available.'}, {'ecosystem': 'Host-associated:Human:Skin:Naris', 'feature_id': 'IPR007298 * IPR011868 * IPR007445', 'feature_label': 'Copper resistance lipoprotein NlpE * Molybdate ABC transporter, ATP-binding protein * Type IV pilus inner membrane component PilO', 'bio_property': 'metal resistance*nutrient uptake*surface adhesion', 'env_property': 'metal availability*nutrient variability*high microbial interaction', 'confidence': 'high', 'explanation': 'Copper resistance proteins and transport systems, along with surface adhesion components, suggest adaptations to an environment with variable metal concentrations and competitive microbial interactions, typical of the human skin where trace metals from sweat and environmental interactions are common.'}, {'ecosystem': 'Host-associated:Human:Skin:Naris', 'feature_id': 'IPR006541 * IPR010133 * IPR019895', 'feature_label': 'Bacteriocin-associated integral membrane protein * Bacteriocin-type signal sequence * Putative bacteriocin export ABC transporter, lactococcin 972 group', 'bio_property': 'bacteriocin production*antimicrobial competition', 'env_property': 'competitive microbial community', 'confidence': 'high', 'explanation': 'The presence of bacteriocin-related proteins suggests that the microbial community is engaged in competitive interactions through the production of antimicrobial peptides, a typical feature of densely populated environments such as the human skin.'}, {'ecosystem': 'Host-associated:Human:Skin:Naris', 'feature_id': 'IPR008557 * IPR017821 * IPR001096', 'feature_label': 'Alkaline phosphatase PhoX * Succinate CoA transferase * Peptidase C13, legumain', 'bio_property': 'phosphate metabolism*TCA cycle*proteolysis', 'env_property': 'variable pH*nutrient processing', 'confidence': 'high', 'explanation': 'The presence of proteins involved in phosphate metabolism, the TCA cycle, and proteolysis indicates adaptations to an environment where pH and nutrient availability may vary, reflecting the dynamic conditions of the human skin.'}, {'ecosystem': 'Host-associated:Human:Skin:Naris', 'feature_id': 'IPR012770 * IPR035364', 'feature_label': 'Trehalose operon transcriptional repressor * Glycosyl hydrolase 101, beta-sandwich domain', 'bio_property': 'sugar signaling and regulation*carbohydrate breakdown', 'env_property': 'nutrient variability', 'confidence': 'high', 'explanation': 'Components involved in sugar regulation and breakdown suggest the ability to adapt to fluctuating nutrient conditions, indicating that the microbial community can efficiently manage and recycle nutrients on the human skin.'}]\n", - "[{'ecosystem': 'Host-associated:Mammals:Digestive system', 'feature_id': 'GO:0004352', 'feature_label': 'glutamate dehydrogenase (NAD+) activity', 'bio_property': 'amino acid metabolism*nitrogen metabolism', 'env_property': 'high protein diet*nitrogen rich', 'confidence': 'high', 'explanation': 'Glutamate dehydrogenase plays a key role in the catabolism of amino acids, converting glutamate to α-ketoglutarate and ammonia. High activity correlates with nitrogen-rich environments due to protein degradation.'}, {'ecosystem': 'Host-associated:Mammals:Digestive system', 'feature_id': 'IPR007210 * GO:0031460', 'feature_label': 'Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport', 'bio_property': 'osmoprotection*stress response', 'env_property': 'high osmolarity*fluctuating moisture levels', 'confidence': 'high', 'explanation': 'Glycine betaine is a known osmoprotectant in high osmolarity environments, aiding microbial cells in coping with osmotic stress.'}, {'ecosystem': 'Host-associated:Mammals:Digestive system', 'feature_id': 'IPR000036 * GO:0006928', 'feature_label': 'Peptidase A26, omptin * obsolete movement of cell or subcellular component', 'bio_property': 'protein degradation*movement regulation', 'env_property': 'microbial competition*dense microbial communities', 'confidence': 'medium', 'explanation': 'Omptins are proteases that modulate cell surfaces and can play roles in microbial interactions and competition, which is significant in densely populated microbial environments.'}, {'ecosystem': 'Host-associated:Mammals:Digestive system', 'feature_id': 'GO:0016539', 'feature_label': 'intein-mediated protein splicing', 'bio_property': 'post-translational modification*protein processing', 'env_property': 'fluctuating environmental conditions*stress adaptation', 'confidence': 'medium', 'explanation': 'Intein-mediated protein splicing is important for protein maturation processes, which can be critical in environments where adaptive response to stress and fluctuating conditions is necessary.'}, {'ecosystem': 'Host-associated:Mammals:Digestive system', 'feature_id': 'IPR014983', 'feature_label': 'GAD-related', 'bio_property': 'glutamate metabolism*neurotransmitter regulation', 'env_property': 'high protein diet*gut-brain axis', 'confidence': 'high', 'explanation': 'The glutamate decarboxylase (GAD)-related proteins are crucial in the conversion of glutamate to GABA, linking amino acid metabolism to gut-brain interactions and nutrient processing.'}, {'ecosystem': 'Host-associated:Mammals:Digestive system', 'feature_id': 'IPR014580', 'feature_label': 'Uncharacterised conserved protein UCP033199', 'bio_property': 'unknown conservation', 'env_property': 'stable long-term conditions*co-evolution with host', 'confidence': 'medium', 'explanation': 'While its function is unknown, conserved proteins may indicate stable, co-evolved symbiotic relationships within the host environment.'}, {'ecosystem': 'Host-associated:Mammals:Digestive system', 'feature_id': 'IPR021505 * sk__Bacteria;k__;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae', 'feature_label': 'Bacteriophage B3, Orf6 * Prevotellaceae', 'bio_property': 'phage-host interaction*microbial regulation', 'env_property': 'microbiome diversity*phage impact on microbial communities', 'confidence': 'high', 'explanation': 'Bacteriophages like B3 can influence microbial population dynamics, impacting species like Prevotellaceae within the gut microbiome.'}, {'ecosystem': 'Host-associated:Mammals:Digestive system', 'feature_id': 'IPR022380 * IPR019235', 'feature_label': 'Glutamyl-Q tRNA(Asp) synthetase * Protein of unknown function DUF2178, transmembrane', 'bio_property': 'tRNA aminoacylation*transmembrane protein function', 'env_property': 'nutrient absorption*cellular communication', 'confidence': 'high', 'explanation': 'Glutamyl-Q tRNA synthetase and transmembrane proteins are essential for proper functioning of translation processes and nutrient transport across cell membranes in nutrient-rich environments.'}]\n", - "[{'ecosystem': 'Host-associated:Mammals:Digestive system:Fecal', 'feature_id': 'GO:0019512 * IPR004300 * sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae', 'feature_label': 'lactose catabolic process via tagatose-6-phosphate * Glycoside hydrolase family 57, N-terminal domain * Firmicutes clostridia', 'bio_property': 'carbohydrate metabolism*glycoside hydrolase activity*lactose degradation', 'env_property': 'high nutrient availability*presence of lactose', 'confidence': 'high', 'explanation': 'Glycoside hydrolase family 57 enzymes are involved in breaking down polysaccharides, and this process is essential in environments rich in carbohydrates, like the mammalian fecal ecosystem where lactose is present.'}, {'ecosystem': 'Host-associated:Mammals:Digestive system:Fecal', 'feature_id': 'GO:0045151 * IPR000675 * sk__Bacteria;k__;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae', 'feature_label': 'acetoin biosynthetic process * Cutinase/acetylxylan esterase * Bacteroidetes bacteroidia', 'bio_property': 'acetoin production*esterase activity', 'env_property': 'anaerobic conditions*presence of fermentation substrates', 'confidence': 'high', 'explanation': 'Acetoin biosynthesis occurs under anaerobic conditions, common in the gut. The presence of cutinase/acetylxylan esterase hints at the ability to break down complex plant materials.'}, {'ecosystem': 'Host-associated:Mammals:Digestive system:Fecal', 'feature_id': 'IPR007210 * sk__Bacteria;k__;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae', 'feature_label': 'Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * Bacteroidetes bacteroidia', 'bio_property': 'osmoprotection*betaine transport', 'env_property': 'stress conditions*variable osmolarity', 'confidence': 'high', 'explanation': 'Glycine betaine serves as an osmoprotectant, which helps microbes survive in variable osmotic conditions in the gut environment.'}, {'ecosystem': 'Host-associated:Mammals:Digestive system:Fecal', 'feature_id': 'IPR003080 * sk__Bacteria;k__;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae', 'feature_label': 'Glutathione S-transferase, alpha class * Bacteroidetes bacteroidia', 'bio_property': 'detoxification*xenobiotic metabolism', 'env_property': 'presence of xenobiotics*oxidative stress', 'confidence': 'high', 'explanation': 'Glutathione S-transferases play a crucial role in detoxifying harmful compounds, which is important in an environment with dietary toxins and endogenous oxidative stress.'}, {'ecosystem': 'Host-associated:Mammals:Digestive system:Fecal', 'feature_id': 'IPR019646 * sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Subdoligranulum', 'feature_label': \"Aminoglycoside-2''-adenylyltransferase * Firmicutes clostridia\", 'bio_property': 'antibiotic resistance*aminoglycoside modification', 'env_property': 'presence of antibiotics*selective pressure', 'confidence': 'high', 'explanation': \"Aminoglycoside-2''-adenylyltransferase confers resistance to aminoglycoside antibiotics, highlighting selective pressure due to antibiotic exposure in the gut.\"}]\n", - "[{'ecosystem': 'Host-associated:Mammals:Digestive system:Large intestine', 'feature_id': 'IPR010106 * IPR026935', 'feature_label': 'Recombination-promoting nuclease RpnA * Butirosin biosynthesis protein H, N-terminal', 'bio_property': 'DNA double-strand break repair*Antibiotic biosynthesis', 'env_property': 'low oxygen*nutrient rich', 'confidence': 'high', 'explanation': 'In the large intestine, the DNA double-strand break repair system is critical for maintaining genetic stability in an anaerobic (low oxygen) yet nutrient-rich environment, where horizontal gene transfer can also occur. The presence of antibiotic biosynthesis-related proteins suggests an ongoing microbial competition for resources.'}, {'ecosystem': 'Host-associated:Mammals:Digestive system:Large intestine', 'feature_id': 'IPR022225 * IPR021725', 'feature_label': 'Phage tail fibre protein * Pathogenicity locus', 'bio_property': 'Phage infection system*Pathogenesis', 'env_property': 'high microbial diversity*high cell density', 'confidence': 'high', 'explanation': 'The interaction between phage proteins and pathogen-related loci indicates a dynamic environment where bacteriophages may contribute to regulating microbial populations within the high-density and diverse microbial ecosystem of the large intestine.'}, {'ecosystem': 'Host-associated:Mammals:Digestive system:Large intestine', 'feature_id': 'IPR023972 * IPR023812', 'feature_label': 'Conserved hypothetical protein CHP04069, acyl carrier-related * Conserved hypothetical protein CHP04002', 'bio_property': 'Lipid metabolism*conserved microbial functions', 'env_property': 'high organic matter', 'confidence': 'medium', 'explanation': 'Proteins involved in acyl carrier-related functions suggest important roles in lipid metabolism, which is crucial in environments rich in organic matter like the large intestine.'}, {'ecosystem': 'Host-associated:Mammals:Digestive system:Large intestine', 'feature_id': 'IPR024522 * IPR032318 * IPR032480 * IPR032511', 'feature_label': 'Protein of unknown function DUF3789 * Protein of unknown function DUF4848 * Domain of unknown function DUF5057 * Protein of unknown function DUF4971', 'bio_property': 'Uncharacterized microbial functions', 'env_property': 'variable nutrient availability*microbial community stability', 'confidence': 'medium', 'explanation': 'Multiple DUF (domain of unknown function) proteins are likely involved in various uncharacterized but essential processes, which ensure stability and adaptation within the microbial community in the large intestine ecosystem where nutrient availability fluctuates.'}, {'ecosystem': 'Host-associated:Mammals:Digestive system:Large intestine', 'feature_id': 'IPR028049', 'feature_label': 'NTF2 fold immunity protein', 'bio_property': 'Immunity-related processes', 'env_property': 'immune pressure*host-microbe interactions', 'confidence': 'high', 'explanation': 'Proteins with NTF2 fold are often involved in immunity-related processes, which are crucial for microbial survival in the large intestine faced with host immune defenses.'}]\n", - "JSON decode error for result: Expecting value: line 1 column 1 (char 0)\n", - "Content that caused the error: Certainly! Let's dive into the observed features in the Host-associated:Mammals:Digestive system:Large intestine:Fecal ecosystem, their biological properties, and how these properties relate to their environment. Below is the analyzed data in JSON format.\n", - "\n", - "\n", - "{\n", - " \"Host-associated:Mammals:Digestive system:Large intestine:Fecal\": {\n", + "[{'ecosystem': 'Host-associated:Human:Digestive system:Oral', 'feature_id': 'IPR001077 * IPR021447', 'feature_label': 'O-methyltransferase domain * Protein of unknown function DUF3097', 'bio_property': 'methylation*structural function', 'env_property': 'microbiome diversity*nutrient-rich', 'confidence': 'high', 'explanation': 'The presence of the O-methyltransferase domain (involved in methylation processes) alongside proteins with unknown functions (DUF3097) indicates a diverse and complex microbial community with potentially unique metabolic capabilities in an environment like the oral cavity rich in various nutrients.'