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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Help - GExplore</title>
<link rel="stylesheet" href="style.css" type="text/css">
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<div class="wrapper">
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<img src="assets/GExplore_logo.png" alt="GExplore Logo" class="logo">
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<li class="active"><a href="home.html"><span class="text">Home</span></a></li>
<li><a><span class="text">Search</span> <span class="angle"></span></a>
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<li><a href="gene_search.html">Genes</a></li>
<li><a href="mutation_search.html">Mutations</a></li>
<li><a href="protein_search.html">Proteins</a></li>
<li><a href="expression_stage_search.html">Stage Expressions</a></li>
<li><a href="expression_tissue_search.html">Tissue Expressions</a></li>
<li><a href="expression_embryo_search.html">Embryo Expressions</a></li>
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<li><a href="about.html"><span class="text">About</span></a></li>
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<!-- Content section -->
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<div class="help-sidebar-title">
<h4>GExplore Documentation</h4>
</div>
<ul>
<li><a href="#user-guide" class="active">GExplore User Guide</a></li>
<li class="has-submenu">
<a href="#introduction">Introduction</a>
<ul>
<li><a href="#gexplore">GExplore</a></li>
<li><a href="#whats-new">What's new?</a></li>
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<a href="#databases">Databases</a>
<ul>
<li><a href="#gene-database">Genes</a></li>
<li><a href="#mutation-database">Mutations</a></li>
<li><a href="#protein-database">Proteins</a></li>
<li><a href="#expression-stages">Expression (Stages)</a></li>
<li><a href="#expression-tissues">Expression (Tissues)</a></li>
<li><a href="#expression-embryo">Expression (Embryo)</a></li>
</ul>
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<a href="#search-fields">Search Fields</a>
<ul>
<li><a href="#general-comments">Overview</a></li>
<li><a href="#gene-search-field">Gene Search Field</a></li>
<li><a href="#protein-domain-search-fields">Protein Domain Search Fields</a></li>
<li><a href="#text-search-fields">Text Search Fields</a></li>
<li><a href="#mutation-search-page">Search Fields on the Mutation Search Page</a></li>
<li><a href="#expression-search-pages">Search Fields on the Expression Search Pages (Stages, Tissues, Embryos)</a></li>
</ul>
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<a href="#display-options">Display Options</a>
<ul>
<li><a href="#general-comments-display">Overview</a></li>
<li><a href="#protein-domain-organization">Protein Domain Organization</a></li>
<li><a href="#display-options-mutations">Special Display Options for Mutations</a></li>
<li><a href="#display-options-expression-data">Special Display Options for Expression Data (Stages, Tissues, Embryo)</a></li>
</ul>
</li>
<li class="has-submenu">
<a href="#tools">Tools</a>
<ul>
<li><a href="#compare-tool">Compare</a></li>
<li><a href="#convert-tool">Convert</a></li>
</ul>
</li>
<li><a href="#domain-abbreviations">Domain Abbreviations</a></li>
<li><a href="#FAQs">FAQs</a></li>
</ul>
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<div id="user-guide" class="help-content-section active">
<div class="date-last-updated">
<h4>Last updated on Sep 20, 2024</h4>
</div>
<div class="help-content-section-title">
<h4>Welcome to the GExplore User Guide</h4>
</div>
<p>Use this guide to help you learn GExplore's features and accelerate your research and analysis. GExplore provides comprehensive data on genes, mutations, proteins, and their expression profiles, making it easier for you to explore and analyze genetic information.</p>
<br>
<p>Start at the beginning, or visit each section individually to work your way through a project session. Each section of this guide provides detailed information and instructions on how to use GExplore's features effectively.</p>
</div>
<!----------------------- Introduction Subpages Start ----------------------->
<div id="introduction" class="help-content-section">
<div class="date-last-updated">
<h4>Last updated on Sep 20, 2024</h4>
</div>
<div class="help-content-section-title">
<h4>Introduction</h4>
</div>
<div id="gexplore">
<h5>GExplore Overview</h5>
<p>GExplore is a tool for large-scale mining of data related to gene or protein function in <em>C. elegans</em>. The interface is simple, and response times are fast to encourage large-scale exploratory searches. GExplore is designed to offer detailed insights into genetic data, enabling researchers and analysts to delve deep into genetic information.</p>
<br>
<p>The database contains selected genome-wide data sets, including protein domain organization, gene expression, and phenotype data, which are important indicators for gene and protein function. Data sets were obtained from WormBase and processed to integrate data and to simplify searches.</p>
<br>
<p>This site should be useful for experimental planning of genome-scale experiments and survey-type queries. With this interface, you should be able to get quick answers to questions such as:</p>
<ul>
<li>How many small secreted proteins are there?</li>
<li>Which putative cell surface receptors are expressed in neurons?</li>
<li>How many kinases expressed in muscle cells have mutants available?</li>
</ul>
<br>
<p>We are continuously improving GExplore and its features. If you have any questions or feedback, please contact <a href="mailto:[email protected]">Dr. Harald Hutter</a>.</p>
</div>
<div id="whats-new">
<h5>Learn what's new in the latest release of GExplore.</h5>
<h6>September 2024 release (version 1.5)</h6>
<p>GExplore version 1.5 is a major update including the following novel data sets and features:</p>
<ul>
<li>All databases were updated to WormBase release 292 (April 2024).</li>
<li>The domain organization for the proteomes of all nine core species in WormBase was added to allow searches for proteins with certain domains in different nematode species.</li>
<li>Gene ontology data were added for all species.</li>
<li>The location of <em>C. elegans</em> mutations was mapped onto the domain organization of the proteins.</li>
<li>SAGE and RNAseq expression data were replaced by new stage-specific expression profiles from the modENCODE project (provided by the Waterston lab).</li>
<li>Best BLAST hits were replaced by orthologs as listed by WormBase; a search option to identify <em>C. elegans</em> orthologs of human, mouse, <em>Drosophila</em>, and yeast genes was added.</li>
</ul>
<br>
<a href="https://academic.oup.com/database" target="_blank" class="update-article-button">Read update article</a>
</div>
</div>
<!----------------------- Introduction Subpages End ----------------------->
<!----------------------- Database Subpages Start ----------------------->
<div id="databases" class="help-content-section">
<div class="date-last-updated">
<h4>Last updated on Sep 20, 2024</h4>
</div>
<div class="help-content-section-title">
<h4>Databases</h4>
<p>GExplore consists of six different databases, each with its own search page.</p>
</div>
<div id="gene-database">
<h5>Genes</h5>
<p>
The gene database contains curated datasets designed to predict the putative functions of genes and proteins. These datasets include:
</p>
<ul style="margin-bottom: 20px;">
<li>Protein domain organization</li>
<li>General gene descriptions</li>
<li>Phenotype and expression data</li>
<li>Gene interaction data</li>
<li>Gene ontology (GO) terms</li>
<li>Disease associations</li>
</ul>
<p>
All data have been sourced from WormBase and are regularly updated. The current version is based on WormBase release 292 (April 2024).
