As Part of Genome Annotation, Proteins are Mapped to Protein Families Called FIGfams

FIGfams enable comparative genomic analysis at PATRIC. They are generated by the Fellowship for Interpretation of Genomes (FIG) and are constructed from careful manual curation of subsystems and automated analysis of closely related strains. FIGfams are based on sequence similarity over the entire protein length, and on the conserved genomic context. Our Protein Family Sorter Tool allows researchers to compare protein families across closely related or diverse groups of genomes, visualize them using an interactive Heatmap, and generate multiple sequence alignments (with phylogenetic trees) for individual families.

Since this is a chart built by D3, this text should be replaced by relevant information from the data file.

Legend: Functional Hypothetical

Find and Analyze Protein Families with PATRIC Tools

View Protein Family Tutorials

  • This tutorial provides an overview of our Protein Family Sorter tool, which enables researchers to compare protein families across closely related or diverse groups of genomes, visualize them using an interactive Heatmap, and generate multiple sequence alignments (with phylogenetic trees) for individual families.

  • This downloadable pdf contains screenshots and detailed step-wise instructions for locating data of interest, such as finding a particular gene, finding the pan-proteome for all Mycobacterium genomes using the Protein Family Sorter and Heatmap, and examining pathways across Mycobacterium using the Comparative Pathway Tool and Heatmap.

  • As a result of the foodborne illness outbreak in Europe in 2011, numerous new E. coli genomes were sequenced and found to have acquired the genes necessary to produce Shiga toxins, which are believed to play a role in the strains’ high virulence. See how to identify and collect these genomes and the full set of Shiga toxins associated with them for further analysis.

  • See how to use PATRIC tables and the Table Toolbar including sorting, downloading, analysis tools, creating persistent column customization, and saving items to your workspace.

  • Between the spring of 2011 and June of 2012, twenty-seven new E. coli genomes were sequenced as a result of a European E. coli outbreak. Learn how we identify areas of these genomes that are different (e.g., missing or unique proteins) when compared to their closest phylogenetically-related E. coli genomes and then search for evidence of lateral transfer in cases where unique proteins were found in new virulent strains.

  • Data in PATRIC is organized in a similar fashion at various taxonomic levels throughout the website.  Follow along in this Mycobacterium example and see what data is available and where to find it for your favorite organisms/genomes/genes.

  • This downloadable pdf contains screenshots and detailed step-wise instructions for locating data of interest, such as finding a particular gene, finding the pan-proteome for all Brucella genomes using the Protein Family Sorter and Heatmap, and examining pathways across Brucella using the Comparative Pathway Tool and Heatmap.

  • Find out more about PATRIC data, analysis tools, and functionality in our Frequently Asked Questions.

How Do We Process and Clean Up Our Data?

How Do We Process and Clean Up Our Data?

Download Data

Annotation Source

File Type