}, {'ecosystem': 'Host-associated:Human:Digestive system:Oral', 'feature_id': 'IPR008013 * sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Eubacteriaceae;g__Eubacterium;s__Eubacterium_sp._oral_clone_FX028', 'feature_label': 'GATA-type transcription activator, N-terminal * Eubacterium sp. oral clone FX028', 'bio_property': 'transcription regulation*bacterial component', 'env_property': 'microbiome diversity*variable pH', 'confidence': 'high', 'explanation': 'GATA-type transcription activators play a role in regulating gene expression. In presence of Eubacterium species, these regulators can be crucial for adapting to the variable pH conditions of the oral cavity.'}, {'ecosystem': 'Host-associated:Human:Digestive system:Oral', 'feature_id': 'IPR019108 * sk__Archaea;k__;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter;s__Methanobrevibacter_oralis', 'feature_label': 'Cytochrome c oxidase caa3-type, assembly factor CtaG-related * Methanobrevibacter oralis', 'bio_property': 'electron transport chain*archaeal component', 'env_property': 'anoxic microenvironments*nutrient-rich', 'confidence': 'high', 'explanation': 'Cytochrome c oxidase assembly factors are essential for electron transport chains in Methanobrevibacter oralis, indicating adaptation to anoxic niches within the oral cavity, where nutrient availability facilitates diverse metabolic interactions.'}, {'ecosystem': 'Host-associated:Human:Digestive system:Oral', 'feature_id': 'IPR026395 * IPR030985', 'feature_label': 'CshA domain * Putative peptide maturation system protein', 'bio_property': 'RNA helicase activity*peptide processing', 'env_property': 'microbiome diversity*temperature stable', 'confidence': 'medium', 'explanation': 'The CshA domain is associated with RNA helicase activity which is vital for microbial RNA processing. Coupled with peptide maturation systems, it highlights the metabolic complexity and adaptability needed to thrive in the stable temperature conditions of the human oral cavity.'}]\n", + "[{'ecosystem': 'Host-associated:Human:Digestive system:Oral:Saliva', 'feature_id': 'GO:0033920 * IPR004300', 'feature_label': '6-phospho-beta-galactosidase activity * Glycoside hydrolase family 57, N-terminal domain', 'bio_property': 'carbohydrate metabolism*glycoside hydrolase activity', 'env_property': 'nutrient-rich*variable pH*presence of dietary sugars', 'confidence': 'high', 'explanation': 'The activity of 6-phospho-beta-galactosidase and glycoside hydrolase are crucial for the breakdown of dietary sugars in the nutrient-rich and variably pH-fluctuating environment of saliva.'}, {'ecosystem': 'Host-associated:Human:Digestive system:Oral:Saliva', 'feature_id': 'IPR010960 * IPR028049', 'feature_label': 'Flavocytochrome c * NTF2 fold immunity protein', 'bio_property': 'electron transport chain*immune-related functions', 'env_property': 'microbiome diversity*divergent redox conditions', 'confidence': 'medium', 'explanation': 'Flavocytochrome c is involved in the electron transport chain which can vary according to different redox conditions in the oral saliva. The NTF2 fold immunity protein plays a role in the microbial competition within a diverse microbiome.'}, {'ecosystem': 'Host-associated:Human:Digestive system:Oral:Saliva', 'feature_id': 'GO:0004352 * IPR022458', 'feature_label': 'glutamate dehydrogenase (NAD+) activity * Conjugative coupling factor TraG/TraD', 'bio_property': 'amino acid metabolism*DNA transfer and replication', 'env_property': 'inter-organism interactions*high microbial turnover', 'confidence': 'medium', 'explanation': 'Glutamate dehydrogenase activity is indicative of amino acid metabolism that supports microbial growth, whereas conjugative coupling factors like TraG/TraD are critical for horizontal gene transfer in environments with high microbial turnover and diversity.'}, {'ecosystem': 'Host-associated:Human:Digestive system:Oral:Saliva', 'feature_id': 'IPR004868 * IPR011119', 'feature_label': 'DNA-directed DNA polymerase, family B, mitochondria/virus * Uncharacterised domain, helicase/relaxase, putative', 'bio_property': 'DNA replication and repair*helicase activity', 'env_property': 'genomic stability*environmental DNA flux', 'confidence': 'high', 'explanation': 'DNA-directed DNA polymerase and helicase/relaxase activity are essential for maintaining genomic stability and managing the high environmental DNA flux common in the complex oral microbiome.'}, {'ecosystem': 'Host-associated:Human:Digestive system:Oral:Saliva', 'feature_id': 'IPR032576 * IPR028962', 'feature_label': 'Domain of unknown function DUF4921 * Immunity protein 10', 'bio_property': 'protein interaction*immunity functions', 'env_property': 'microbial competition*host immune response', 'confidence': 'medium', 'explanation': 'The prevalence of immunity-related proteins and various protein domains of unknown function suggests adaptation strategies to cope with microbial competition and host immune response in the oral environment.'}, {'ecosystem': 'Host-associated:Human:Digestive system:Oral:Saliva', 'feature_id': 'IPR035576 * IPR021505', 'feature_label': 'Type VI secretion system TssC * Bacteriophage B3, Orf6', 'bio_property': 'bacterial pathogenicity*phage interaction', 'env_property': 'interspecies microbial warfare*dynamic microbial populations', 'confidence': 'high', 'explanation': 'The Type VI secretion system (TssC) and bacteriophage proteins are indicative of interspecies microbial warfare and dynamic microbial population structures typical in the saliva ecosystem.'}, {'ecosystem': 'Host-associated:Human:Digestive system:Oral:Saliva', 'feature_id': 'IPR028962 * IPR015304', 'feature_label': 'Immunity protein 10 * ZinT domain', 'bio_property': 'immune defenses*zinc transport', 'env_property': 'trace metal availability*host-microbe interactions', 'confidence': 'medium', 'explanation': 'Immunity protein and zinc transport-related domains reflect adaptation mechanisms to manage trace metal availability and enhanced host-microbe interactions within the oral environment.'}]\n", + "[{'ecosystem': 'Host-associated:Human:Skin', 'feature_id': 'IPR010706 * GO:0004037 * IPR010945 * IPR010518 * IPR017821', 'feature_label': 'Fatty acid cis-trans isomerase * allantoicase activity * Malate dehydrogenase, type 2 * Flagellar regulatory protein FleQ * Succinate CoA transferase', 'bio_property': 'fatty acid metabolism*allantoate degradation*malate oxidation*flagellar regulation*succinate conversion', 'env_property': 'exposure to UV radiation*presence of fatty acids*need for motility*variable hydration levels', 'confidence': 'high', 'explanation': \"Fatty acid cis-trans isomerase and malate dehydrogenase are involved in fatty acid metabolism and oxidation essential for energy production in fluctuating hydration levels. Flagellar regulatory protein FleQ is important for motility, aiding bacteria to navigate the host skin's complex environment. Succinate CoA transferase is significant for succinate conversion in energy pathways. Allantoate degradation is pertinent due to the breakdown of nitrogenous compounds on skin.\"}, {'ecosystem': 'Host-associated:Human:Skin', 'feature_id': 'IPR000938 * IPR009272 * IPR012706 * IPR022387 * IPR031631', 'feature_label': 'CAP Gly-rich domain * Protein of unknown function DUF929 * Rib/alpha/Esp surface antigen * Carbohydrate ABC transporter substrate-binding, CPR0540 * Glycosyl hydrolase family 63, N-terminal', 'bio_property': 'adhesion*unknown function*antigenic variation*carbohydrate transport*carbohydrate metabolism', 'env_property': 'host immune response*nutrient utilization*microbial community interaction', 'confidence': 'high', 'explanation': 'The CAP Gly-rich domain is crucial for adhesion, aiding microbial persistence in the host habitat. The Rib/alpha/Esp surface antigen participates in immune evasion through antigenic variation. Carbohydrate ABC transporters and glycosyl hydrolases are essential for nutrient acquisition and metabolism on the skin, supporting microbial survival and growth.'}, {'ecosystem': 'Host-associated:Human:Skin', 'feature_id': 'sk__Bacteria;k__;p__Proteobacteria;c__Betaproteobacteria;o__Neisseriales;f__Neisseriaceae;g__Neisseria;s__Neisseria_meningitidis * IPR019949 * IPR032124 * IPR032191 * IPR032193', 'feature_label': 'Neisseria meningitidis * Luciferase family oxidoreductase, group 1 * Bacteriophage F116-like holin * CCR4-NOT transcription complex subunit 1, CAF1-binding domain * CCR4-NOT transcription complex subunit 1, TTP binding domain', 'bio_property': 'pathogenicity*bioluminescence*phage function*transcriptional regulation', 'env_property': 'pathogenic potential*interaction with viruses', 'confidence': 'high', 'explanation': 'Neisseria meningitidis is a known pathogen with the ability to evade host defenses. Luciferase family oxidoreductases contribute to oxidative stress responses. Bacteriophage holins are important for phage cycle regulation, impacting bacterial-viral interactions on the skin. CCR4-NOT transcription complex is involved in transcriptional regulation, crucial for bacterial adaptability in response to environmental stressors.'}, {'ecosystem': 'Host-associated:Human:Skin', 'feature_id': 'IPR014984 * IPR017523 * IPR031636', 'feature_label': 'HopJ type III effector protein * Conserved hypothetical protein CHP03089 * Protein kinase G, tetratricopeptide repeat containing domain', 'bio_property': 'effector function*conserved protein function*phosphorylation signaling', 'env_property': 'bacterial-host interaction*signal transduction', 'confidence': 'medium', 'explanation': 'HopJ type III effector proteins play a role in pathogenicity via manipulation of host processes. Conserved hypothetical proteins suggest essential but unknown functions. Protein kinase G with TPR domains is involved in signal transduction, essential for microbial responses to environmental cues on the skin.'}, {'ecosystem': 'Host-associated:Human:Skin', 'feature_id': 'IPR032576 * IPR021250 * IPR018067', 'feature_label': 'Domain of unknown function DUF4921 * Protein of unknown function DUF2789 * Protein phosphatase 2A regulatory subunit PR55, conserved site', 'bio_property': 'unknown function*regulatory function', 'env_property': 'desiccation resistance*nutrient variability', 'confidence': 'medium', 'explanation': 'While functions of DUF4921 and DUF2789 remain unknown, their presence indicates potential roles in stress response and survival. Protein phosphatase 2A regulatory subunits are involved in regulatory activities, suggesting a response to nutrient variability and environmental stress on the skin.'}]\n", + "[{'ecosystem': 'Host-associated:Human:Skin:Naris', 'feature_id': 'GO:0019317 * GO:0019512 * GO:0033920', 'feature_label': 'fucose catabolic process * lactose catabolic process via tagatose-6-phosphate * 6-phospho-beta-galactosidase activity', 'bio_property': 'carbohydrate metabolism', 'env_property': 'nutrient-rich', 'confidence': 'high', 'explanation': 'The skin has a variety of oligosaccharides and polysaccharides derived from human secretion and microbial sources. These enzymes indicate the presence of catabolic pathways to utilize these complex carbohydrates as nutrient sources.'}, {'ecosystem': 'Host-associated:Human:Skin:Naris', 'feature_id': 'IPR007298 * IPR008557', 'feature_label': 'Copper resistance lipoprotein NlpE * Alkaline phosphatase PhoX', 'bio_property': 'metal ion homeostasis*phosphate metabolism', 'env_property': 'high metal ion concentration*nutrient availability', 'confidence': 'high', 'explanation': 'Copper and phosphate regulation are crucial for microbial survival in the skin environment, which is known to contain various metal ions and nutrient levels from sweat and other secretions.'}, {'ecosystem': 'Host-associated:Human:Skin:Naris', 'feature_id': 'IPR006541 * IPR010133 * IPR019895', 'feature_label': 'Bacteriocin-associated integral membrane protein * Bacteriocin-type signal sequence * Putative bacteriocin export ABC transporter, lactococcin 972 group', 'bio_property': 'bacteriocin production and export', 'env_property': 'competitive microbial environment', 'confidence': 'high', 'explanation': 'Bacteriocins are antimicrobial peptides produced to inhibit the growth of competing bacteria, which is significant in the dense and competitive microbial communities on human skin.'}, {'ecosystem': 'Host-associated:Human:Skin:Naris', 'feature_id': 'GO:0004352 * IPR010945 * IPR017821', 'feature_label': 'glutamate dehydrogenase (NAD+) activity * Malate dehydrogenase, type 2 * Succinate CoA transferase', 'bio_property': 'amino acid metabolism*TCA cycle', 'env_property': 'oxygen availability*metabolic flexibility', 'confidence': 'high', 'explanation': 'These enzymes participate in the TCA cycle and amino acid metabolism which are crucial for energy production and metabolic adaptability in the fluctuating aerobic-anaerobic conditions present on the skin.'}, {'ecosystem': 'Host-associated:Human:Skin:Naris', 'feature_id': 'IPR011868 * IPR018148 * IPR026359', 'feature_label': 'Molybdate ABC transporter, ATP-binding protein * Methylglyoxal synthase, active site * SasC/Mrp/FmtB intercellular aggregation domain', 'bio_property': 'molybdate transport*stress response*cell aggregation', 'env_property': 'trace element presence*cellular stress*biofilm formation', 'confidence': 'high', 'explanation': 'Transport of trace elements like molybdate, stress response mechanisms, and cell aggregation are critical for survival and persistence in the skin ecosystem, which is exposed to environmental stressors and requires microbial aggregation for biofilm formation.'