Download NMPDRposter - Edwards @ SDSU

National Microbial Pathogen Data Resource
Robert Edwards, Leslie McNeil, Folker Meyer, Ross Overbeek, Bob Olson, Veronika Vonstein, Rick Stevens
About us
Organisms
Campylobacter
Chlamydia
Chlamydophila
Haemophilus
Listeria
Mycoplasma
Neisseria
Staphylococcus
Streptococcus
Treponema
Ureaplasma
Vibrio
Using NMPDR
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.
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
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.
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.
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.
Search results
provide links to
other databases
that contain
information about
the same gene.
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.
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.
subsystems
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
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
FELLOWSHIP FOR
INTERPRETATION OF
GENOMES
compare regions
www.nmpdr.org
funding