</p>
<p>
The search interface allows users to quickly identify groups of genes that share specific features, such as kinases expressed in muscle cells. Alternatively, users can input large lists (hundreds or thousands) of candidate genes and filter them based on certain characteristics.
</p>
<p>
The system’s fast response time and flexible output options make it easy to perform efficient, survey-type queries with large groups of genes in both the input and output.
</p>
</div>
<div id="mutation-database">
<h5>Mutations</h5>
<p>
Mutation data were downloaded from WormBase release 292 (April 2024). The dataset includes only exonic alleles and alleles affecting splice junctions, while SNPs from wildtype isolates have been excluded. This curated list of mutations is enriched for alleles likely to affect protein function.
</p>
<p>
The location of the mutations is mapped onto the domain organization of the protein, providing a visual display of both the location and nature of the mutations. For deletions, a color code is used to distinguish between in-frame deletions (purple) and frameshift deletions (red). Mutations are mapped to all known splice variants of the gene, enabling easy identification of splice-variant-specific alleles.
</p>
<p>
For deletions, the endpoints are indicated as being located either 'outside' the gene, in an 'intron', or in an 'exon'. Display options also include the ability to show the protein sequence with the affected amino acids highlighted.
</p>
<p>
The WS292 version of the database contains:
</p>
<ul>
<li>227,110 alleles in 19,661 genes (28,240 splice variants)</li>
<li>12,998 deletions</li>
<li>183,547 missense alleles</li>
<li>10,014 nonsense alleles</li>
<li>An additional 8,763 alleles without molecular information</li>
</ul>
</div>
<div id="protein-database">
<h5>Proteins</h5>
<p>
The protein database contains data from 13 <i>Caenorhabditis</i> species (<i>C. becei</i>, <i>C. brenneri</i>, <i>C. briggsae</i>, <i>C. elegans</i>, <i>C. japonica</i>, <i>C. parvicauda</i>, <i>C. quiockensis</i>, <i>C. remanei</i>, <i>C. sulstoni</i>, <i>C. uteleia</i>, <i>C. tropicalis</i>, <i>C. waitukubuli</i>, <i>C. zanzibari</i>), representing all branches of the <i>Caenorhabditis</i> phylogenetic tree.
</p>
<p>
In addition, the database contains proteome data from 7 other nematode species (<i>B. malayi</i>, <i>O. tipulae</i>, <i>O. volvulus</i>, <i>P. pacificus</i>, <i>P. redivivus</i>, <i>S. ratti</i>, <i>T. muris</i>) that have high-quality data available. For comparison, the database also includes the proteomes of major model organisms (<i>S. cerevisiae</i>, <i>D. melanogaster</i>, <i>D. rerio</i>, <i>M. musculus</i>, <i>H. sapiens</i>).
</p>
<p>
Protein data were downloaded either from WormBase (for nematode species) or from the <a href="https://www.ebi.ac.uk/reference_proteomes/" target="_blank">reference proteome site</a> for model organisms. <a href="http://smart.embl-heidelberg.de/" target="_blank">SMART</a> was used for protein domain prediction.
</p>
<p>
To facilitate comparisons across species, the database also contains information about homologs in all species included in the database. The search interface allows users to select proteins with specific protein domains or domain arrangements for a chosen species. The output can be limited to proteins with homologs in one or more other species, enabling quick identification of either nematode-specific genes or evolutionarily conserved genes of a certain type (e.g. kinases).
</p>
</div>
<div id="expression-database">
<h5>Expressions</h5>
<div id="expression-stages">
<h6>Expression (Stages)</h6>
<p>
The expression data for the different stages of the life cycle of <i>C. elegans</i> were obtained as part of the NHGRI modENCODE project, in collaboration with the Waterston (Max Boeck, Chau Huynh, LaDeana Hillier, University of Washington), Reinke (Guilin Wang, Dionna Kasper, Yale University), and Miller (Clay Spencer, Vanderbilt University) labs<sup>1,2,3,4</sup>. Briefly, 18 samples were analyzed using RNA-seq. The results provided here represent a subset of that data, derived from synchronized whole animals at embryonic and post-embryonic stages.
</p>
<p>
For post-embryonic stages, two or more biological replicates were obtained, and weighted averages are provided. For embryonic stages, four independent time series were collected, with samples taken every 30 minutes (though some samples were lost due to technical failures). For detailed data collection and analysis, refer to reference 4.
</p>
<p>
Expression for each gene is provided in dcpm units (depth of coverage per million 35 base reads)<sup>1</sup>. This measure offers base-pair resolution, which simplifies the analysis of shorter features such as exons and splice junctions. A dcpm value of 1.5 represents an average expression level. Values between 0.003 and 0.1 generally indicate significant expression. To approximate rpkm values, use the following equation: <code>rpkm = dcpm * 1000 / 35</code>.