}]\n", + "[{'ecosystem': 'Host-associated:Mammals:Digestive system', 'feature_id': 'GO:0004352 * IPR003563', 'feature_label': 'glutamate dehydrogenase (NAD+) activity * Oxidized purine nucleoside triphosphate', 'bio_property': 'amino acid metabolism*nucleic acid repair', 'env_property': 'nutrient-rich*variable pH', 'confidence': 'high', 'explanation': 'Glutamate dehydrogenase activity is involved in amino acid metabolism, important in nutrient-rich environments like the digestive system where amino acids are abundant. Oxidized purine nucleoside triphosphate repair is significant for maintaining genomic integrity in variable pH conditions.'}, {'ecosystem': 'Host-associated:Mammals:Digestive system', 'feature_id': 'IPR000036 * GO:0006928', 'feature_label': 'Peptidase A26, omptin * obsolete movement of cell or subcellular component', 'bio_property': 'proteolysis*cellular migration', 'env_property': 'dynamic microbial communities*high microbial load', 'confidence': 'high', 'explanation': 'Peptidase A26 is crucial for proteolysis and processing proteins in environments with high microbial interactions. Cellular migration, although obsolete, indicates a dynamic environment with constant microbial movement.'}, {'ecosystem': 'Host-associated:Mammals:Digestive system', 'feature_id': 'IPR007117 * IPR008983', 'feature_label': 'Expansin, cellulose-binding-like domain * Tumour necrosis factor-like domain superfamily', 'bio_property': 'cell wall degradation*immune response modulation', 'env_property': 'high fiber diet*host immune interactions', 'confidence': 'high', 'explanation': \"Expansins play roles in degrading cellulose in high fiber diets. Tumour necrosis factor-like domains suggest interactions with the host's immune system.\"}, {'ecosystem': 'Host-associated:Mammals:Digestive system', 'feature_id': 'IPR012657 * IPR014583', 'feature_label': '23S rRNA-intervening sequence protein * Uncharacterised conserved protein UCP033199', 'bio_property': 'ribosome biogenesis*conserved domain functions', 'env_property': 'complex microbial interactions*optimized protein synthesis', 'confidence': 'medium', 'explanation': 'Ribo-bases are essential for protein synthesis in environments with complex microbial interactions. Conserved proteins may play roles in maintaining essential functions amidst diverse microbial communities.'}, {'ecosystem': 'Host-associated:Mammals:Digestive system', 'feature_id': 'IPR014983 * GO:0017148', 'feature_label': 'GAD-related * negative regulation of translation', 'bio_property': 'glutamate regulation*translational control', 'env_property': 'fluctuating nutrient availability*environmental stress', 'confidence': 'medium', 'explanation': 'GAD-related proteins are involved in glutamate regulation under variable nutrient conditions. Negative regulation of translation responds to environmental stressors.'}, {'ecosystem': 'Host-associated:Mammals:Digestive system', 'feature_id': 'sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae * sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae', 'feature_label': 'Lachnospiraceae * Ruminococcaceae', 'bio_property': 'polysaccharide fermentation*butyrate production', 'env_property': 'high fiber diet*anaerobic conditions', 'confidence': 'high', 'explanation': 'Lachnospiraceae and Ruminococcaceae members are key polysaccharide fermenters producing butyrate in high fiber diets typical of anaerobic environments in the digestive system.'}, {'ecosystem': 'Host-associated:Mammals:Digestive system', 'feature_id': 'IPR024405 * IPR035408', 'feature_label': 'Prophage protein BhlA/UviB * Phage single-stranded DNA-binding protein', 'bio_property': 'phage DNA integration*DNA stabilization', 'env_property': 'high microbial turnover*phage-host interactions', 'confidence': 'high', 'explanation': 'Prophage integrations and DNA-binding proteins are indicative of high microbial turnover rates and frequent phage-host interactions in the digestive system.'}]\n", + "[{'ecosystem': 'Host-associated:Mammals:Digestive system:Fecal', 'feature_id': 'GO:0019512 * IPR004501', 'feature_label': 'lactose catabolic process via tagatose-6-phosphate * Phosphotransferase system, EIIC component, type 3', 'bio_property': 'Carbohydrate metabolism*Lactose degradation', 'env_property': 'high nutrient availability*anaerobic conditions', 'confidence': 'high', 'explanation': 'The lactose catabolic process via tagatose-6-phosphate and Phosphotransferase system EIIC component are involved in carbohydrate metabolism that is essential in the mammalian gut where lactose from diet is metabolized.'}, {'ecosystem': 'Host-associated:Mammals:Digestive system:Fecal', 'feature_id': 'IPR000675 * IPR004300', 'feature_label': 'Cutinase/acetylxylan esterase * Glycoside hydrolase family 57, N-terminal domain', 'bio_property': 'Polysaccharide degradation*Xenobiotic degradation', 'env_property': 'high fiber diet*complex carbohydrate presence', 'confidence': 'high', 'explanation': 'The presence of Cutinase/acetylxylan esterase and Glycoside hydrolase family 57 domains indicates a system specialized in breaking down complex polysaccharides likely derived from a high fiber diet found in fecal matter.'}, {'ecosystem': 'Host-associated:Mammals:Digestive system:Fecal', 'feature_id': 'IPR003080 * IPR010106', 'feature_label': 'Glutathione S-transferase, alpha class * Recombination-promoting nuclease RpnA', 'bio_property': 'Detoxification*DNA repair', 'env_property': 'fluctuating toxicity levels*reactive oxygen species', 'confidence': 'high', 'explanation': 'Glutathione S-transferase, alpha class enzyme, and RpnA provide defense against oxidative stress and DNA damage, vital in environments like the gut where reactive oxygen species and other toxins can be present.'}, {'ecosystem': 'Host-associated:Mammals:Digestive system:Fecal', 'feature_id': 'GO:0045151 * IPR019646', 'feature_label': \"acetoin biosynthetic process * Aminoglycoside-2''-adenylyltransferase\", 'bio_property': 'Fermentation*antibiotic resistance', 'env_property': 'anaerobic conditions*presence of antibiotics', 'confidence': 'high', 'explanation': \"Acetoin biosynthesis is involved in anaerobic fermentation processes in the gut, and Aminoglycoside-2''-adenylyltransferase indicates resistance to antibiotics, reflecting the selective pressures of such compounds in this environment.\"}, {'ecosystem': 'Host-associated:Mammals:Digestive system:Fecal', 'feature_id': 'IPR022339 * GO:0017148', 'feature_label': 'MHC class II-associated invariant chain * negative regulation of translation', 'bio_property': 'Immune modulation*gene expression control', 'env_property': 'immune system interaction*microbial competition', 'confidence': 'medium', 'explanation': 'The MHC class II-associated invariant chain and regulatory translation processes underline the dynamic interaction between the gut microbiota and the host immune system, as well as competitive interactions among microbial species.'}]\n", + "JSON decode error for result: Extra data: line 39 column 1 (char 3075)\n", + "Content that caused the error: {\n", + " \"Host-associated:Mammals:Digestive system:Large intestine\": {\n", " \"1\": {\n", - " \"feature_id\": \"GO:0008740 * IPR004759 * IPR006879\",\n", - " \"feature_label\": \"L-rhamnose isomerase activity * Glutamate:g-aminobutyrate antiporter * Carbohydrate deacetylase YdjC-like\",\n", - " \"bio_property\": \"carbohydrate metabolism * nutrient assimilation * stress response\",\n", - " \"env_property\": \"nutrient rich * acidic pH\",\n", + " \"feature_id\": \"IPR010106 * IPR021725 * IPR022225\",\n", + " \"feature_label\": \"Recombination-promoting nuclease RpnA * Pathogenicity locus * Phage tail fibre protein\",\n", + " \"bio_property\": \"genomic recombination * pathogenicity * viral infection mechanisms\",\n", + " \"env_property\": \"complex microbiome * high bacterial diversity * immune interaction\",\n", " \"confidence\": \"high\",\n", - " \"explanation\": \"These features are involved in carbohydrate metabolism and nutrient assimilation, processes that are crucial in the nutrient-rich but acidic environment of the large intestine.\"\n", + " \"explanation\": \"Recombination-promoting nucleases and pathogenicity loci are often associated with gene transfer and bacterial adaptation in diverse microbial communities, while phage tail fiber proteins are indicative of presence of bacteriophages which interact with host immunity and microbial competition.\"\n", " },\n", " \"2\": {\n", - " \"feature_id\": \"IPR004813 * IPR025479 * GO:0015307\",\n", - " \"feature_label\": \"Oligopeptide transporter, OPT superfamily * Domain of unknown function DUF4329 * obsolete drug:proton antiporter activity\",\n", - " \"bio_property\": \"peptide transport * stress response\",\n", - " \"env_property\": \"high microbial competition * anaerobic condition\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Peptide transport systems help bacteria survive in competitive environments like the gut, where anaerobic conditions prevail.\"\n", + " \"feature_id\": \"IPR014580 * IPR023812 * IPR023972 * IPR024522 * IPR032318 * IPR032480 * IPR032511\",\n", + " \"feature_label\": \"Uncharacterised conserved protein UCP033199 * Conserved hypothetical protein CHP04002 * Conserved hypothetical protein CHP04069, acyl carrier-related * Protein of unknown function DUF3789 * Protein of unknown function DUF4848 * Domain of unknown function DUF5057 * Protein of unknown function DUF4971\",\n", + " \"bio_property\": \"conserved protein functions * potential biosynthetic pathways * unknown cellular roles\",\n", + " \"env_property\": \"complex nutrient interactions * high microbial metabolism\",\n", + " \"confidence\": \"medium\",\n", + " \"explanation\": \"Many conserved and hypothetical proteins suggest the presence of unique or specialized metabolic processes that are not fully understood but are likely to play a role in the high metabolic activity and nutrient processing typical of the large intestine environment.\"\n", " },\n", " \"3\": {\n", - " \"feature_id\": \"IPR007210 * GO:0031460 * IPR016300\",\n", - " \"feature_label\": \"Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * glycine betaine transport * Arsenical pump ATPase, ArsA/GET3\",\n", - " \"bio_property\": \"osmoprotection * detoxification * stress response\",\n", - " \"env_property\": \"high osmolarity * presence of xenobiotics\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Features related to osmoprotection and detoxification indicate adaptation to high osmolarity and presence of harmful substances in the gut.\"\n", - " },\n", - " \"4\": {\n", - " \"feature_id\": \"IPR012706 * IPR018669 * IPR012657\",\n", - " \"feature_label\": \"Rib/alpha/Esp surface antigen * carbohydrate-binding protein * 23S rRNA-intervening sequence protein\",\n", - " \"bio_property\": \"immune system interaction * cellular adhesion\",\n", - " \"env_property\": \"high bacterial load * host immune activity\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Surface antigens and carbohydrate-binding proteins enable microorganisms to interact with the host's immune system and adhere to gut surfaces.\"\n", - " },\n", - " \"5\": {\n", - " \"feature_id\": \"IPR025123 * IPR025399 * IPR025479\",\n", - " \"feature_label\": \"Domain of unknown function DUF4049 * Domain of unknown function DUF4372 * Domain of unknown function DUF4329\",\n", - " \"bio_property\": \"potential regulatory function\",\n", - " \"env_property\": \"variable environmental conditions\",\n", + " \"feature_id\": \"IPR028049\",\n", + " \"feature_label\": \"NTF2 fold immunity protein\",\n", + " \"bio_property\": \"immune response modulation\",\n", + " \"env_property\": \"immune interaction * microbial homeostasis\",\n", " \"confidence\": \"medium\",\n", - " \"explanation\": \"While their exact functions are unknown, domains of unknown function (DUFs) likely serve regulatory roles that allow adaptation to the variable conditions in the gut.\"\n", - " },\n", - " \"6\": {\n", - " \"feature_id\": \"IPR030984 * IPR032507\",\n", - " \"feature_label\": \"Bacterial microcompartment shell protein PduB * GH32, BT1760-like, C-terminal domain\",\n", - " \"bio_property\": \"compartmentalization * polysaccharide degradation\",\n", - " \"env_property\": \"high polysaccharide content\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Bacterial microcompartments and polysaccharide degrading enzymes are crucial for breaking down complex carbohydrates present in the gut.\"\n", + " \"explanation\": \"NTF2 fold immunity proteins are implicated in immune responses, which are crucial in maintaining microbial balance and preventing overgrowth of harmful bacteria in the host-associated gut environment.\"\n", " },\n", - " \"7\": {\n", - " \"feature_id\": \"sk__Bacteria;k__;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae * sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae\",\n", - " \"feature_label\": \"Prevotellaceae * Ruminococcaceae\",\n", - " \"bio_property\": \"cellulose metabolism * short-chain fatty acid production\",\n", - " \"env_property\": \"fiber-rich diet\",\n", + " \"4\": {\n", + " \"feature_id\": \"sk__Bacteria;k__;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae\",\n", + " \"feature_label\": \"Bacterial taxonomy: Firmicutes; Clostridia; Clostridiales; Ruminococcaceae\",\n", + " \"bio_property\": \"fermentation * short-chain fatty acids production\",\n", + " \"env_property\": \"anaerobic conditions * fiber-rich diet\",\n", " \"confidence\": \"high\",\n", - " \"explanation\": \"Prevotellaceae and Ruminococcaceae are known for their capacity to metabolize cellulose and produce short-chain fatty acids, key processes in fiber-rich diets.