Accessing EC Search on the PATRIC Website
An advanced search, described below, may be conducted from the “Searches and Tools” tab at the top of the PATRIC site and from the “Search Tools” box on any Organism Landing page. To learn about Organism Landing pages, see the PATRIC Data Organization Overview tutorial.
- Note: Searches conducted using EC Search from the “Search Tools” box on an Organism Landing page will be pre-scoped to the taxonomic level of the page.
EC Search Overview
The Enzyme Commission (EC) number is a numerical classification scheme for enzymes based on the chemical reactions they catalyze. Our EC Search tool enables researchers to locate proteins annotated with specified EC criteria.
Using EC Search
To begin, select your phylum, class, order, family, genus, species, or genomes of interest via the Taxonomy Tree tab, the Alphabetized Organism tab, or begin typing in the “Jump to” field. Additionally, if you are a registered PATRIC user, you may access any of your previously saved Organism data via the My Groups tab. You may also chose to filter your search via entering a Keyword, EC Number, EC Name, or Annotation Source. Then click on the Search button. You will be taken to an initial EC Search Results Table. Note: Larger searches may take PATRIC several minutes.
EC Search Results Table
- All tables accessed via EC Search may be sorted as described in Feature Table FAQs.
- Search results may be filtered by keyword or various Metatdata categories, such as Annotation using the “Filter By” panel on the left. For an explanation of various annotation sources, see Annotation FAQs.
- You may click on links in the EC Search Results Table within rows to navigate to specific PATRIC genome pages (Genome Name), NCBI nucleotide page for that genome (Accession), specific PATRIC locus pages (Locus Tag), the ExPASy page for a specific EC Number (EC Number), or a PATRIC Pathways Table for your selected EC Number (Pathways). Note: The Accession column in not shown in the default view. For information on what you may do from a PATRIC Pathways Table see Comparative Pathway Tool FAQs. For more information on the ExPASy page for a specific EC number, visit the ExPASy (Expert Protein Analysis System) website.
- You may utilize the EC Search Table Toolbar, located in the light blue row to:
- Save selected items to groups within your Workspace by clicking the Add Feature(s) button. To learn more about how to save data for future visits and utilize your personal Workspace see Workspace FAQs.
- View or download selected DNA and/or protein sequence data in FASTA format. The table itself, or selected data within it, are also downloadable in both excel and .txt file formats.
- View pathways and associated pathway information for your selected genes by clicking the Pathway Summary button.
- Conduct Multiple Sequence Alignment analysis on selected items by clicking the Multiple Sequence Alignment button. For more details on this tool see Multiple Sequence Alignment FAQs.
- Utilize the ID Mapping Tool on selected items by clicking the Map IDs button. For more information on this tool see ID Mapping FAQs.
- Customize columns shown/hidden in your results table with the Columns button
- Access the PATRIC FAQs glossary within PATRIC eNews by clicking on the PATRIC FAQs button.