</p>
<div >
<h2>References</h2>
<ol style="margin-bottom: 40px;">
<li style="margin-bottom: 10px;">Hillier LW, Reinke V, Green P, Hirst M, Marra MA, Waterston RH. Massively parallel sequencing of the polyadenylated transcriptome of <i>C. elegans</i>. Genome Res. 2009 Apr;19(4):657-66. PMID: 19181841 PMCID: PMC2665784. DOI: <a href="https://doi.org/10.1101/gr.088112.108" target="_blank">10.1101/gr.088112.108</a></li>
<li style="margin-bottom: 10px;">Gerstein MB, Lu ZJ, Van Nostrand EL, et al. Integrative analysis of the <i>Caenorhabditis elegans</i> genome by the modENCODE project. Science. 2010 Dec 24;330(6012):1775-87. PMID: 21177976 PMCID: PMC3142569 DOI: <a href="https://doi.org/10.1126/science.1196914" target="_blank">10.1126/science.1196914</a></li>
<li style="margin-bottom: 10px;">Gerstein MB, Rozowsky J, Yan K, Wang D, et al. Comparative analysis of the transcriptome across distant species. Nature. 2014 Aug 28;512(7515):445-8. PMID: 25164755 PMCID: PMC4155737 DOI: <a href="https://doi.org/10.1038/nature13424" target="_blank">10.1038/nature13424</a></li>
<li>Boeck, M et al. The time-resolved transcriptome of <i>C. elegans</i>. Genome Res. 2016 Oct;26(10):1441-1450. PMID: 27531719 PMCID: PMC5052054 DOI: <a href="https://doi.org/10.1101/gr.202663.115" target="_blank">10.1101/gr.202663.115</a></li>
</ol>
</div>
</div>
<div id="expression-tissues">
<h6>Expression (Tissues)</h6>
<p>
The expression data for cells and tissues at the L2 larval stage were generated using Single-cell Combinatorial Indexing RNA-seq (sci-RNA-seq). For details on data collection and analysis, refer to Cao et al. (2017). In brief, the expression profiles of nearly 50,000 cells from the L2 stage were determined using sci-RNA-seq. From this dataset, consensus expression profiles for 27 cell types were defined.
</p>
<p>
The profiles available through GExplore correspond to the data in Tables S2 to S4 of Cao et al. (2017), while images of the expression profiles align with Figure S14. Expression levels for each gene are presented in transcripts per million (TPM).
</p>
<p>
Enrichment data were pre-calculated and are presented as the "ratio" of a gene's expression in the most highly expressing cell type compared to the second-most highly expressing cell type. "qval" represents the false detection rate (FDR) at which the gene is considered differentially expressed between the highest and second-highest expressing cell types.
</p>
<p style="margin-bottom: 40px;">
For reference, in Cao et al. (2017), a gene is labeled as "cell type enriched" if the <code>ratio >= 5</code> and <code>q-val < 0.05</code>.
</p>
</div>
<div id="expression-embryo">
<h6>Expression (Embryo)</h6>
<p>
The expression data for embryonic tissues were generated using RNA-seq. For detailed information on data collection and analysis, refer to Warner et al. (2019). In brief, synchronized populations of embryos expressing tissue-specific fluorescent markers were sampled at 90-minute intervals over five time points, starting 120 minutes after embryo isolation (about halfway through gastrulation, referred to as t<sub>0</sub>).
</p>
<p>
The final time point (480 minutes after isolation, t<sub>4</sub>) corresponds to the early 3-fold stage, when cells begin terminal differentiation, but before cuticle formation. Time series data were collected for five different tissues/organs—hypodermis, intestine, pharynx, muscle, and neurons—as well as for two lineage-specific populations (ABa and ABala).
</p>
<p>
Expression levels are reported in transcripts per million (TPM).
</p>
</div>
</div>
</div>
<!----------------------- Database Subpages End ----------------------->
<!----------------------- Search Fields Subpages Start ----------------------->
<div id="search-fields" class="help-content-section">
<div class="date-last-updated">
<h4>Last updated on Sep 20, 2024</h4>
</div>
<div class="help-content-section-title">
<h4>Search Fields</h4>
</div>
<!-- Serach Fields: Overview Start -->
<div id="general-comments">
<h5>Overview</h5>
<p>
You only need to enter search terms in <strong>one</strong> of the search fields. If you enter search terms in multiple fields, they will be combined for an <strong>AND Search</strong> (the result will contain only genes that fulfill all search criteria).
</p>
<p>
Text search fields on the "Genes" search page (Description, Phenotype, Expression, Gene Ontology, and Disease Associations) will return any match to the search term(s). You can:
</p>
<ul>
<li>Use <strong>comma-separated lists</strong> for an <strong>OR Search</strong></li>
<li>Use <strong>Boolean logic</strong> to combine search terms: <code>((axon <strong>and</strong> dendrite) <strong>or</strong> neuron) <strong>not</strong> muscle</code></li>
</ul>
<div class="table-wrapper">
<table>
<thead>
<tr>
<th class="search_type">Search Type</th>
<th class="example">Example</th>
<th>Result</th>
<th>Use Case</th>
</tr>
</thead>
<tbody>
<tr>
<td class="search_type">AND Search</td>
<td class="example"><code>axon <strong>and</strong> dendrite</code></td>
<td>Only results containing both "axon" and "dendrite".</td>
<td>Use when you want to narrow down results to items that meet all criteria. This gives fewer, more specific results.</td>
</tr>
<tr>
<td class="search_type">OR Search</td>
<td class="example"><code>axon <strong>or</strong> dendrite</code></td>
<td>Results containing either "axon", or "dendrite", or both.</td>
<td>Use when you want to broaden the search to include items that match any of the criteria, increasing the number of results.</td>
</tr>
</tbody>
</table>
</div>
<h6>What to expect?</h6>
<p>
On the output page, search terms for the text search fields will be <span class="highlight_style">highlighted</span> for easier recognition.
</p>
<p>
Once the search is executed, the results will be displayed in table format. On the output page, you can:
</p>
<ul>
<li>Choose which additional data to display.</li>
<li>Determine the output format (example: table columns, export options).</li>
</ul>
</div>
<!-- Serach Fields: Overview End -->
<!-- Serach Fields: Gene Search Field Start -->
<div id="gene-search-field">
<h5>Gene Search Field</h5>
<p>The gene search field accepts the following identifiers (or any combination):</p>
<ul>
<li>WormBase gene ID: <code>WBGene00003738</code></li>
<li>Gene sequence name: <code>F54F3.1</code></li>
<li>Locus name: <code>nid-1</code></li>
<li>Protein sequence name: <code>F54F3.1a</code></li>
</ul>
<p>Names can be separated by commas or any whitespace character (space, tab, newline). You can enter (or copy) a list of thousands of gene names for a single search.</p>
<p><code>*</code> can be used as a wildcard character. For example, <code>unc-*</code> means all gene names beginning with <code>unc-</code>.