\"\n", + " \"explanation\": \"The Ruminococcaceae family is well-known for its role in fermenting complex carbohydrates and producing short-chain fatty acids under anaerobic conditions, which are typical properties of the large intestine environment enriched with dietary fibers.\"\n", " }\n", " }\n", "}\n", "\n", "\n", - "### Summary\n", - "\n", - "In the Host-associated:Mammals:Digestive system:Large intestine:Fecal ecosystem, the data show several key relationships between the identified features and the environmental conditions. Features related to carbohydrate metabolism, osmoprotection, detoxification, immune system interaction, and microbial competition are prevalent. These features support the high microbial diversity, high osmolarity, the presence of xenobiotics, and high competition for resources characteristic of the large intestine environment. This curated digest provides comprehensive and reliable associations with a high level of confidence.\n", + "I have compiled and analyzed the relationships between observed microbial metagenomic features and environmental properties specific to the Host-associated:Mammals:Digestive system:Large intestine ecosystem. The focus was on interpreting the implications of these features regarding the biological activities and environmental conditions characteristic of this niche. Each relationship is supported by well-established associations and is presented with a confidence estimation based on the strength of available evidence.\n", "[]\n", - "[{'ecosystem': 'Host-associated:Mammals:Respiratory system', 'feature_id': 'GO:0004144 * IPR006322', 'feature_label': 'diacylglycerol O-acyltransferase activity * Glutathione reductase, eukaryote/bacterial', 'bio_property': 'lipid metabolism*oxidative stress response', 'env_property': 'low oxygen*variable nutrient levels', 'confidence': 'high', 'explanation': 'Diacylglycerol O-acyltransferase is involved in lipid biosynthesis which is crucial in bacteria thriving in nutrient-variable environments like the mammalian respiratory tract. Glutathione reductase plays a key role in protecting cells from oxidative damage, hinting at low oxygen conditions where oxidative stress management is critical.'}, {'ecosystem': 'Host-associated:Mammals:Respiratory system', 'feature_id': 'GO:0019512 * IPR007037', 'feature_label': 'lactose catabolic process via tagatose-6-phosphate * Siderophore-interacting protein, C-terminal domain', 'bio_property': 'carbohydrate metabolism*iron acquisition', 'env_property': 'high nutrient variability*iron limitation', 'confidence': 'high', 'explanation': 'The ability to catabolize lactose via the tagatose-6-phosphate pathway indicates adaptation to utilize diverse carbon sources, a necessity in the variable nutrient conditions of the respiratory tract. Siderophore-interacting proteins are essential for acquiring iron in iron-limited environments, which is a common challenge in host-associated locales.'}, {'ecosystem': 'Host-associated:Mammals:Respiratory system', 'feature_id': 'GO:0045151 * IPR007445', 'feature_label': 'acetoin biosynthetic process * Type IV pilus inner membrane component PilO', 'bio_property': 'secondary metabolite production*cell adhesion', 'env_property': 'mucosal surfaces*host interaction', 'confidence': 'medium', 'explanation': 'Acetoin biosynthesis is part of the metabolic complexity needed for survival in diverse conditions. Type IV pili are essential for bacterial adhesion to host cells and mucosal surfaces, facilitating colonization and persistence in the respiratory system.'}, {'ecosystem': 'Host-associated:Mammals:Respiratory system', 'feature_id': 'IPR007210 * GO:0046797', 'feature_label': 'Glycine betaine/proline betaine transport system ATP-binding protein ProV-like * viral procapsid maturation', 'bio_property': 'osmoprotection*viral assembly', 'env_property': 'high osmolarity*host immune response', 'confidence': 'high', 'explanation': 'The ProV-like protein is associated with compatibility solutes transport that helps in osmoprotection, essential in fluctuating osmolarity conditions. Viral procapsid maturation refers to the assembly stages of viral replication, which are relevant in understanding host-pathogen dynamics and immune evasion strategies in the respiratory system.'}, {'ecosystem': 'Host-associated:Mammals:Respiratory system', 'feature_id': 'IPR012706 * IPR011118', 'feature_label': 'Rib/alpha/Esp surface antigen * Tannase/feruloyl esterase', 'bio_property': 'surface antigens*degradation of complex organic compounds', 'env_property': 'host immune evasion*complex nutrient environment', 'confidence': 'high', 'explanation': 'Surface antigens like Rib/alpha/Esp play roles in immune evasion and modulation, which are crucial for persistence in the respiratory system. Tannase/feruloyl esterase indicates the ability to degrade complex organic compounds, suggesting adaptation to a nutrient-diverse environment.'}]\n", - "[{'ecosystem': 'Host-associated:Plants', 'feature_id': 'GO:0017148 * GO:0042176 * IPR001208 * IPR032191 * IPR032193', 'feature_label': 'negative regulation of translation * regulation of protein catabolic process * MCM domain * CCR4-NOT transcription complex subunit 1, CAF1-binding domain * CCR4-NOT transcription complex subunit 1, TTP binding domain', 'bio_property': 'protein regulation*transcription regulation*protein degradation', 'env_property': 'nutrient variation*biotic stress', 'confidence': 'high', 'explanation': 'Protein and transcription regulation mechanisms, including the CCR4-NOT complex, are crucial adaptations for plants facing fluctuating nutrients and biotic stress from pathogens or symbionts.'}, {'ecosystem': 'Host-associated:Plants', 'feature_id': 'IPR018040', 'feature_label': 'Pectinesterase, Tyr active site', 'bio_property': 'cell wall modification*pectin degradation', 'env_property': 'biotic stress*symbiosis', 'confidence': 'high', 'explanation': 'Pectinesterase enzymes play a key role in modifying plant cell walls, often in response to pathogen attack or during interactions with symbiotic organisms.'}, {'ecosystem': 'Host-associated:Plants', 'feature_id': 'IPR004813', 'feature_label': 'Oligopeptide transporter, OPT superfamily', 'bio_property': 'nutrient uptake*peptide transport', 'env_property': 'nutrient poor', 'confidence': 'high', 'explanation': 'Oligopeptide transporters facilitate the uptake of peptides, a crucial adaptation for plants in nutrient-limited environments to maximize available resources.'}, {'ecosystem': 'Host-associated:Plants', 'feature_id': 'IPR001096 * IPR033126', 'feature_label': 'Peptidase C13, legumain * Glycosyl hydrolases family 9, Asp/Glu active sites', 'bio_property': 'protein degradation*carbohydrate degradation', 'env_property': 'nutrient cycling*decomposition', 'confidence': 'high', 'explanation': 'Peptidases and glycosyl hydrolases are essential for breaking down proteins and carbohydrates, respectively, contributing to nutrient cycling and decomposition in soil associated with plants.'}]\n", - "[{'ecosystem': 'Host-associated:Plants:Phylloplane', 'feature_id': 'GO:0042176 * IPR006652', 'feature_label': 'regulation of protein catabolic process * Kelch repeat type 1', 'bio_property': 'protein degradation*structural protein interactions', 'env_property': 'nutrient limited*exposure to microbial competition', 'confidence': 'high', 'explanation': 'The regulation of protein catabolic processes and Kelch repeat proteins are essential for maintaining protein turnover and structural functions in nutrient-limited environments where efficient resource utilization is critical.'}, {'ecosystem': 'Host-associated:Plants:Phylloplane', 'feature_id': 'IPR000036 * GO:0033890', 'feature_label': 'Peptidase A26, omptin * ribonuclease D activity', 'bio_property': 'protein degradation*RNA processing', 'env_property': 'high microbial diversity*exposure to pathogenic attack', 'confidence': 'high', 'explanation': 'Peptidases and ribonucleases are necessary for breaking down proteins and RNA, respectively, providing a quick response to microbial competition and pathogen attacks in a diverse microbial environment.'}, {'ecosystem': 'Host-associated:Plants:Phylloplane', 'feature_id': 'GO:0003950 * IPR033126', 'feature_label': 'NAD+ ADP-ribosyltransferase activity * Glycosyl hydrolases family 9, Asp/Glu active sites', 'bio_property': 'DNA repair*carbohydrate metabolism', 'env_property': 'exposure to UV light*abundant plant polysaccharides', 'confidence': 'high', 'explanation': 'NAD+ ADP-ribosyltransferase activity is key for DNA repair mechanisms, which is critical in environments exposed to UV light, while glycosyl hydrolases aid in polysaccharide breakdown, prevalent on plant surfaces.'}, {'ecosystem': 'Host-associated:Plants:Phylloplane', 'feature_id': 'IPR033762', 'feature_label': 'MCM OB domain', 'bio_property': 'DNA replication', 'env_property': 'high cellular turnover*exposure to DNA-damaging agents', 'confidence': 'high', 'explanation': 'The MCM OB domain is integral to DNA replication processes, necessary for maintaining genomic stability in environments with high cellular turnover and exposure to DNA-damaging agents.'}]\n", - "JSON decode error for result: Expecting value: line 1 column 1 (char 0)\n", - "Content that caused the error: Sure, let's break this down based on the required analysis for the Host-associated:Plants:Rhizosphere ecosystem in your observed features. \n", - "\n", - "\n", - "{\n", - " \"Host-associated:Plants:Rhizosphere\": {\n", - " \"1\": {\n", - " \"feature_id\": \"IPR000675\",\n", - " \"feature_label\": \"Cutinase/acetylxylan esterase\",\n", - " \"bio_property\": \"cutin degradation * hydrolysis of plant cell wall polymers\",\n", - " \"env_property\": \"nutrient cycling * decomposing plant material\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Cutinases and esterases are crucial for breaking down plant cutin and other polymers, facilitating nutrient cycling and decomposition.\"\n", - " },\n", - " \"2\": {\n", - " \"feature_id\": \"GO:0005871\",\n", - " \"feature_label\": \"kinesin complex\",\n", - " \"bio_property\": \"microtubule-based movement * intracellular transport\",\n", - " \"env_property\": \"soil structure interaction\",\n", - " \"confidence\": \"medium\",\n", - " \"explanation\": \"Kinesin complexes are involved in cellular movement and transport, which could influence interactions within the complex soil matrix.\"\n", - " },\n", - " \"3\": {\n", - " \"feature_id\": \"GO:0006011\",\n", - " \"feature_label\": \"UDP-glucose metabolic process\",\n", - " \"bio_property\": \"carbohydrate metabolism * cell wall biosynthesis\",\n", - " \"env_property\": \"nutrient availability\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"UDP-glucose is a crucial intermediate in carbohydrate metabolism and is important for plant and microbial cell wall biosynthesis, affecting nutrient cycles.\"\n", - " },\n", - " \"4\": {\n", - " \"feature_id\": \"IPR007312\",\n", - " \"feature_label\": \"Phosphoesterase\",\n", - " \"bio_property\": \"nucleotide metabolism * phosphorus cycle\",\n", - " \"env_property\": \"nutrient rich * decomposing organic material\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Phosphoesterases are involved in breaking down phosphoester bonds, playing a key role in phosphorus cycling in environments rich in organic matter.\"\n", - " },\n", - " \"5\": {\n", - " \"feature_id\": \"IPR012727\",\n", - " \"feature_label\": \"Glycine oxidase ThiO\",\n", - " \"bio_property\": \"amino acid metabolism * detoxification\",\n", - " \"env_property\": \"high nitrogen * organic-rich\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Glycine oxidase is involved in amino acid metabolism and detoxification processes, which are significant in nitrogen-rich, organic-rich environments.\"\n", - " },\n", - " \"6\": {\n", - " \"feature_id\": \"IPR004300\",\n", - " \"feature_label\": \"Glycoside hydrolase family 57, N-terminal domain\",\n", - " \"bio_property\": \"polysaccharide degradation * metabolic flexibility\",\n", - " \"env_property\": \"plant root vicinity * decomposing cellulose/hemicellulose\",\n", - " \"confidence\": \"high\",\n", - " \"explanation\": \"Glycoside hydrolases degrade complex polysaccharides like cellulose and hemicellulose, which are abundant near plant roots and decomposing organic matter.\"\n", - " },\n", - " \"7\": {\n", - " \"feature_id\": \"sk__Bacteria;k__;p__Verrucomicrobia;c__Spartobacteria;o__Chthoniobacterales;f__Chthoniobacteraceae;g__Candidatus_Udaeobacter\",\n", - " \"feature_label\": \"Candidatus_Udaeobacter (Verrucomicrobia)\",\n", - " \"bio_property\": \"soil bacterial community * organic matter breakdown\",\n", - " \"env_property\": \"decomposing organic matter * rhizosphere\",\n", - " \"confidence\": \"medium\",\n", - " \"explanation\": \"Candidatus_Udaeobacter is part of soil bacterial communities known for breaking down organic matter, which is essential for nutrient cycling in the rhizosphere.\"\n", - " }\n", + "[{'ecosystem': 'Host-associated:Mammals:Digestive system:Large intestine:Fecal', 'feature_id': 'GO:0008740 * IPR004759 * IPR026419', 'feature_label': 'L-rhamnose isomerase activity * Glutamate:g-aminobutyrate antiporter * Glycosyltransferase, GG-Bacteroidales peptide system', 'bio_property': 'carbohydrate metabolism*amino acid metabolism*glycosylation', 'env_property': 'nutrient-rich*anaerobic', 'confidence': 'high', 'explanation': 'The large intestine is rich in diverse carbohydrates which require specific enzymes for their metabolism. These microbial features support the digestion and absorption of diverse nutrients in an anaerobic environment.'