Comparative Pathway Tool¶
Accessing the Comparative Pathway Tool 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 Comparative Pathway Tool from the “Search Tools” box on an Organism Landing page will be pre-scoped to the taxonomic level of the page.
Comparative Pathway Tool Overview¶
The Comparative Pathway Tool allows you to identify a set of pathways based on taxonomy, EC number, pathway ID, pathway name and/or specific annotation type. The Comparative Pathway Tool displays a table of unique pathways that match the search criteria. From there, you can select specific pathways of interest and view the Comparative Pathway KEGG Map and the Comparative Pathway Heatmap.
Using the Comparative Pathway Tool¶
To begin, conduct an initial search by 1) selecting 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 2) utilizing the Keyword search functionality, or 3) a combination of both. Then click on the Search button. Note: Larger searches may take PATRIC several minutes. For an explanation of various annotation sources, please see Annotation FAQs.
Results will be shown in a Pathway table. From here you may do the following:
- Use the three tabs (Pathways, EC number, and Genes) at the top of
the table to navigate your search results. Click on links within
rows under each tab to navigate to the various pages:
- From the Pathway tab you can navigate within rows to a specific PATRIC Pathway Map page (Pathway Name), a table with all the EC numbers annotated in a particular pathway (Unique EC Count), and a table with all the genes in a particular pathway (Unique Gene Count).
- From the EC Number tab you can navigate within rows to a specific PATRIC Pathway Map page (Pathway Name), a table with all the genes for a particular EC number (Unique Gene Count).
- From the Genes tab you can navigate within rows to specific
PATRIC genome pages (Genome Name), NCBI nucleotide pages for
that genome (Accession), specific PATRIC locus pages (Locus
Tag), or a specific PATRIC Pathway Map page (Pathway Name).
- Note: The Accession column is not shown in the default view.
- Use the column headers to sort your search results.
- Use the Pathway Table Toolbar, located in the light blue row at the
top of the table 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 please 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 features by clicking the Multiple Sequence Alignment button. For more details on this tool please see Multiple Sequence Alignment FAQs.
- Utilize the ID Mapping Tool on selected features by clicking the Map IDs button. For more information on this tool please see ID Mapping FAQs.
- Customize columns shown/hidden in your results table with the Columns button.
- Click on any Pathway Name to view results via the default KEGG Map tab or the Heatmap Tab. For details on how to use these tools, please see Comparative KEGG Map FAQs and Comparative Pathway Heatmap FAQs.
Comparative Pathway Tool Information¶
- Genome Count: This gives the number of genomes that have some genes present in this pathway at the taxonomic level chosen.
- Unique Gene Count: This provides a list of all the genes in all the genomes that belong to this pathway. Clicking on any number in this column will provide a list of the annotated genes in each genome that belong to this family.
- Unique EC Count: The Enzyme Commission number (EC number) is a numerical classification scheme for enzymes, based on the chemical reactions they catalyze and in a given KEGG metabolic pathway, each step has an EC number assigned to it. In a given genome there may be several genes that have been assigned the same EC number, meaning that several different genes have the possibility of doing the same job. The unique EC count tells how many steps within the pathway have at least one gene behind them.
- EC Conservation %: For a single pathway (row), this number gives the percent of unique EC numbers present in all selected genomes. 100% describes a situation in which all unique EC numbers are present in all selected genomes. Smaller numbers indicate that there is one or more genomes are missing some EC numbers.
- Gene Conservation: A genome can have several genes that have been assigned the same EC number. Gene conservation provides an estimate of pathways where there might be redundancies, or where EC numbers are missing. Numbers greater than one mean that in at least one genome, there is more than one gene that has been assigned a particular EC number. Numbers less than one mean indicate that in at least one genome, a particular EC number is missing. This provides a quick way to see which pathways have perfect conservation across all genomes (Gene Conservation = 1) to those pathways where there are differences among the genomes. Users can then explore these differences by drilling down on either the Unique Gene Count, or the Unique EC Count.