</p>
</div>
<!-- Serach Fields: Gene Search Field End -->
<!-- Serach Fields: Gene search field Start -->
<div id="protein-domain-search-fields">
<h5>Protein Domain Search Fields</h5>
<div id="domain-search-field">
<h6>Domain</h6>
<p>Enter one or more of the domain abbreviations from the <a href="help.html#domain-abbreviations" target="_blank">table of abbreviations</a> or SMART/Pfam identifiers (example: <code>SM00273</code>, <code>PF12423</code>).</p>
</div>
<div id="domain-pattern-search-field">
<h6>Domain Pattern</h6>
<p>Use this field to search for certain domain combinations. Think of a protein as a linear sequence of domains like <code>IG IG IG FN3 FN3 TM 324</code>. Domain abbreviations in this field (but not in the domain field) are case-sensitive! You can use wildcards (<code>*</code> acts as a wildcard for 0 or more domains) and numbers (but no Boolean terms) in the following way:</p>
<!-- Adding a div wrapper around the table -->
<div class="table-wrapper">
<table>
<thead>
<tr>
<th>Pattern Input</th>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr>
<td><code>IG IG IG</code></td>
<td>3 IGs in a row with no other domain in between.</td>
</tr>
<tr>
<td><code>IG*FN3</code></td>
<td>The IG domain is eventually followed by an FN3 domain.</td>
</tr>
<tr>
<td><code>3IG</code></td>
<td>Expanded to <code>IG IG IG</code>: 3 IG domains in a row. Ensure there’s no space between the number and the domain abbreviation.</td>
</tr>
<tr>
<td><code>3IG%</code></td>
<td>Represents <code>IG*IG*IG</code>: 3 IGs with other domains interspersed (<code>%</code> acts as a wildcard during expansion).</td>
</tr>
<tr>
<td><code>3-5IG</code></td>
<td>Represents 3 to 5 IG domains: <code>IG IG IG</code>, <code>IG IG IG IG</code>, or <code>IG IG IG IG IG</code>.</td>
</tr>
<tr>
<td><code><3IG FN3</code></td>
<td>Translated as <code>IG FN3</code> or <code>IG IG FN3</code>: meaning at least 1 but no more than 2 IGs followed by FN3.</td>
</tr>
<tr>
<td><code>>3IG FN3</code></td>
<td>Translated as <code>IG IG IG IG*FN3</code>: meaning at least 4 IGs followed by FN3.</td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
<div id="text-search-fields" class="help-section">
<h5>Text Search Fields</h5>
<p>
On the output page, search terms for the text search fields will be <span class="highlight_style">highlighted</span> for easier recognition.
</p>
<!-- Description Search Field -->
<div id="description-search-field">
<h6>Description Search Field</h6>
<p>
The Legacy Description is equivalent to the "Legacy manual gene description" in WormBase, while the Automated Description is the top-level description under the “Overview” tab in WormBase.
</p>
<!-- Image Section -->
<div class="image-wrapper">
<img src="assets/Wormbase_Descriptions.png" alt="Wormbase Descriptions" class="description-image">
</div>
</div>
<!-- Phenotype and Expression Search Fields -->
<div id="phenotype-expression-search-fields">
<h6>Phenotype and Expression Search Fields</h6>
<p>
The Phenotype and Expression search fields use WormBase-defined vocabularies. These fields include an autosuggest function, which suggests search terms as you type. You are not required to use the suggested terms—you can search using any word, and GExplore will find matches containing your search word.
</p>
<p>
The Tissues and Stages (Genomic Studies) search field refers to data from single-cell RNAseq studies or enrichment analysis of high-throughput studies, where expression in specific tissues is compared to whole animals.
</p>
</div>
<!-- Gene Ontology and Disease Association Search Fields -->
<div id="ontology-disease-fields">
<h6>Gene Ontology and Disease Association Search Fields</h6>
<p>
These search fields also use predefined vocabularies and feature an autosuggest function to help find relevant terms.
</p>
</div>
</div>
<div id="mutation-search-page" class="help-section">
<h5>Search Fields on the Mutation Search Page</h5>
<!-- Checkbox: Do Not Show Deletions Affecting More Than One Gene -->
<h6>Checkbox: "Do not show deletions affecting more than one gene"</h6>
<p>
Some deletions are large and affect multiple genes. If your goal is to identify mutations in a single gene, you can use this checkbox to exclude large deletions that affect more than one gene.
</p>
<!-- Mutation Type -->
<h6>Mutation Type</h6>
<p>
The Mutation Type checkboxes allow you to limit the output to mutations that significantly impact the protein. Nonsense and Deletion mutation types give you more flexibility:
</p>
<p><code>Nonsenses removing greater than x%</code> and <code>Deletions removing greater than x%</code>:</p>
<p>Limits the output to nonsense allele/deletions that truncate the proteins by at least <code>x%</code>. This might be useful to identify putative null alleles by eliminating alleles that only affect the C-terminus of the protein.</p>
<!-- Mutation Source -->
<h6>Mutation Source (Million Mutation Project, KO Consortium, Other)</h6>
<p>
The Mutation Source field allows you to filter mutations based on their origin:
</p>
<ul>
<li><strong>Million Mutation Project</strong>: A large number of mutations were identified by whole-genome sequencing. However, many of these mutations might not result in strong loss-of-function (lof) alleles.</li>
<li><strong>KO Consortium</strong>: Mutations from the KO Consortium were designed to be putative null alleles, typically resulting in complete gene knockouts.</li>
<li><strong>Other Sources</strong>: Includes mutations from other research projects, which may vary in their functional impact.</li>
</ul>
</div>
<div id="expression-search-pages">
<h5>Search Fields on the Expression Search Pages (Stages, Tissues, Embryos)</h5>
<p>Each of the three pages has unique search fields based on the underlying expression database. Details can be found directly on the search pages.</p>
</div>
</div>
<!----------------------- Search Fields Subpages Start ----------------------->
<!----------------------- Display Options Subpages Start ----------------------->
<div id="display-options" class="help-content-section">
<div class="date-last-updated">
<h4>Last updated on Sep 20, 2024</h4>
</div>
<div class="help-content-section-title">
<h4>Display Options</h4>
</div>
<div id="general-comments-display">
<h5>General Comments</h5>
<p>
All result pages are now displayed in HTML format, providing a webpage with various display options and data presented in a table format. Users can export the results to <strong>TXT</strong> or <strong>CSV</strong> using the available export options for further processing locally.