}, {'ecosystem': 'Host-associated:Mammals:Digestive system:Large intestine:Fecal', 'feature_id': 'IPR004813 * IPR008016 * IPR030984', 'feature_label': 'Oligopeptide transporter, OPT superfamily * Portal protein Gp10 * Bacterial microcompartment shell protein PduB', 'bio_property': 'peptide transport*viral assembly*microcompartment formation', 'env_property': 'host-associated*high bacterial density', 'confidence': 'high', 'explanation': 'These features highlight the complex roles of transport systems, bacterial microcompartments, and interactions with bacteriophages in a densely populated gut environment.'}, {'ecosystem': 'Host-associated:Mammals:Digestive system:Large intestine:Fecal', 'feature_id': 'IPR006879 * IPR009677 * IPR032830', 'feature_label': 'Carbohydrate deacetylase YdjC-like * Protein of unknown function DUF1266 * Helicase XPB/Ssl2, N-terminal domain', 'bio_property': 'carbohydrate processing*protein function unknown*DNA repair', 'env_property': 'biotic interactions*chemical signal processing', 'confidence': 'high', 'explanation': 'Carbohydrate deacetylases and helicases play essential roles in processing and modifying polysaccharides and DNA, vital in the microbe-rich and chemically dynamic environment of the large intestine.'}, {'ecosystem': 'Host-associated:Mammals:Digestive system:Large intestine:Fecal', 'feature_id': 'GO:0005871 * GO:0015307 * IPR031636', 'feature_label': 'kinesin complex * obsolete drug:proton antiporter activity * Protein kinase G, tetratricopeptide repeat containing domain', 'bio_property': 'cellular transport*ion transport*protein phosphorylation', 'env_property': 'fluid-dynamic conditions*chemical gradients', 'confidence': 'high', 'explanation': 'Kinesin complexes and antiporters are crucial for maintaining cellular and ionic balance, driven by the dynamic fluid environment and chemical gradients in the gut.'}]\n", + "[{'ecosystem': 'Host-associated:Mammals:Respiratory system', 'feature_id': 'GO:0004144 * IPR007037 * IPR007445', 'feature_label': 'diacylglycerol O-acyltransferase activity * Siderophore-interacting protein, C-terminal domain * Type IV pilus inner membrane component PilO', 'bio_property': 'lipid metabolism*iron acquisition*bacterial adhesion', 'env_property': 'mucosal surfaces*competitive microenvironment*host immune interactions', 'confidence': 'high', 'explanation': 'Diacylglycerol O-acyltransferase is involved in lipid metabolism crucial for microbial energy storage and membrane fluidity. Siderophore-interacting proteins mediate iron acquisition, critical in the iron-limited environments of respiratory mucosa. Type IV pili are implicated in bacterial adhesion to mucosal surfaces, aiding colonization in the competitive and immune-challenging respiratory tract.'}, {'ecosystem': 'Host-associated:Mammals:Respiratory system', 'feature_id': 'GO:0019512 * IPR011118 * IPR004624', 'feature_label': 'lactose catabolic process via tagatose-6-phosphate * Tannase/feruloyl esterase * Protein YjdM', 'bio_property': 'carbohydrate metabolism*aromatic compound degradation*protein function unknown', 'env_property': 'mucosal surfaces*presence of host sugars*variable nutrient availability', 'confidence': 'medium', 'explanation': 'The lactose catabolic process facilitates utilization of host-derived sugars, crucial for microbial survival in mucosa. Tannase/feruloyl esterase degrades aromatic compounds, potentially sourced from dietary elements. Protein YjdM functionality remains unclear but may play a regulatory or structural role in such an environment.'}, {'ecosystem': 'Host-associated:Mammals:Respiratory system', 'feature_id': 'GO:0046797 * IPR032124 * IPR014984', 'feature_label': 'viral procapsid maturation * Bacteriophage F116-like holin * HopJ type III effector protein', 'bio_property': 'viral replication*bacteriophage function*immune system evasion', 'env_property': 'host-virus interaction*microbial ecosystem dynamics*immune evasion', 'confidence': 'high', 'explanation': 'Viral procapsid maturation is critical for virus assembly within host cells. Bacteriophage-associated holins regulate host cell lysis, influencing bacterial population dynamics. Type III effector proteins enable bacteria to manipulate host immune responses, vital for survival within the immune-active respiratory tract.'}, {'ecosystem': 'Host-associated:Mammals:Respiratory system', 'feature_id': 'IPR007920 * IPR021250 * IPR021361 * IPR023845', 'feature_label': 'Protein of unknown function UPF0223 * Protein of unknown function DUF2789 * Protein of unknown function DUF2829 * Domain of unknown function DUF3817, transmembrane', 'bio_property': 'unknown protein functions*potential structural roles*possible regulatory functions', 'env_property': 'highly dynamic*host-derived nutrient conditions*microbial competition', 'confidence': 'medium', 'explanation': 'These proteins of unknown function likely contribute to structural, regulatory, or adaptive responses essential for survival and competition within the respiratory tract’s dynamic and nutrient-variable environment.'}]\n", + "JSON decode error for result: Extra data: line 47 column 1 (char 3147)\n", + "Content that caused the error: {\n", + " \"Host-associated:Plants\": {\n", + " \"1\": {\n", + " \"feature_id\": \"IPR018040 * IPR033126\",\n", + " \"feature_label\": \"Pectinesterase, Tyr active site * Glycosyl hydrolases family 9, Asp/Glu active sites\",\n", + " \"bio_property\": \"polysaccharide degradation * cell wall modification * carbohydrate metabolism\",\n", + " \"env_property\": \"rich in plant cell wall materials * varied carbohydrate availability\",\n", + " \"confidence\": \"high\",\n", + " \"explanation\": \"Pectinesterase and Glycosyl hydrolases are involved in the degradation and modification of plant cell wall components, commonly found in plant-associated environments.\"\n", + " },\n", + " \"2\": {\n", + " \"feature_id\": \"IPR000477 * IPR004264\",\n", + " \"feature_label\": \"Reverse transcriptase domain * Transposase, Tnp1/En/Spm-like\",\n", + " \"bio_property\": \"genetic element mobility * genome maintenance * DNA recombination\",\n", + " \"env_property\": \"dynamic genomic environment * presence of mobile genetic elements\",\n", + " \"confidence\": \"high\",\n", + " \"explanation\": \"Reverse transcriptase and Transposase domains are associated with the mobility of genetic elements, which is crucial in dynamic plant-associated environments where genetic adaptations can be advantageous.\"\n", + " },\n", + " \"3\": {\n", + " \"feature_id\": \"GO:0017148 * GO:0042176\",\n", + " \"feature_label\": \"negative regulation of translation * regulation of protein catabolic process\",\n", + " \"bio_property\": \"protein homeostasis * stress response * cellular regulation\",\n", + " \"env_property\": \"variable nutrient conditions * fluctuating environmental stressors\",\n", + " \"confidence\": \"medium\",\n", + " \"explanation\": \"Regulatory processes like the negative regulation of translation and protein catabolism are important in maintaining cellular homeostasis under variable nutrient conditions and environmental stress commonly encountered in plant-associated environments.\"\n", + " },\n", + " \"4\": {\n", + " \"feature_id\": \"IPR001096 * IPR032191\",\n", + " \"feature_label\": \"Peptidase C13, legumain * CCR4-NOT transcription complex subunit 1, CAF1-binding domain\",\n", + " \"bio_property\": \"protein degradation * mRNA regulation * post-transcriptional modification\",\n", + " \"env_property\": \"nutrient cycling * high symbiotic activity\",\n", + " \"confidence\": \"medium\",\n", + " \"explanation\": \"Enzymes like Peptidase legumain and components of the CCR4-NOT complex are involved in protein degradation and mRNA regulation, which are key in nutrient cycling and maintaining symbiotic interactions in plant-associated environments.\"\n", + " },\n", + " \"5\": {\n", + " \"feature_id\": \"IPR001320 * IPR004813\",\n", + " \"feature_label\": \"Ionotropic glutamate receptor, C-terminal * Oligopeptide transporter, OPT superfamily\",\n", + " \"bio_property\": \"signal transduction * nutrient uptake * intercellular communication\",\n", + " \"env_property\": \"rich in signaling molecules * diverse nutrient availability\",\n", + " \"confidence\": \"high\",\n", + " \"explanation\": \"Ionotropic glutamate receptors and oligopeptide transporters play roles in signal transduction and nutrient uptake, which are essential in environments rich in signaling molecules and diverse nutrients, typical of plant-associated ecosystems.\"\n", " }\n", + " }\n", "}\n", "\n", "\n", - "This JSON structure provides an exhaustive summary linking observed microbial metagenomic features to biological properties and relevant environmental properties with varying levels of confidence. These associations form a foundational understanding of the interactions within the rhizosphere ecosystem, aiding in further environmental and ecological studies.\n", - "[]\n" + "**Explanation**:\n", + "- The selected features and their subsets were chosen based on their biological properties and relevance to the plant-associated environment.\n", + "- The relationships between features and environmental properties were inferred based on known functions of the features and characteristics of plant-associated ecosystems.\n", + "- Only medium to high confidence associations were reported, ensuring reliability.\n", + "- This JSON structure groups the features by their shared biological and environmental properties, providing a thorough and exhaustive list of reliable relationships.\n", + "[]\n", + "[{'ecosystem': 'Host-associated:Plants:Phylloplane', 'feature_id': 'GO:0003950 * IPR033126', 'feature_label': 'NAD+ ADP-ribosyltransferase activity * Glycosyl hydrolases family 9, Asp/Glu active sites', 'bio_property': 'post-translational modification*carbohydrate metabolism', 'env_property': 'high nutrient availability*complex organic matter', 'confidence': 'high', 'explanation': 'The NAD+ ADP-ribosyltransferase activity relates to post-translational modifications, which are critical for regulating intracellular processes in a nutrient-rich environment like the phylloplane. Glycosyl hydrolases are involved in breaking down complex carbohydrates, indicating the presence of diverse organic matter on plant surfaces.'}, {'ecosystem': 'Host-associated:Plants:Phylloplane', 'feature_id': 'GO:0033890 * IPR000036', 'feature_label': 'ribonuclease D activity * Peptidase A26, omptin', 'bio_property': 'RNA processing*protein degradation', 'env_property': 'microbial community complexity*organic matter turnover', 'confidence': 'high', 'explanation': 'Ribonuclease D is involved in RNA processing, suggesting active turnover of genetic material, complemented by Omptin peptidases which degrade proteins, both pointing to high microbial community dynamics and organic matter turnover in the phylloplane.'}, {'ecosystem': 'Host-associated:Plants:Phylloplane', 'feature_id': 'GO:0042176 * IPR033762', 'feature_label': 'regulation of protein catabolic process * MCM OB domain', 'bio_property': 'protein catabolism regulation*DNA replication initiation', 'env_property': 'stress adaptation*dynamic microenvironment', 'confidence': 'high', 'explanation': 'The regulation of protein catabolic process is crucial for managing cellular stress, while MCM OB domains are key in DNA replication initiation, indicating adaptation to environmental stress and a dynamic microenvironment on the plant surface.'}, {'ecosystem': 'Host-associated:Plants:Phylloplane', 'feature_id': 'IPR006652 * IPR019060', 'feature_label': 'Kelch repeat type 1 * Domain of unknown function DUF2382', 'bio_property': 'protein-protein interactions*unknown', 'env_property': 'complex microbial interactions*potential novel functionalities', 'confidence': 'medium', 'explanation': \"Kelch repeats are involved in protein-protein interactions, suggesting complex microbial interactions within the phylloplane. The DUF2382 domain's unknown function highlights potential novel functionalities adapted to this environment.\"}]\n", + "[{'ecosystem': 'Host-associated:Plants:Rhizosphere', 'feature_id': 'GO:0005871 * GO:0006011 * GO:0019068', 'feature_label': 'kinesin complex * UDP-glucose metabolic process * virion assembly', 'bio_property': 'microbial motility complex*carbohydrate metabolism*virus lifecycle', 'env_property': 'nutrient-rich*high microbial diversity', 'confidence': 'high', 'explanation': 'The kinesin complex is vital for intracellular transport, including in plant root interactions. UDP-glucose metabolism fuels various biosynthetic processes that are crucial in a nutrient-rich rhizosphere. Virion assembly indicates the potential for viral interactions within a diverse microbial community.'}, {'ecosystem': 'Host-associated:Plants:Rhizosphere', 'feature_id': 'IPR000675 * IPR007941 * IPR012727', 'feature_label': 'Cutinase/acetylxylan esterase * Protein of unknown function DUF726 * Glycine oxidase ThiO', 'bio_property': 'plant polymer degradation*unknown protein function*amino acid metabolism', 'env_property': 'organic matter-rich*nitrogen cycling', 'confidence': 'high', 'explanation': 'Cutinase and acetylxylan esterase are essential for breaking down plant polymers, crucial in rhizospheres rich in organic matter from root exudates. Glycine oxidase participates in nitrogen cycling by degrading glycine.'}, {'ecosystem': 'Host-associated:Plants:Rhizosphere', 'feature_id': 'IPR001320 * IPR004264 * IPR007312', 'feature_label': 'Ionotropic glutamate receptor, C-terminal * Transposase, Tnp1/En/Spm-like * Phosphoesterase', 'bio_property': 'neurotransmitter-like signaling*genetic element mobility*phosphate metabolism', 'env_property': 'microbe-plant signaling*high horizontal gene transfer*phosphorus availability', 'confidence': 'high', 'explanation': 'Ionotropic glutamate receptors, akin to plant signaling molecules, play a role in microbe-plant interactions. Transposases reflect high genetic mobility, common in microbe-rich environments like the rhizosphere. Phosphoesterase activity is related to phosphorus cycling, essential in soil ecosystems.'