1. National Microbial Pathogen Data Resource www.nmpdr.org About us NMPDR is a Bioinformatics Resource Center dedicated to the thorough understanding of core organisms assigned by the National Institute of Allergy and Infectious Diseases. NMPDR is an environment for the comparative functional analysis of genomes. Organisms Campylobacter Chlamydia Chlamydophila Haemophilus Listeria Mycoplasma Neisseria Staphylococcus Streptococcus Treponema Ureaplasma Vibrio The database now includes the complete genomes of more than 150 strains of pathogenic bacteria that are the core focus of NMPDR annotators: Campylobacter, Chlamydia, Chlamydophila, Haemophilus, Listeria, Mycoplasma, Neisseria, Staphylococcus, Streptococcus, Treponema, Ureaplasma, and Vibrio. Also included are complete genomes from more than 500 other organisms that provide a broad context for comparative analysis. All genomes are queried by searching from the home page. Each group of NMPDR core pathogens is linked to a page that will limit the search to that set of genomes. Using NMPDR Begin with a keyword search for the gene/protein of interest. In this case, a gene in the sulfonamide resistance (folate synthesis) operon, was located by searching for “EC 2.7.6.3” from the Streptococcus page. The search function joins terms with “AND.” Genes that match all terms in the search are returned in a table. To analyze the gene of interest in the context of its neighbors in the genome, click on the NMPDR button. Search results provide links to other databases that contain information about the same gene. Clicking the GBrowse button displays a layout of genes against the genome. You can zoom in and out. You may select to map pathogenicity islands, homologous regions from related genomes, and so forth. Clicking on a gene of interest in this display will open the NMPDR context page, just like clicking on the NMPDR button in the results table. Clustering of genes on prokaryotic genomes is frequently caused by a functional relationship shared by the neighboring genes. The genomic context of the focus gene (highlighted green) is displayed in both a table and graphic, in which blue neighbors frequently cluster across other genomes, and red neighbors do not. The table provides links to precomputed functional clustering scores, fc-sc, which is a measure of the frequency that the genes are co-localized in genomes, along with the phylogenetic distance between those genomes. Clicking on the score will display a table of genomes in which the gene of interest is likely to have a functional relationship with its neighbor. Even if the gene of focus is not functionally clustered in the genome under inspection, it may be clustered in other genomes. To find best clusters in other genomes, click on the CL button NMPDR tools genomic context functional clusters compare regions Clicking on the option Show Compare Regions provides a visual comparison of your gene (in red) with its five closest homologs. This tool may be reset to display a wider or narrower view of the region matched to more or fewer other genomes. Sets of homologous genes share the same label and color. Tables listing these sets are provided by the commentary button. The genes in the display are linked to their respective context pages, so by clicking on the red arrow in the last genome displayed under Strep pneumo, the context of the cluster in Fusobacterium nucleatum is displayed. In this organism, the cluster has been reduced to three of the five enzymatic functions found in the sulfonamide resistance operon of Strep pneumo. The original function we searched for, EC 2.7.6.3, is a separate gene in pyogenes, but it has fused with the next function in the pathway, EC 4.1.2.25, in both pneumo and Fus. nuc. The different structures of the operons in the two species of Strep may provide insight to differing sulfonamide resistance in these organisms. The most exciting tool available in the NMPDR will compare two sets of genomes and display either the set of genes in common, or the set of genes that distinguish the organisms in set 1 from those in set 2. For example, the genes contained in Strep pneumo that are absent in Strep pyogenes number 1,044, of which 36 are RNAs and about a third encode hypothetical proteins. signature genes subsystems If the gene of interest plays a role that has been included in a subsystem, meaning metabolic or regulatory pathway or structural complex, then that subsystem and its variants in other genomes may be viewed in a table with one click. The subsystems annotated in NMPDR are constructed by experts in the biochemistry of the given system, rather than by a curator who focuses on all systems of a given organism. Links are provided to metabolic maps in KEGG. This work was funded by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract HHSN266200400042C funding Robert Edwards, Leslie McNeil, Folker Meyer, Ross Overbeek, Bob Olson, Veronika Vonstein, Rick Stevens