</p>
<p>
The <strong>"List of proteins/genes found"</strong> section contains the list of genes or proteins that meet the search criteria. This list can be copied and used to compare different search results using the <strong>Compare</strong> tool (refer to the Tools section for details).
</p>
<p>
Most display options add an extra column to the results table with the relevant data. The names of these options are generally self-explanatory.
</p>
</div>
<div id="protein-domain-organization">
<h5>Protein Domain Organization</h5>
<p>
Protein domains, such as <strong>SMART</strong> or <strong>Pfam</strong> domains, are displayed as small rectangles containing a unique domain abbreviation. Larger meta-domains, like <code>7TM_chemorcpt_1</code>, which typically span the entire protein, are represented as larger rectangles. Note that the size of the rectangle does not correspond to the actual size of the domain.
</p>
<p>
A <a href="help.html#domain-abbreviations" target="_blank">table of abbreviations</a> is used for selected domains that are found in multiple proteins. SMART/Pfam domains that are not listed in the abbreviation table are shown as gray rectangles with the SMART/Pfam identifier inside. These rectangles link to the corresponding SMART or Pfam entry.
</p>
<p>
Numbers within the rectangles represent the number of amino acids and indicate parts of the protein that are not assigned to any domain. To improve performance, images representing the domain organization of all proteins were pre-calculated for faster response times.
</p>
<p>
Gaps between domains that are smaller than 30 amino acids are suppressed, as they likely reflect artificial boundaries of the consensus sequences used to predict domains, which tend to be smaller than the actual domain. For example, an Immunoglobulin (IG) domain is approximately 125 amino acids in size, while the consensus sequence for the SMART IG domain (SM000409) is only 100 amino acids.
</p>
<p>
On the mutation results page, users can adjust the suppression of gaps to a smaller value for more precise output.
</p>
</div>
<div id="display-options-mutations">
<h5>Special Display Options for Mutations</h5>
<p>
<code>Wrap after x domains</code>:
Some proteins contain a large number of domains, which can make it challenging to view them all on a single line. This option allows users to specify the maximum number of domains to display per line for better visualization.
</p>
<p>
<code>Show gaps > x amino acids</code>:
By default, gaps greater than 30 amino acids are suppressed (as explained above). If a more precise location of the mutation is needed, users can lower this threshold to show smaller gaps between domains.
</p>
</div>
<div id="display-options-expression-data">
<h5>Special Display Options for Expression Data (Stages, Tissues, Embryo)</h5>
<p>
<strong>Checkboxes:</strong>
Each of the three expression data sets (stages, tissues, embryo) has a graphic display of expression data for each gene. To provide a complete overview of these data sets, each results page includes checkboxes that allow users to <strong>also</strong> display the graphs for:
</p>
<ul style="margin-bottom: 20px;">
<li><code><strong>Stage-specific</strong> expression graph</code></li>
<li><code><strong>L2 tissue</strong> expression graph</code></li>
<li><code><strong>Embryonic tissue</strong> expression graph</code></li>
</ul>
<p>
By selecting these options, users can easily access all three graphical representations, offering a comprehensive view of the gene expression across different stages, tissues, and embryonic development.
</p>
</div>
</div>
<!----------------------- Display Options Subpages End ----------------------->
<!----------------------- Tools Subpages Start ----------------------->
<div id="tools" class="help-content-section">
<div class="date-last-updated">
<h4>Last updated on Sep 20, 2024</h4>
</div>
<div class="help-content-section-title">
<h4>Tools</h4>
</div>
<div id="compare-tool">
<h5>Compare Tool</h5>
<p>Compare provides an easy way to find unique and common genes within two sets of genes (two lists of terms of any kind). The input fields accept a comma-separated list of terms such as the "list of genes/proteins" found on the results pages of GExplore. The out consists of three lists: the common genes and the unique genes from each of the two input sets. </p>
</div>
<div id="convert-tool">
<h5>Convert Tool</h5>
<p>The convert input field accepts any combination of <em>C. elegans</em> gene identifiers:</p>
<ul style="margin-bottom: 20px;">
<li>Locus Name: <code>nid-1</code></li>
<li>Gene Sequence Name: <code>F54F3.1</code></li>
<li>WormBase Gene ID: <code>WBGene00003738</code></li>
<li>Protein Sequence Name: <code>F54F3.1a</code></li>
<li>Wormpep ID: <code>CE18731</code></li>
<li>Uniprot ID: <code>Q93791</code></li>
</ul>
<p>The output consists of a table with all the identifiers for all the genes in the input field. This can be used to standardize identifiers that come from different sources or to convert one set of identifiers into another one.</p>
</div>
</div>
<!----------------------- Tools Subpages End ----------------------->
<!----------------------- Domain Abbreviations Start ----------------------->
<div id="domain-abbreviations" class="help-content-section">
<div class="date-last-updated">
<h4>Last updated on Sep 25, 2024</h4>
</div>
<div class="help-content-section-title">
<h4>Table of Domain Abbreviations</h4>
</div>
<p>
Domains are depicted as small rectangles containing a unique domain abbreviation. Meta-domains like <code>7TM_chemorcpt_1</code>, which typically cover the entire protein, are displayed as larger rectangles. The size of the rectangle does not reflect the actual domain size.