}, {'ecosystem': 'Host-associated:Plants:Rhizosphere', 'feature_id': 'IPR004300 * IPR014983 * IPR017523', 'feature_label': 'Glycoside hydrolase family 57, N-terminal domain * GAD-related * Conserved hypothetical protein CHP03089', 'bio_property': 'polysaccharide breakdown*putative decarboxylase activity*uncharacterized but conserved function', 'env_property': 'carbohydrate-rich*multiple nutrient cycles', 'confidence': 'medium', 'explanation': 'Glycoside hydrolases break down polysaccharides, pivotal in a carbohydrate-rich rhizosphere. GAD-related proteins may be involved in amino acid metabolism, contributing to nutrient cycling. Conserved hypothetical proteins often have key ecological roles despite unknown specific functions.'}, {'ecosystem': 'Host-associated:Plants:Rhizosphere', 'feature_id': 'IPR028962 * sk__Bacteria;k__;p__Verrucomicrobia;c__Spartobacteria;o__Chthoniobacterales;f__Chthoniobacteraceae;g__Candidatus_Udaeobacter', 'feature_label': 'Immunity protein 10 * Candidatus_Udaeobacter', 'bio_property': 'microbial defense mechanisms*actinobacterium association', 'env_property': 'pathogen-rich*microbe-microbe interactions', 'confidence': 'medium', 'explanation': 'Immunity protein 10 suggests microbial defense in pathogen-rich environments, common in the rhizosphere. Candidatus_Udaeobacter, part of Verrucomicrobia, indicates specific microbial associations beneficial to plant roots.'}]\n" ] }, { @@ -7702,53 +7122,53 @@ " \n", " \n", " 0\n", - " Engineered:Bioremediation:Terephthalate:Wastew...\n", - " GO:0004114 * IPR004501\n", - " 3',5'-cyclic-nucleotide phosphodiesterase acti...\n", - " signal transduction*sugar transport\n", - " high organic load*nutrient dense\n", + " Engineered:Bioreactor\n", + " GO:0018551 * IPR005126\n", + " dissimilatory sulfite reductase activity * Nap...\n", + " anaerobic respiration*sulfur metabolism\n", + " anoxic*sulfur-rich\n", " high\n", - " Systems involved in signal transduction and su...\n", + " Dissimilatory sulfite reductase and associated...\n", " \n", " \n", " 1\n", - " Engineered:Bioremediation:Terephthalate:Wastew...\n", - " GO:0008901 * IPR010960\n", - " ferredoxin hydrogenase activity * Flavocytochr...\n", - " electron transport chain*anaerobic respiration\n", - " oxygen-limited*high organic load\n", + " Engineered:Bioreactor\n", + " GO:0031460 * IPR004763\n", + " glycine betaine transport * Cation efflux syst...\n", + " osmoprotection*ion transport\n", + " osmotic stress*metal-rich\n", " high\n", - " Ferredoxin hydrogenase and Flavocytochrome c a...\n", + " Glycine betaine transport and cation efflux sy...\n", " \n", " \n", " 2\n", - " Engineered:Bioremediation:Terephthalate:Wastew...\n", - " GO:0019512 * IPR004300\n", - " lactose catabolic process via tagatose-6-phosp...\n", - " lactose metabolism*carbohydrate degradation\n", - " high organic load*carbohydrate-rich conditions\n", - " high\n", - " These features are involved in carbohydrate me...\n", + " Engineered:Bioreactor\n", + " IPR007117 * IPR011868\n", + " Expansin, cellulose-binding-like domain * Moly...\n", + " cell wall modification*molybdenum transport\n", + " organic-rich*high molybdate availability\n", + " medium\n", + " The presence of expansin for cell wall modific...\n", " \n", " \n", " 3\n", - " Engineered:Bioremediation:Terephthalate:Wastew...\n", - " GO:0004037 * IPR017813\n", - " allantoicase activity * Mycothiol acetyltransf...\n", - " amino acid metabolism*detoxification\n", - " nutrient dense*potentially toxin-rich\n", + " Engineered:Bioreactor\n", + " IPR016300 * IPR019949\n", + " Arsenical pump ATPase, ArsA/GET3 * Luciferase ...\n", + " arsenic resistance*oxidative stress response\n", + " toxic metal contamination*high oxidative stress\n", " medium\n", - " Enzymes involved in amino acid metabolism and ...\n", + " Arsenical pump ATPase and luciferase family ox...\n", " \n", " \n", " 4\n", - " Engineered:Bioremediation:Terephthalate:Wastew...\n", - " IPR014580 * IPR014984\n", - " Uncharacterised conserved protein UCP033199 * ...\n", - " unknown function*pathogenicity\n", - " diverse microbial community*complex interactions\n", + " Engineered:Bioreactor\n", + " GO:0008743 * IPR001360\n", + " L-threonine 3-dehydrogenase activity * Glycosi...\n", + " amino acid metabolism*carbohydrate degradation\n", + " nutrient cycling*high organic load\n", " medium\n", - " Presence of pathogenicity-related proteins ind...\n", + " L-threonine 3-dehydrogenase and glycoside hydr...\n", " \n", " \n", " ...\n", @@ -7761,143 +7181,143 @@ " ...\n", " \n", " \n", - " 131\n", - " Host-associated:Plants\n", - " IPR001096 * IPR033126\n", - " Peptidase C13, legumain * Glycosyl hydrolases ...\n", - " protein degradation*carbohydrate degradation\n", - " nutrient cycling*decomposition\n", + " 147\n", + " Host-associated:Plants:Rhizosphere\n", + " GO:0005871 * GO:0006011 * GO:0019068\n", + " kinesin complex * UDP-glucose metabolic proces...\n", + " microbial motility complex*carbohydrate metabo...\n", + " nutrient-rich*high microbial diversity\n", " high\n", - " Peptidases and glycosyl hydrolases are essenti...\n", + " The kinesin complex is vital for intracellular...\n", " \n", " \n", - " 132\n", - " Host-associated:Plants:Phylloplane\n", - " GO:0042176 * IPR006652\n", - " regulation of protein catabolic process * Kelc...\n", - " protein degradation*structural protein interac...\n", - " nutrient limited*exposure to microbial competi...\n", + " 148\n", + " Host-associated:Plants:Rhizosphere\n", + " IPR000675 * IPR007941 * IPR012727\n", + " Cutinase/acetylxylan esterase * Protein of unk...\n", + " plant polymer degradation*unknown protein func...\n", + " organic matter-rich*nitrogen cycling\n", " high\n", - " The regulation of protein catabolic processes ...\n", + " Cutinase and acetylxylan esterase are essentia...\n", " \n", " \n", - " 133\n", - " Host-associated:Plants:Phylloplane\n", - " IPR000036 * GO:0033890\n", - " Peptidase A26, omptin * ribonuclease D activity\n", - " protein degradation*RNA processing\n", - " high microbial diversity*exposure to pathogeni...\n", + " 149\n", + " Host-associated:Plants:Rhizosphere\n", + " IPR001320 * IPR004264 * IPR007312\n", + " Ionotropic glutamate receptor, C-terminal * Tr...\n", + " neurotransmitter-like signaling*genetic elemen...\n", + " microbe-plant signaling*high horizontal gene t...\n", " high\n", - " Peptidases and ribonucleases are necessary for...\n", + " Ionotropic glutamate receptors, akin to plant ...\n", " \n", " \n", - " 134\n", - " Host-associated:Plants:Phylloplane\n", - " GO:0003950 * IPR033126\n", - " NAD+ ADP-ribosyltransferase activity * Glycosy...\n", - " DNA repair*carbohydrate metabolism\n", - " exposure to UV light*abundant plant polysaccha...\n", - " high\n", - " NAD+ ADP-ribosyltransferase activity is key fo...\n", + " 150\n", + " Host-associated:Plants:Rhizosphere\n", + " IPR004300 * IPR014983 * IPR017523\n", + " Glycoside hydrolase family 57, N-terminal doma...\n", + " polysaccharide breakdown*putative decarboxylas...\n", + " carbohydrate-rich*multiple nutrient cycles\n", + " medium\n", + " Glycoside hydrolases break down polysaccharide...\n", " \n", " \n", - " 135\n", - " Host-associated:Plants:Phylloplane\n", - " IPR033762\n", - " MCM OB domain\n", - " DNA replication\n", - " high cellular turnover*exposure to DNA-damagin...\n", - " high\n", - " The MCM OB domain is integral to DNA replicati...\n", + " 151\n", + " Host-associated:Plants:Rhizosphere\n", + " IPR028962 * sk__Bacteria;k__;p__Verrucomicrobi...\n", + " Immunity protein 10 * Candidatus_Udaeobacter\n", + " microbial defense mechanisms*actinobacterium a...\n", + " pathogen-rich*microbe-microbe interactions\n", + " medium\n", + " Immunity protein 10 suggests microbial defense...\n", " \n", " \n", "\n", - "

136 rows × 7 columns

\n", + "

152 rows × 7 columns

\n", "" ], "text/plain": [ - " ecosystem \\\n", - "0 Engineered:Bioremediation:Terephthalate:Wastew... \n", - "1 Engineered:Bioremediation:Terephthalate:Wastew... \n", - "2 Engineered:Bioremediation:Terephthalate:Wastew... \n", - "3 Engineered:Bioremediation:Terephthalate:Wastew... \n", - "4 Engineered:Bioremediation:Terephthalate:Wastew... \n", - ".. ... \n", - "131 Host-associated:Plants \n", - "132 Host-associated:Plants:Phylloplane \n", - "133 Host-associated:Plants:Phylloplane \n", - "134 Host-associated:Plants:Phylloplane \n", - "135 Host-associated:Plants:Phylloplane \n", + " ecosystem \\\n", + "0 Engineered:Bioreactor \n", + "1 Engineered:Bioreactor \n", + "2 Engineered:Bioreactor \n", + "3 Engineered:Bioreactor \n", + "4 Engineered:Bioreactor \n", + ".. ... \n", + "147 Host-associated:Plants:Rhizosphere \n", + "148 Host-associated:Plants:Rhizosphere \n", + "149 Host-associated:Plants:Rhizosphere \n", + "150 Host-associated:Plants:Rhizosphere \n", + "151 Host-associated:Plants:Rhizosphere \n", "\n", - " feature_id \\\n", - "0 GO:0004114 * IPR004501 \n", - "1 GO:0008901 * IPR010960 \n", - "2 GO:0019512 * IPR004300 \n", - "3 GO:0004037 * IPR017813 \n", - "4 IPR014580 * IPR014984 \n", - ".. ... \n", - "131 IPR001096 * IPR033126 \n", - "132 GO:0042176 * IPR006652 \n", - "133 IPR000036 * GO:0033890 \n", - "134 GO:0003950 * IPR033126 \n", - "135 IPR033762 \n", + " feature_id \\\n", + "0 GO:0018551 * IPR005126 \n", + "1 GO:0031460 * IPR004763 \n", + "2 IPR007117 * IPR011868 \n", + "3 IPR016300 * IPR019949 \n", + "4 GO:0008743 * IPR001360 \n", + ".. ... \n", + "147 GO:0005871 * GO:0006011 * GO:0019068 \n", + "148 IPR000675 * IPR007941 * IPR012727 \n", + "149 IPR001320 * IPR004264 * IPR007312 \n", + "150 IPR004300 * IPR014983 * IPR017523 \n", + "151 IPR028962 * sk__Bacteria;k__;p__Verrucomicrobi... \n", "\n", " feature_label \\\n", - "0 3',5'-cyclic-nucleotide phosphodiesterase acti... \n", - "1 ferredoxin hydrogenase activity * Flavocytochr... \n", - "2 lactose catabolic process via tagatose-6-phosp... \n", - "3 allantoicase activity * Mycothiol acetyltransf... \n", - "4 Uncharacterised conserved protein UCP033199 * ... \n", + "0 dissimilatory sulfite reductase activity * Nap... \n", + "1 glycine betaine transport * Cation efflux syst... \n", + "2 Expansin, cellulose-binding-like domain * Moly... \n", + "3 Arsenical pump ATPase, ArsA/GET3 * Luciferase ... \n", + "4 L-threonine 3-dehydrogenase activity * Glycosi... \n", ".. ... \n", - "131 Peptidase C13, legumain * Glycosyl hydrolases ... \n", - "132 regulation of protein catabolic process * Kelc... \n", - "133 Peptidase A26, omptin * ribonuclease D activity \n", - "134 NAD+ ADP-ribosyltransferase activity * Glycosy... \n", - "135 MCM OB domain \n", + "147 kinesin complex * UDP-glucose metabolic proces... \n", + "148 Cutinase/acetylxylan esterase * Protein of unk... \n", + "149 Ionotropic glutamate receptor, C-terminal * Tr... \n", + "150 Glycoside hydrolase family 57, N-terminal doma... \n", + "151 Immunity protein 10 * Candidatus_Udaeobacter \n", "\n", " bio_property \\\n", - "0 signal transduction*sugar transport \n", - "1 electron transport chain*anaerobic respiration \n", - "2 lactose metabolism*carbohydrate degradation \n", - "3 amino acid metabolism*detoxification \n", - "4 unknown function*pathogenicity \n", + "0 anaerobic respiration*sulfur metabolism \n", + "1 osmoprotection*ion transport \n", + "2 cell wall modification*molybdenum transport \n", + "3 arsenic resistance*oxidative stress response \n", + "4 amino acid metabolism*carbohydrate degradation \n", ".. ... \n", - "131 protein degradation*carbohydrate degradation \n", - "132 protein degradation*structural protein interac... \n", - "133 protein degradation*RNA processing \n", - "134 DNA repair*carbohydrate metabolism \n", - "135 DNA replication \n", + "147 microbial motility complex*carbohydrate metabo... \n", + "148 plant polymer degradation*unknown protein func... \n", + "149 neurotransmitter-like signaling*genetic elemen... \n", + "150 polysaccharide breakdown*putative decarboxylas... \n", + "151 microbial defense mechanisms*actinobacterium a... \n", "\n", " env_property confidence \\\n", - "0 high organic load*nutrient dense high \n", - "1 oxygen-limited*high organic load high \n", - "2 high organic load*carbohydrate-rich conditions high \n", - "3 nutrient dense*potentially toxin-rich medium \n", - "4 diverse microbial community*complex interactions medium \n", + "0 anoxic*sulfur-rich high \n", + "1 osmotic stress*metal-rich high \n", + "2 organic-rich*high molybdate availability medium \n", + "3 toxic metal contamination*high oxidative stress medium \n", + "4 nutrient cycling*high organic load medium \n", ".. ... ... \n", - "131 nutrient cycling*decomposition high \n", - "132 nutrient limited*exposure to microbial competi... high \n", - "133 high microbial diversity*exposure to pathogeni... high \n", - "134 exposure to UV light*abundant plant polysaccha... high \n", - "135 high cellular turnover*exposure to DNA-damagin... high \n", + "147 nutrient-rich*high microbial diversity high \n", + "148 organic matter-rich*nitrogen cycling high \n", + "149 microbe-plant signaling*high horizontal gene t... high \n", + "150 carbohydrate-rich*multiple nutrient cycles medium \n", + "151 pathogen-rich*microbe-microbe interactions medium \n", "\n", " explanation \n", - "0 Systems involved in signal transduction and su... \n", - "1 Ferredoxin hydrogenase and Flavocytochrome c a... \n", - "2 These features are involved in carbohydrate me... \n", - "3 Enzymes involved in amino acid metabolism and ... \n", - "4 Presence of pathogenicity-related proteins ind... \n", + "0 Dissimilatory sulfite reductase and associated... \n", + "1 Glycine betaine transport and cation efflux sy... \n", + "2 The presence of expansin for cell wall modific... \n", + "3 Arsenical pump ATPase and luciferase family ox... \n", + "4 L-threonine 3-dehydrogenase and glycoside hydr... \n", ".. ... \n", - "131 Peptidases and glycosyl hydrolases are essenti... \n", - "132 The regulation of protein catabolic processes ... \n", - "133 Peptidases and ribonucleases are necessary for... \n", - "134 NAD+ ADP-ribosyltransferase activity is key fo... \n", - "135 The MCM OB domain is integral to DNA replicati... \n", + "147 The kinesin complex is vital for intracellular... \n", + "148 Cutinase and acetylxylan esterase are essentia... \n", + "149 Ionotropic glutamate receptors, akin to plant ... \n", + "150 Glycoside hydrolases break down polysaccharide... \n", + "151 Immunity protein 10 suggests microbial defense... \n", "\n", - "[136 rows x 7 columns]" + "[152 rows x 7 columns]" ] }, - "execution_count": 190, + "execution_count": 196, "metadata": {}, "output_type": "execute_result" } @@ -7980,7 +7400,7 @@ }, { "cell_type": "code", - "execution_count": 191, + "execution_count": 197, "id": "7893b8d9-1566-4e36-aec3-e6b9d4435f51", "metadata": {}, "outputs": [ @@ -8017,53 +7437,53 @@ " \n", " \n", " 0\n", - " Engineered:Bioremediation:Terephthalate:Wastew...\n", - " GO:0004114 * IPR004501\n", - " 3',5'-cyclic-nucleotide phosphodiesterase acti...\n", - " signal transduction*sugar transport\n", - " high organic load*nutrient dense\n", + " Engineered:Bioreactor\n", + " GO:0018551 * IPR005126\n", + " dissimilatory sulfite reductase activity * Nap...\n", + " anaerobic respiration*sulfur metabolism\n", + " anoxic*sulfur-rich\n", " high\n", - " Systems involved in signal transduction and su...\n", + " Dissimilatory sulfite reductase and associated...\n", " \n", " \n", " 1\n", - " Engineered:Bioremediation:Terephthalate:Wastew...\n", - " GO:0008901 * IPR010960\n", - " ferredoxin hydrogenase activity * Flavocytochr...\n", - " electron transport chain*anaerobic respiration\n", - " oxygen-limited*high organic load\n", + " Engineered:Bioreactor\n", + " GO:0031460 * IPR004763\n", + " glycine betaine transport * Cation efflux syst...\n", + " osmoprotection*ion transport\n", + " osmotic stress*metal-rich\n", " high\n", - " Ferredoxin hydrogenase and Flavocytochrome c a...\n", + " Glycine betaine transport and cation efflux sy...\n", " \n", " \n", " 2\n", - " Engineered:Bioremediation:Terephthalate:Wastew...\n", - " GO:0019512 * IPR004300\n", - " lactose catabolic process via tagatose-6-phosp...\n", - " lactose metabolism*carbohydrate degradation\n", - " high organic load*carbohydrate-rich conditions\n", - " high\n", - " These features are involved in carbohydrate me...\n", + " Engineered:Bioreactor\n", + " IPR007117 * IPR011868\n", + " Expansin, cellulose-binding-like domain * Moly...\n", + " cell wall modification*molybdenum transport\n", + " organic-rich*high molybdate availability\n", + " medium\n", + " The presence of expansin for cell wall modific...\n", " \n", " \n", " 3\n", - " Engineered:Bioremediation:Terephthalate:Wastew...\n", - " GO:0004037 * IPR017813\n", - " allantoicase activity * Mycothiol acetyltransf...\n", - " amino acid metabolism*detoxification\n", - " nutrient dense*potentially toxin-rich\n", + " Engineered:Bioreactor\n", + " IPR016300 * IPR019949\n", + " Arsenical pump ATPase, ArsA/GET3 * Luciferase ...\n", + " arsenic resistance*oxidative stress response\n", + " toxic metal contamination*high oxidative stress\n", " medium\n", - " Enzymes involved in amino acid metabolism and ...\n", + " Arsenical pump ATPase and luciferase family ox...\n", " \n", " \n", " 4\n", - " Engineered:Bioremediation:Terephthalate:Wastew...\n", - " IPR014580 * IPR014984\n", - " Uncharacterised conserved protein UCP033199 * ...\n", - " unknown function*pathogenicity\n", - " diverse microbial community*complex interactions\n", + " Engineered:Bioreactor\n", + " GO:0008743 * IPR001360\n", + " L-threonine 3-dehydrogenase activity * Glycosi...\n", + " amino acid metabolism*carbohydrate degradation\n", + " nutrient cycling*high organic load\n", " medium\n", - " Presence of pathogenicity-related proteins ind...\n", + " L-threonine 3-dehydrogenase and glycoside hydr...\n", " \n", " \n", " ...\n", @@ -8076,143 +7496,143 @@ " ...\n", " \n", " \n", - " 131\n", - " Host-associated:Plants\n", - " IPR001096 * IPR033126\n", - " Peptidase C13, legumain * Glycosyl hydrolases ...\n", - " protein degradation*carbohydrate degradation\n", - " nutrient cycling*decomposition\n", + " 147\n", + " Host-associated:Plants:Rhizosphere\n", + " GO:0005871 * GO:0006011 * GO:0019068\n", + " kinesin complex * UDP-glucose metabolic proces...\n", + " microbial motility complex*carbohydrate metabo...\n", + " nutrient-rich*high microbial diversity\n", " high\n", - " Peptidases and glycosyl hydrolases are essenti...\n", + " The kinesin complex is vital for intracellular...\n", " \n", " \n", - " 132\n", - " Host-associated:Plants:Phylloplane\n", - " GO:0042176 * IPR006652\n", - " regulation of protein catabolic process * Kelc...\n", - " protein degradation*structural protein interac...\n", - " nutrient limited*exposure to microbial competi...\n", + " 148\n", + " Host-associated:Plants:Rhizosphere\n", + " IPR000675 * IPR007941 * IPR012727\n", + " Cutinase/acetylxylan esterase * Protein of unk...\n", + " plant polymer degradation*unknown protein func...\n", + " organic matter-rich*nitrogen cycling\n", " high\n", - " The regulation of protein catabolic processes ...\n", + " Cutinase and acetylxylan esterase are essentia...\n", " \n", " \n", - " 133\n", - " Host-associated:Plants:Phylloplane\n", - " IPR000036 * GO:0033890\n", - " Peptidase A26, omptin * ribonuclease D activity\n", - " protein degradation*RNA processing\n", - " high microbial diversity*exposure to pathogeni...\n", + " 149\n", + " Host-associated:Plants:Rhizosphere\n", + " IPR001320 * IPR004264 * IPR007312\n", + " Ionotropic glutamate receptor, C-terminal * Tr...\n", + " neurotransmitter-like signaling*genetic elemen...\n", + " microbe-plant signaling*high horizontal gene t...\n", " high\n", - " Peptidases and ribonucleases are necessary for...\n", + " Ionotropic glutamate receptors, akin to plant ...\n", " \n", " \n", - " 134\n", - " Host-associated:Plants:Phylloplane\n", - " GO:0003950 * IPR033126\n", - " NAD+ ADP-ribosyltransferase activity * Glycosy...\n", - " DNA repair*carbohydrate metabolism\n", - " exposure to UV light*abundant plant polysaccha...\n", - " high\n", - " NAD+ ADP-ribosyltransferase activity is key fo...\n", + " 150\n", + " Host-associated:Plants:Rhizosphere\n", + " IPR004300 * IPR014983 * IPR017523\n", + " Glycoside hydrolase family 57, N-terminal doma...\n", + " polysaccharide breakdown*putative decarboxylas...\n", + " carbohydrate-rich*multiple nutrient cycles\n", + " medium\n", + " Glycoside hydrolases break down polysaccharide...\n", " \n", " \n", - " 135\n", - " Host-associated:Plants:Phylloplane\n", - " IPR033762\n", - " MCM OB domain\n", - " DNA replication\n", - " high cellular turnover*exposure to DNA-damagin...\n", - " high\n", - " The MCM OB domain is integral to DNA replicati...\n", + " 151\n", + " Host-associated:Plants:Rhizosphere\n", + " IPR028962 * sk__Bacteria;k__;p__Verrucomicrobi...\n", + " Immunity protein 10 * Candidatus_Udaeobacter\n", + " microbial defense mechanisms*actinobacterium a...\n", + " pathogen-rich*microbe-microbe interactions\n", + " medium\n", + " Immunity protein 10 suggests microbial defense...\n", " \n", " \n", "\n", - "

136 rows × 7 columns

\n", + "

152 rows × 7 columns

\n", "" ], "text/plain": [ - " ecosystem \\\n", - "0 Engineered:Bioremediation:Terephthalate:Wastew... \n", - "1 Engineered:Bioremediation:Terephthalate:Wastew... \n", - "2 Engineered:Bioremediation:Terephthalate:Wastew... \n", - "3 Engineered:Bioremediation:Terephthalate:Wastew... \n", - "4 Engineered:Bioremediation:Terephthalate:Wastew... \n", - ".. ... \n", - "131 Host-associated:Plants \n", - "132 Host-associated:Plants:Phylloplane \n", - "133 Host-associated:Plants:Phylloplane \n", - "134 Host-associated:Plants:Phylloplane \n", - "135 Host-associated:Plants:Phylloplane \n", + " ecosystem \\\n", + "0 Engineered:Bioreactor \n", + "1 Engineered:Bioreactor \n", + "2 Engineered:Bioreactor \n", + "3 Engineered:Bioreactor \n", + "4 Engineered:Bioreactor \n", + ".. ... \n", + "147 Host-associated:Plants:Rhizosphere \n", + "148 Host-associated:Plants:Rhizosphere \n", + "149 Host-associated:Plants:Rhizosphere \n", + "150 Host-associated:Plants:Rhizosphere \n", + "151 Host-associated:Plants:Rhizosphere \n", "\n", - " feature_id \\\n", - "0 GO:0004114 * IPR004501 \n", - "1 GO:0008901 * IPR010960 \n", - "2 GO:0019512 * IPR004300 \n", - "3 GO:0004037 * IPR017813 \n", - "4 IPR014580 * IPR014984 \n", - ".. ... \n", - "131 IPR001096 * IPR033126 \n", - "132 GO:0042176 * IPR006652 \n", - "133 IPR000036 * GO:0033890 \n", - "134 GO:0003950 * IPR033126 \n", - "135 IPR033762 \n", + " feature_id \\\n", + "0 GO:0018551 * IPR005126 \n", + "1 GO:0031460 * IPR004763 \n", + "2 IPR007117 * IPR011868 \n", + "3 IPR016300 * IPR019949 \n", + "4 GO:0008743 * IPR001360 \n", + ".. ... \n", + "147 GO:0005871 * GO:0006011 * GO:0019068 \n", + "148 IPR000675 * IPR007941 * IPR012727 \n", + "149 IPR001320 * IPR004264 * IPR007312 \n", + "150 IPR004300 * IPR014983 * IPR017523 \n", + "151 IPR028962 * sk__Bacteria;k__;p__Verrucomicrobi... \n", "\n", " feature_label \\\n", - "0 3',5'-cyclic-nucleotide phosphodiesterase acti... \n", - "1 ferredoxin hydrogenase activity * Flavocytochr... \n", - "2 lactose catabolic process via tagatose-6-phosp... \n", - "3 allantoicase activity * Mycothiol acetyltransf... \n", - "4 Uncharacterised conserved protein UCP033199 * ... \n", + "0 dissimilatory sulfite reductase activity * Nap... \n", + "1 glycine betaine transport * Cation efflux syst... \n", + "2 Expansin, cellulose-binding-like domain * Moly... \n", + "3 Arsenical pump ATPase, ArsA/GET3 * Luciferase ... \n", + "4 L-threonine 3-dehydrogenase activity * Glycosi... \n", ".. ... \n", - "131 Peptidase C13, legumain * Glycosyl hydrolases ... \n", - "132 regulation of protein catabolic process * Kelc... \n", - "133 Peptidase A26, omptin * ribonuclease D activity \n", - "134 NAD+ ADP-ribosyltransferase activity * Glycosy... \n", - "135 MCM OB domain \n", + "147 kinesin complex * UDP-glucose metabolic proces... \n", + "148 Cutinase/acetylxylan esterase * Protein of unk... \n", + "149 Ionotropic glutamate receptor, C-terminal * Tr... \n", + "150 Glycoside hydrolase family 57, N-terminal doma... \n", + "151 Immunity protein 10 * Candidatus_Udaeobacter \n", "\n", " bio_property \\\n", - "0 signal transduction*sugar transport \n", - "1 electron transport chain*anaerobic respiration \n", - "2 lactose metabolism*carbohydrate degradation \n", - "3 amino acid metabolism*detoxification \n", - "4 unknown function*pathogenicity \n", + "0 anaerobic respiration*sulfur metabolism \n", + "1 osmoprotection*ion transport \n", + "2 cell wall modification*molybdenum transport \n", + "3 arsenic resistance*oxidative stress response \n", + "4 amino acid metabolism*carbohydrate degradation \n", ".. ... \n", - "131 protein degradation*carbohydrate degradation \n", - "132 protein degradation*structural protein interac... \n", - "133 protein degradation*RNA processing \n", - "134 DNA repair*carbohydrate metabolism \n", - "135 DNA replication \n", + "147 microbial motility complex*carbohydrate metabo... \n", + "148 plant polymer degradation*unknown protein func... \n", + "149 neurotransmitter-like signaling*genetic elemen... \n", + "150 polysaccharide breakdown*putative decarboxylas... \n", + "151 microbial defense mechanisms*actinobacterium a... \n", "\n", " env_property confidence \\\n", - "0 high organic load*nutrient dense high \n", - "1 oxygen-limited*high organic load high \n", - "2 high organic load*carbohydrate-rich conditions high \n", - "3 nutrient dense*potentially toxin-rich medium \n", - "4 diverse microbial community*complex interactions medium \n", + "0 anoxic*sulfur-rich high \n", + "1 osmotic stress*metal-rich high \n", + "2 organic-rich*high molybdate availability medium \n", + "3 toxic metal contamination*high oxidative stress medium \n", + "4 nutrient cycling*high organic load medium \n", ".. ... ... \n", - "131 nutrient cycling*decomposition high \n", - "132 nutrient limited*exposure to microbial competi... high \n", - "133 high microbial diversity*exposure to pathogeni... high \n", - "134 exposure to UV light*abundant plant polysaccha... high \n", - "135 high cellular turnover*exposure to DNA-damagin... high \n", + "147 nutrient-rich*high microbial diversity high \n", + "148 organic matter-rich*nitrogen cycling high \n", + "149 microbe-plant signaling*high horizontal gene t... high \n", + "150 carbohydrate-rich*multiple nutrient cycles medium \n", + "151 pathogen-rich*microbe-microbe interactions medium \n", "\n", " explanation \n", - "0 Systems involved in signal transduction and su... \n", - "1 Ferredoxin hydrogenase and Flavocytochrome c a... \n", - "2 These features are involved in carbohydrate me... \n", - "3 Enzymes involved in amino acid metabolism and ... \n", - "4 Presence of pathogenicity-related proteins ind... \n", + "0 Dissimilatory sulfite reductase and associated... \n", + "1 Glycine betaine transport and cation efflux sy... \n", + "2 The presence of expansin for cell wall modific... \n", + "3 Arsenical pump ATPase and luciferase family ox... \n", + "4 L-threonine 3-dehydrogenase and glycoside hydr... \n", ".. ... \n", - "131 Peptidases and glycosyl hydrolases are essenti... \n", - "132 The regulation of protein catabolic processes ... \n", - "133 Peptidases and ribonucleases are necessary for... \n", - "134 NAD+ ADP-ribosyltransferase activity is key fo... \n", - "135 The MCM OB domain is integral to DNA replicati... \n", + "147 The kinesin complex is vital for intracellular... \n", + "148 Cutinase and acetylxylan esterase are essentia... \n", + "149 Ionotropic glutamate receptors, akin to plant ... \n", + "150 Glycoside hydrolases break down polysaccharide... \n", + "151 Immunity protein 10 suggests microbial defense... \n", "\n", - "[136 rows x 7 columns]" + "[152 rows x 7 columns]" ] }, - "execution_count": 191, + "execution_count": 197, "metadata": {}, "output_type": "execute_result" } @@ -8223,7 +7643,7 @@ }, { "cell_type": "code", - "execution_count": 192, + "execution_count": 198, "id": "9d60b516-cd04-4931-b6cc-06ba3ae6509a", "metadata": {}, "outputs": [ @@ -8260,53 +7680,53 @@ " \n", " \n", " 0\n", - " Engineered:Bioremediation:Terephthalate:Wastew...