</p>
<!-- Table Structure -->
<div class="table-wrapper">
<table>
<thead>
<tr>
<th>Abbreviation</th>
<th>Display</th>
<th>Pfam</th>
<th>SMART</th>
<th>Description</th>
</tr>
</thead>
<tbody><tr>
<td class="abbrev_col"><a name="14_3_3" id="14_3_3"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=14_3_3&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">14_3_3</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/14_3_3.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF00244/">PF00244</a> </td>
<td class="ipr_col"><a href="http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=SM00101">SM00101</a> </td>
<td class="description_col">14_3_3 domain</td>
</tr>
<tr>
<td class="abbrev_col"><a name="3b-HSD" id="3b-HSD"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=3b-HSD&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">3b-HSD</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/3b-HSD.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF01073/">PF01073</a> </td>
<td class="ipr_col"></td>
<td class="description_col">3-beta hydroxysteroid dehydrogenase/isomerase family</td>
</tr>
<tr>
<td class="abbrev_col"><a name="7TM_GPCR_Sra" id="7TM_GPCR_Sra"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=7TM_GPCR_Sra&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">7TM_GPCR_Sra</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/7TM_GPCR_Sra.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF02117/">PF02117</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Nematode chemoreceptor, Sra</td>
</tr>
<tr>
<td class="abbrev_col"><a name="7TM_GPCR_Srab" id="7TM_GPCR_Srab"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=7TM_GPCR_Srab&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">7TM_GPCR_Srab</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/7TM_GPCR_Srab.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF10292/">PF10292</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Serpentine type 7TM GPCR receptor class Srab</td>
</tr>
<tr>
<td class="abbrev_col"><a name="7TM_GPCR_Srb" id="7TM_GPCR_Srb"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=7TM_GPCR_Srb&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">7TM_GPCR_Srb</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/7TM_GPCR_Srb.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF02175/">PF02175</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Serpentine beta receptor</td>
</tr>
<tr>
<td class="abbrev_col"><a name="7TM_GPCR_Srbc" id="7TM_GPCR_Srbc"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=7TM_GPCR_Srbc&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">7TM_GPCR_Srbc</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/7TM_GPCR_Srbc.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF10316/">PF10316</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Serpentine type 7TM GPCR chemoreceptor Srbc</td>
</tr>
<tr>
<td class="abbrev_col"><a name="7TM_GPCR_Sre" id="7TM_GPCR_Sre"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=7TM_GPCR_Sre&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">7TM_GPCR_Sre</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/7TM_GPCR_Sre.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF03125/">PF03125</a> </td>
<td class="ipr_col"></td>
<td class="description_col">C. elegans Sre G protein-coupled chemoreceptor</td>
</tr>
<tr>
<td class="abbrev_col"><a name="7TM_GPCR_Srg" id="7TM_GPCR_Srg"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=7TM_GPCR_Srg&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">7TM_GPCR_Srg</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/7TM_GPCR_Srg.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF02118">PF02118</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Serpentine gamma receptor, Caenorhabditis species</td>
</tr>
<tr>
<td class="abbrev_col"><a name="7TM_GPCR_Srh" id="7TM_GPCR_Srh"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=7TM_GPCR_Srh&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">7TM_GPCR_Srh</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/7TM_GPCR_Srh.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF10318">PF10318</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Serpentine type 7TM GPCR receptor class Srh</td>
</tr>
<tr>
<td class="abbrev_col"><a name="7TM_GPCR_Sri" id="7TM_GPCR_Sri"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=7TM_GPCR_Sri&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">7TM_GPCR_Sri</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/7TM_GPCR_Sri.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF10327">PF10327</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Serpentine type 7TM GPCR receptor class Sri</td>
</tr>
<tr>
<td class="abbrev_col"><a name="7TM_GPCR_Srj" id="7TM_GPCR_Srj"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=7TM_GPCR_Srj&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">7TM_GPCR_Srj</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/7TM_GPCR_Srj.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF10319">PF10319</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Serpentine type 7TM GPCR receptor class Srj</td>
</tr>
<tr>
<td class="abbrev_col"><a name="7TM_GPCR_Srr" id="7TM_GPCR_Srr"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=7TM_GPCR_Srr&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">7TM_GPCR_Srr</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/7TM_GPCR_Srr.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF03268">PF03268</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Domain of unknown function DUF267</td>
</tr>
<tr>
<td class="abbrev_col"><a name="7TM_GPCR_Srsx" id="7TM_GPCR_Srsx"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=7TM_GPCR_Srsx&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">7TM_GPCR_Srsx</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/7TM_GPCR_Srsx.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF10320">PF10320</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Serpentine type 7TM GPCR receptor class Srsx</td>
</tr>
<tr>
<td class="abbrev_col"><a name="7TM_GPCR_Srt" id="7TM_GPCR_Srt"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=7TM_GPCR_Srt&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">7TM_GPCR_Srt</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/7TM_GPCR_Srt.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF10321">PF10321</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Serpentine type 7TM GPCR receptor class Srt</td>
</tr>
<tr>
<td class="abbrev_col"><a name="7TM_GPCR_Sru" id="7TM_GPCR_Sru"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=7TM_GPCR_Sru&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">7TM_GPCR_Sru</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/7TM_GPCR_Sru.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF10322">PF10322</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Serpentine type 7TM GPCR receptor class Sru</td>
</tr>
<tr>
<td class="abbrev_col"><a name="7TM_GPCR_Srv" id="7TM_GPCR_Srv"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=7TM_GPCR_Srv&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">7TM_GPCR_Srv</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/7TM_GPCR_Srv.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF10323">PF10323</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Serpentine type 7TM GPCR receptor class Srv</td>
</tr>
<tr>
<td class="abbrev_col"><a name="7TM_GPCR_Srw" id="7TM_GPCR_Srw"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=7TM_GPCR_Srw&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">7TM_GPCR_Srw</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/7TM_GPCR_Srw.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF10324">PF10324</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Serpentine type 7TM GPCR receptor class Srw</td>
</tr>
<tr>
<td class="abbrev_col"><a name="7TM_GPCR_Srx" id="7TM_GPCR_Srx"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=7TM_GPCR_Srx&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">7TM_GPCR_Srx</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/7TM_GPCR_Srx.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF10328">PF10328</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Serpentine type 7TM GPCR receptor class Srx</td>
</tr>
<tr>
<td class="abbrev_col"><a name="7TM_GPCR_Srxa" id="7TM_GPCR_Srxa"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=7TM_GPCR_Srxa&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">7TM_GPCR_Srxa</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/7TM_GPCR_Srxa.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF03383">PF03383</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Serpentine type 7TM GPCR receptor class Srxa</td>
</tr>
<tr>