\n", - " GO:0004114 * IPR004501\n", - " 3',5'-cyclic-nucleotide phosphodiesterase acti...\n", - " signal transduction*sugar transport\n", - " high organic load*nutrient dense\n", + " Engineered:Bioreactor\n", + " GO:0018551 * IPR005126\n", + " dissimilatory sulfite reductase activity * Nap...\n", + " anaerobic respiration*sulfur metabolism\n", + " anoxic*sulfur-rich\n", " high\n", - " Systems involved in signal transduction and su...\n", + " Dissimilatory sulfite reductase and associated...\n", " \n", " \n", " 1\n", - " Engineered:Bioremediation:Terephthalate:Wastew...\n", - " GO:0008901 * IPR010960\n", - " ferredoxin hydrogenase activity * Flavocytochr...\n", - " electron transport chain*anaerobic respiration\n", - " oxygen-limited*high organic load\n", + " Engineered:Bioreactor\n", + " GO:0031460 * IPR004763\n", + " glycine betaine transport * Cation efflux syst...\n", + " osmoprotection*ion transport\n", + " osmotic stress*metal-rich\n", " high\n", - " Ferredoxin hydrogenase and Flavocytochrome c a...\n", + " Glycine betaine transport and cation efflux sy...\n", " \n", " \n", - " 2\n", + " 6\n", " Engineered:Bioremediation:Terephthalate:Wastew...\n", - " GO:0019512 * IPR004300\n", - " lactose catabolic process via tagatose-6-phosp...\n", - " lactose metabolism*carbohydrate degradation\n", - " high organic load*carbohydrate-rich conditions\n", + " GO:0008743 * IPR001360 * GO:0019512\n", + " L-threonine 3-dehydrogenase activity * Glycosi...\n", + " amino acid metabolism*carbohydrate metabolism*...\n", + " organic carbon-rich*nutrient recycling*polluta...\n", " high\n", - " These features are involved in carbohydrate me...\n", + " The presence of enzymes involved in the metabo...\n", " \n", " \n", - " 6\n", + " 8\n", " Engineered:Bioremediation:Terephthalate:Wastew...\n", - " sk__Bacteria;k__;p__Bacteroidetes;c__Bacteroid...\n", - " Bacteroides * Collinsella\n", - " complex carbohydrate breakdown*secondary metab...\n", - " high fiber*complex organic matter\n", + " IPR000036 * IPR006391\n", + " Peptidase A26, omptin * P-type ATPase, B chain...\n", + " protein degradation*ion transport\n", + " high metal ion concentration\n", " high\n", - " Bacteroides and Collinsella are known for thei...\n", + " P-type ATPases are involved in ion transport a...\n", " \n", " \n", - " 7\n", - " Engineered:Built environment\n", - " IPR009413\n", - " Hemolysin, aegerolysin type\n", - " cell lysis*pathogenicity\n", - " humid*high dust load\n", + " 10\n", + " Engineered:Bioremediation:Terephthalate:Wastew...\n", + " IPR010106 * IPR017813\n", + " Recombination-promoting nuclease RpnA * Mycoth...\n", + " DNA repair*antioxidative stress response\n", + " chemical stress*oxidative stress\n", " high\n", - " Hemolysins like aegerolysin type are often ass...\n", + " These proteins are involved in cellular defens...\n", " \n", " \n", " ...\n", @@ -8319,143 +7739,143 @@ " ...\n", " \n", " \n", - " 131\n", - " Host-associated:Plants\n", - " IPR001096 * IPR033126\n", - " Peptidase C13, legumain * Glycosyl hydrolases ...\n", - " protein degradation*carbohydrate degradation\n", - " nutrient cycling*decomposition\n", + " 144\n", + " Host-associated:Plants:Phylloplane\n", + " GO:0033890 * IPR000036\n", + " ribonuclease D activity * Peptidase A26, omptin\n", + " RNA processing*protein degradation\n", + " microbial community complexity*organic matter ...\n", " high\n", - " Peptidases and glycosyl hydrolases are essenti...\n", + " Ribonuclease D is involved in RNA processing, ...\n", " \n", " \n", - " 132\n", + " 145\n", " Host-associated:Plants:Phylloplane\n", - " GO:0042176 * IPR006652\n", - " regulation of protein catabolic process * Kelc...\n", - " protein degradation*structural protein interac...\n", - " nutrient limited*exposure to microbial competi...\n", + " GO:0042176 * IPR033762\n", + " regulation of protein catabolic process * MCM ...\n", + " protein catabolism regulation*DNA replication ...\n", + " stress adaptation*dynamic microenvironment\n", " high\n", - " The regulation of protein catabolic processes ...\n", + " The regulation of protein catabolic process is...\n", " \n", " \n", - " 133\n", - " Host-associated:Plants:Phylloplane\n", - " IPR000036 * GO:0033890\n", - " Peptidase A26, omptin * ribonuclease D activity\n", - " protein degradation*RNA processing\n", - " high microbial diversity*exposure to pathogeni...\n", + " 147\n", + " Host-associated:Plants:Rhizosphere\n", + " GO:0005871 * GO:0006011 * GO:0019068\n", + " kinesin complex * UDP-glucose metabolic proces...\n", + " microbial motility complex*carbohydrate metabo...\n", + " nutrient-rich*high microbial diversity\n", " high\n", - " Peptidases and ribonucleases are necessary for...\n", + " The kinesin complex is vital for intracellular...\n", " \n", " \n", - " 134\n", - " Host-associated:Plants:Phylloplane\n", - " GO:0003950 * IPR033126\n", - " NAD+ ADP-ribosyltransferase activity * Glycosy...\n", - " DNA repair*carbohydrate metabolism\n", - " exposure to UV light*abundant plant polysaccha...\n", + " 148\n", + " Host-associated:Plants:Rhizosphere\n", + " IPR000675 * IPR007941 * IPR012727\n", + " Cutinase/acetylxylan esterase * Protein of unk...\n", + " plant polymer degradation*unknown protein func...\n", + " organic matter-rich*nitrogen cycling\n", " high\n", - " NAD+ ADP-ribosyltransferase activity is key fo...\n", + " Cutinase and acetylxylan esterase are essentia...\n", " \n", " \n", - " 135\n", - " Host-associated:Plants:Phylloplane\n", - " IPR033762\n", - " MCM OB domain\n", - " DNA replication\n", - " high cellular turnover*exposure to DNA-damagin...\n", + " 149\n", + " Host-associated:Plants:Rhizosphere\n", + " IPR001320 * IPR004264 * IPR007312\n", + " Ionotropic glutamate receptor, C-terminal * Tr...\n", + " neurotransmitter-like signaling*genetic elemen...\n", + " microbe-plant signaling*high horizontal gene t...\n", " high\n", - " The MCM OB domain is integral to DNA replicati...\n", + " Ionotropic glutamate receptors, akin to plant ...\n", " \n", " \n", "\n", - "

94 rows × 7 columns

\n", + "

106 rows × 7 columns

\n", "" ], "text/plain": [ " ecosystem \\\n", - "0 Engineered:Bioremediation:Terephthalate:Wastew... \n", - "1 Engineered:Bioremediation:Terephthalate:Wastew... \n", - "2 Engineered:Bioremediation:Terephthalate:Wastew... \n", + "0 Engineered:Bioreactor \n", + "1 Engineered:Bioreactor \n", "6 Engineered:Bioremediation:Terephthalate:Wastew... \n", - "7 Engineered:Built environment \n", + "8 Engineered:Bioremediation:Terephthalate:Wastew... \n", + "10 Engineered:Bioremediation:Terephthalate:Wastew... \n", ".. ... \n", - "131 Host-associated:Plants \n", - "132 Host-associated:Plants:Phylloplane \n", - "133 Host-associated:Plants:Phylloplane \n", - "134 Host-associated:Plants:Phylloplane \n", - "135 Host-associated:Plants:Phylloplane \n", + "144 Host-associated:Plants:Phylloplane \n", + "145 Host-associated:Plants:Phylloplane \n", + "147 Host-associated:Plants:Rhizosphere \n", + "148 Host-associated:Plants:Rhizosphere \n", + "149 Host-associated:Plants:Rhizosphere \n", "\n", - " feature_id \\\n", - "0 GO:0004114 * IPR004501 \n", - "1 GO:0008901 * IPR010960 \n", - "2 GO:0019512 * IPR004300 \n", - "6 sk__Bacteria;k__;p__Bacteroidetes;c__Bacteroid... \n", - "7 IPR009413 \n", - ".. ... \n", - "131 IPR001096 * IPR033126 \n", - "132 GO:0042176 * IPR006652 \n", - "133 IPR000036 * GO:0033890 \n", - "134 GO:0003950 * IPR033126 \n", - "135 IPR033762 \n", + " feature_id \\\n", + "0 GO:0018551 * IPR005126 \n", + "1 GO:0031460 * IPR004763 \n", + "6 GO:0008743 * IPR001360 * GO:0019512 \n", + "8 IPR000036 * IPR006391 \n", + "10 IPR010106 * IPR017813 \n", + ".. ... \n", + "144 GO:0033890 * IPR000036 \n", + "145 GO:0042176 * IPR033762 \n", + "147 GO:0005871 * GO:0006011 * GO:0019068 \n", + "148 IPR000675 * IPR007941 * IPR012727 \n", + "149 IPR001320 * IPR004264 * IPR007312 \n", "\n", " feature_label \\\n", - "0 3',5'-cyclic-nucleotide phosphodiesterase acti... \n", - "1 ferredoxin hydrogenase activity * Flavocytochr... \n", - "2 lactose catabolic process via tagatose-6-phosp... \n", - "6 Bacteroides * Collinsella \n", - "7 Hemolysin, aegerolysin type \n", + "0 dissimilatory sulfite reductase activity * Nap... \n", + "1 glycine betaine transport * Cation efflux syst... \n", + "6 L-threonine 3-dehydrogenase activity * Glycosi... \n", + "8 Peptidase A26, omptin * P-type ATPase, B chain... \n", + "10 Recombination-promoting nuclease RpnA * Mycoth... \n", ".. ... \n", - "131 Peptidase C13, legumain * Glycosyl hydrolases ... \n", - "132 regulation of protein catabolic process * Kelc... \n", - "133 Peptidase A26, omptin * ribonuclease D activity \n", - "134 NAD+ ADP-ribosyltransferase activity * Glycosy... \n", - "135 MCM OB domain \n", + "144 ribonuclease D activity * Peptidase A26, omptin \n", + "145 regulation of protein catabolic process * MCM ... \n", + "147 kinesin complex * UDP-glucose metabolic proces... \n", + "148 Cutinase/acetylxylan esterase * Protein of unk... \n", + "149 Ionotropic glutamate receptor, C-terminal * Tr... \n", "\n", " bio_property \\\n", - "0 signal transduction*sugar transport \n", - "1 electron transport chain*anaerobic respiration \n", - "2 lactose metabolism*carbohydrate degradation \n", - "6 complex carbohydrate breakdown*secondary metab... \n", - "7 cell lysis*pathogenicity \n", + "0 anaerobic respiration*sulfur metabolism \n", + "1 osmoprotection*ion transport \n", + "6 amino acid metabolism*carbohydrate metabolism*... \n", + "8 protein degradation*ion transport \n", + "10 DNA repair*antioxidative stress response \n", ".. ... \n", - "131 protein degradation*carbohydrate degradation \n", - "132 protein degradation*structural protein interac... \n", - "133 protein degradation*RNA processing \n", - "134 DNA repair*carbohydrate metabolism \n", - "135 DNA replication \n", + "144 RNA processing*protein degradation \n", + "145 protein catabolism regulation*DNA replication ... \n", + "147 microbial motility complex*carbohydrate metabo... \n", + "148 plant polymer degradation*unknown protein func... \n", + "149 neurotransmitter-like signaling*genetic elemen... \n", "\n", " env_property confidence \\\n", - "0 high organic load*nutrient dense high \n", - "1 oxygen-limited*high organic load high \n", - "2 high organic load*carbohydrate-rich conditions high \n", - "6 high fiber*complex organic matter high \n", - "7 humid*high dust load high \n", + "0 anoxic*sulfur-rich high \n", + "1 osmotic stress*metal-rich high \n", + "6 organic carbon-rich*nutrient recycling*polluta... high \n", + "8 high metal ion concentration high \n", + "10 chemical stress*oxidative stress high \n", ".. ... ... \n", - "131 nutrient cycling*decomposition high \n", - "132 nutrient limited*exposure to microbial competi... high \n", - "133 high microbial diversity*exposure to pathogeni... high \n", - "134 exposure to UV light*abundant plant polysaccha... high \n", - "135 high cellular turnover*exposure to DNA-damagin... high \n", + "144 microbial community complexity*organic matter ... high \n", + "145 stress adaptation*dynamic microenvironment high \n", + "147 nutrient-rich*high microbial diversity high \n", + "148 organic matter-rich*nitrogen cycling high \n", + "149 microbe-plant signaling*high horizontal gene t... high \n", "\n", " explanation \n", - "0 Systems involved in signal transduction and su... \n", - "1 Ferredoxin hydrogenase and Flavocytochrome c a... \n", - "2 These features are involved in carbohydrate me... \n", - "6 Bacteroides and Collinsella are known for thei... \n", - "7 Hemolysins like aegerolysin type are often ass... \n", + "0 Dissimilatory sulfite reductase and associated... \n", + "1 Glycine betaine transport and cation efflux sy... \n", + "6 The presence of enzymes involved in the metabo... \n", + "8 P-type ATPases are involved in ion transport a... \n", + "10 These proteins are involved in cellular defens... \n", ".. ... \n", - "131 Peptidases and glycosyl hydrolases are essenti... \n", - "132 The regulation of protein catabolic processes ... \n", - "133 Peptidases and ribonucleases are necessary for... \n", - "134 NAD+ ADP-ribosyltransferase activity is key fo... \n", - "135 The MCM OB domain is integral to DNA replicati... \n", + "144 Ribonuclease D is involved in RNA processing, ... \n", + "145 The regulation of protein catabolic process is... \n", + "147 The kinesin complex is vital for intracellular... \n", + "148 Cutinase and acetylxylan esterase are essentia... \n", + "149 Ionotropic glutamate receptors, akin to plant ... \n", "\n", - "[94 rows x 7 columns]" + "[106 rows x 7 columns]" ] }, - "execution_count": 192, + "execution_count": 198, "metadata": {}, "output_type": "execute_result" } @@ -8466,12 +7886,12 @@ }, { "cell_type": "code", - "execution_count": 193, + "execution_count": 199, "id": "5df219e6-8484-42e7-9ff0-60cfbd786582", "metadata": {}, "outputs": [], "source": [ - "llm_results_df.to_csv(\"ecosystem_characteristics_llm_results_df_v5.tsv\",sep=\"\\t\",header=True)" + "llm_results_df.to_csv(\"ecosystem_characteristics_llm_results_df_v7.tsv\",sep=\"\\t\",header=True)" ] }, {