<td class="abbrev_col"><a name="7TM_GPCR_Srz" id="7TM_GPCR_Srz"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=7TM_GPCR_Srz&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">7TM_GPCR_Srz</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/7TM_GPCR_Srz.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF10325">PF10325</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Serpentine type 7TM GPCR receptor class Srz</td>
</tr>
<tr>
<td class="abbrev_col"><a name="7TM_GPCR_Str" id="7TM_GPCR_Str"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=7TM_GPCR_Str&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">7TM_GPCR_Str</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/7TM_GPCR_Str.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF10326">PF10326</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Serpentine type 7TM GPCR receptor class Str</td>
</tr>
<tr>
<td class="abbrev_col"><a name="AA_perm" id="AA_perm"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=AA_perm&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">AA_perm</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/AA_perm.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF00324">PF00324</a> </td>
<td class="ipr_col"></td>
<td class="description_col">amino acid permease</td>
</tr>
<tr>
<td class="abbrev_col"><a name="Aa_trans" id="Aa_trans"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=Aa_trans&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">Aa_trans</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/Aa_trans.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF01490">PF01490</a> </td>
<td class="ipr_col"></td>
<td class="description_col">amino acid transporter</td>
</tr>
<tr>
<td class="abbrev_col"><a name="AAA" id="AAA"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=AAA&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">AAA</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/AAA.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF00004">PF00004</a> </td>
<td class="ipr_col"><a href="http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=SM00382">SM00382</a> </td>
<td class="description_col">AAA ATPase</td>
</tr>
<tr>
<td class="abbrev_col"><a name="ABC2_m" id="ABC2_m"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=ABC2_m&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">ABC2_m</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/ABC2_m.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF01061">PF01061</a> </td>
<td class="ipr_col"></td>
<td class="description_col">ABC-2 type transporter</td>
</tr>
<tr>
<td class="abbrev_col"><a name="ABC_transporter" id="ABC_transporter"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=ABC_transporter&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">ABC_transporter</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/ABC_transporter.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF00005">PF00005</a> </td>
<td class="ipr_col"></td>
<td class="description_col">ABC transporter related </td>
</tr>
<tr>
<td class="abbrev_col"><a name="ABC_transporter_TM" id="ABC_transporter_TM"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=ABC_transporter_TM&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">ABC_transporter_TM</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/ABC_transporter_TM.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF00664">PF00664</a> <a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF06472">PF06472</a> </td>
<td class="ipr_col"></td>
<td class="description_col">ABC transporter, transmembrane region, type 1</td>
</tr>
<tr>
<td class="abbrev_col"><a name="ABHyd" id="ABHyd"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=ABHyd&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">ABHyd</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/ABHyd.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF00561">PF00561</a> </td>
<td class="ipr_col"></td>
<td class="description_col">alpha/beta hydrolase fold</td>
</tr>
<tr>
<td class="abbrev_col"><a name="AbHyd3" id="AbHyd3"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=AbHyd3&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">AbHyd3</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/AbHyd3.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF07859">PF07859</a> </td>
<td class="ipr_col"></td>
<td class="description_col">alpha/beta hydrolase fold</td>
</tr>
<tr>
<td class="abbrev_col"><a name="ACBP" id="ACBP"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=ACBP&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">ACBP</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/ACBP.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF00887">PF00887</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Acyl CoA binding protein</td>
</tr>
<tr>
<td class="abbrev_col"><a name="AcCoA_dh" id="AcCoA_dh"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=AcCoA_dh&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">AcCoA_dh</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/AcCoA_dh.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF00441">PF00441</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Acyl-CoA dehydrogenase, C-terminal domain</td>
</tr>
<tr>
<td class="abbrev_col"><a name="actin" id="actin"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=actin&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">actin</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/actin.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF00022">PF00022</a> </td>
<td class="ipr_col"><a href="http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=SM00268">SM00268</a> </td>
<td class="description_col">Actin/actin-like</td>
</tr>
<tr>
<td class="abbrev_col"><a name="Acy_dh2" id="Acy_dh2"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=Acy_dh2&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">Acy_dh2</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/Acy_dh2.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF08028">PF08028</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Acyl-CoA dehydrogenase, C-terminal domain</td>
</tr>
<tr>
<td class="abbrev_col"><a name="Acy_dh_M" id="Acy_dh_M"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=Acy_dh_M&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">Acy_dh_M</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/Acy_dh_M.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF02770">PF02770</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Acyl-CoA dehydrogenase, middle domain</td>
</tr>
<tr>
<td class="abbrev_col"><a name="Acy_dh_N" id="Acy_dh_N"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=Acy_dh_N&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">Acy_dh_N</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/Acy_dh_N.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF02771">PF02771</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Acyl-CoA dehydrogenase, N-terminal domain</td>
</tr>
<tr>
<td class="abbrev_col"><a name="AcylT" id="AcylT"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=AcylT&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">AcylT</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/AcylT.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF00583">PF00583</a> </td>
<td class="ipr_col"></td>
<td class="description_col">AhpC/TSA family</td>
</tr>
<tr>
<td class="abbrev_col"><a name="Acyltransferase" id="Acyltransferase"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=Acyltransferase&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">Acyltransferase</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/Acyltransferase.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF01757">PF01757</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Acyltransferase 3</td>
</tr>
<tr>
<td class="abbrev_col"><a name="AD" id="AD"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=AD&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">AD</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/AD.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF01421">PF01421</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Peptidase M12B, ADAM/reprolysin</td>
</tr>
<tr>
<td class="abbrev_col"><a name="ADH_N" id="ADH_N"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=ADH_N&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">ADH_N</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/ADH_N.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF00107">PF00107</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Zinc-binding dehydrogenase</td>
</tr>
<tr>
<td class="abbrev_col"><a name="Ah_perox" id="Ah_perox"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=Ah_perox&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">Ah_perox</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/Ah_perox.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF03098">PF03098</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Animal haem peroxidase</td>
</tr>
<tr>
<td class="abbrev_col"><a name="AhpC" id="AhpC"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=AhpC&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">AhpC</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/AhpC.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF00578">PF00578</a> </td>
<td class="ipr_col"></td>
<td class="description_col">AhpC/TSA family</td>
</tr>
<tr>
<td class="abbrev_col"><a name="AKR" id="AKR"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=AKR&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">AKR</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/AKR.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF00248">PF00248</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Aldo/keto reductase family</td>
</tr>
<tr>
<td class="abbrev_col"><a name="Aldedh" id="Aldedh"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=Aldedh&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">Aldedh</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/Aldedh.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF00171">PF00171</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Aldehyde dehydrogenase family</td>
</tr>
<tr>
<td class="abbrev_col"><a name="AMPB" id="AMPB"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=AMPB&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">AMPB</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/AMPB.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF00501">PF00501</a> </td>
<td class="ipr_col"></td>
<td class="description_col">AMP-binding enzyme</td>
</tr>
<tr>
<td class="abbrev_col"><a name="ANFR" id="ANFR"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=ANFR&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">ANFR</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/ANFR.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF01094">PF01094</a> </td>
<td class="ipr_col"></td>
<td class="description_col">receptor family ligand binding region</td>
</tr>
<tr>
<td class="abbrev_col"><a name="Ankyr" id="Ankyr"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=Ankyr&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">Ankyr</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/Ankyr.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF00023">PF00023</a> </td>
<td class="ipr_col"><a href="http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=SM00248">SM00248</a> </td>
<td class="description_col">Ankyrin repeat</td>
</tr>
<tr>
<td class="abbrev_col"><a name="APH" id="APH"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=APH&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">APH</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/APH.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF01636">PF01636</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Phosphotransferase enzyme family</td>
</tr>
<tr>
<td class="abbrev_col"><a name="Apple" id="Apple"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=Apple&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">Apple</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/Apple.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF00024">PF00024</a> </td>
<td class="ipr_col"><a href="http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=SM00223">SM00223</a> <a href="http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=SM00473">SM00473</a> </td>
<td class="description_col">apple</td>
</tr>
<tr>
<td class="abbrev_col"><a name="Arm" id="Arm"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=Arm&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">Arm</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/Arm.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF00514">PF00514</a> </td>
<td class="ipr_col"><a href="http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=SM00185">SM00185</a> </td>
<td class="description_col">armadillo repeat</td>
</tr>
<tr>
<td class="abbrev_col"><a name="Arre_C" id="Arre_C"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=Arre_C&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">Arre_C</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/Arre_C.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF02752">PF02752</a> </td>
<td class="ipr_col"><a href="http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=SM01017">SM01017</a> </td>
<td class="description_col">Arrestin (or S-antigen), C-terminal domain</td>
</tr>
<tr>
<td class="abbrev_col"><a name="Arre_N" id="Arre_N"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=Arre_N&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">Arre_N</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/Arre_N.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF00339">PF00339</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Arrestin (or S-antigen), N-terminal domain</td>
</tr>
<tr>
<td class="abbrev_col"><a name="Asp" id="Asp"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=Asp&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">Asp</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/Asp.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF00026">PF00026</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Aspartate protease</td>
</tr>
<tr>
<td class="abbrev_col"><a name="AT" id="AT"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=AT&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">AT</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/AT.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF01821">PF01821</a> </td>
<td class="ipr_col"><a href="http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=SM00104">SM00104</a> </td>
<td class="description_col">Anaphylatoxin/fibulin</td>
</tr>
<tr>
<td class="abbrev_col"><a name="AT_12" id="AT_12"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=AT_12&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">AT_12</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/AT_12.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF00155">PF00155</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Aminotransferase class I and II</td>
</tr>
<tr>
<td class="abbrev_col"><a name="AT_5" id="AT_5"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=AT_5&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">AT_5</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/AT_5.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF00266">PF00266</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Aminotransferase class-V</td>
</tr>
<tr>
<td class="abbrev_col"><a name="AT_hook" id="AT_hook"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=AT_hook&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">AT_hook</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/AT_hook.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF02178">PF02178</a> </td>
<td class="ipr_col"><a href="http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=SM00384">SM00384</a> </td>
<td class="description_col">DNA binding domain with preference for A/T rich regions</td>
</tr>
<tr>
<td class="abbrev_col"><a name="B4_1N" id="B4_1N"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=B4_1N&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">B4_1N</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/B4_1N.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF00373">PF00373</a> </td>
<td class="ipr_col"><a href="http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=SM00295">SM00295</a> </td>
<td class="description_col">Band 4.1, N-terminal</td>
</tr>
<tr>
<td class="abbrev_col"><a name="BACK" id="BACK"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=BACK&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">BACK</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/BACK.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF07707">PF07707</a> </td>
<td class="ipr_col"><a href="http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=SM00875">SM00875</a> </td>
<td class="description_col">BTB And C-terminal Kelch</td>
</tr>
<tr>
<td class="abbrev_col"><a name="Band_7" id="Band_7"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=Band_7&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">Band_7</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/Band_7.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF01145">PF01145</a> </td>
<td class="ipr_col"><a href="http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=SM00244">SM00244</a> </td>
<td class="description_col">Band 7 protein (found in stomatin)</td>
</tr>
<tr>
<td class="abbrev_col"><a name="Bestrophin" id="Bestrophin"></a><a href="../cgi-bin/gexplore/gexplore.pl?abbrev=Bestrophin&search_page=combined&aaThres=30&db=WB250&domain_display=ON&sizeThres=ON&meta=ON">Bestrophin</a></td><td class="abbrev_col"><div style=" text-align: center;"><img src="domain_img/Bestrophin.png"></div></td>
<td class="ipr_col"><a href="https://www.ebi.ac.uk/interpro/entry/pfam/PF01062">PF01062</a> </td>
<td class="ipr_col"></td>
<td class="description_col">Bestrophin</td>
</tr>