Database Authors
J. Bashkin1, Jonathan Wagg1, Nan Guo1, Peter Karp1, Ron Caspi1
1SRI International
Summary The primary data source for this dataset is the full genome sequence of Bacillus anthracis Ames [Read03], derived from Genbank accession NC_003997.

This Pathway/Genome Database (PGDB) was created from the annotated genome using the PathoLogic [Karp11, Karp19] component of the Pathway Tools software and the MetaCyc reference database [Caspi20]. The PGDB, which integrates the biochemical reaction network and metabolic pathways of the organism with the genome, was improved by limited manual curation.

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
Chromosome 15,4395,31112805,227,293RefSeq:NC_003997
Ames Plasmid PX0120420400181,677RefSeq:NC_007322
Ames Plasmid PX021041040094,830RefSeq:NC_007323
Total:5,7475,61912805,503,800
Ortholog data available?Yes
Database Contents
Genes5,747
Pathways310
Enzymatic Reactions1,443
Transport Reactions82
Polypeptides5,621
Protein Complexes85
Enzymes922
Transporters480
Compounds1,122
Transcription Units4,075
tRNAs99
Protein Features822
Database Version29.0 [History of Updates]
Synonyms Bacillus anthracis AmesGenbank entry NC_003997
Bacillus anthracis strain Ames
Bacillus anthracis Ames
Bacillus anthracis str. Ames
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Bacilli
Bacillales
Bacillaceae
Bacillus <firmicutes>
Bacillus cereus group
Bacillus anthracis
Bacillus anthracis Ames
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
GOLD0000640
NCBI-Taxonomy198094
Relationship to Oxygenfacultative
Trophic Levelheterotroph
Temperature Rangemesophile
Biotic Relationshipfree-living
Pathogenicityanimal
NCBI Genome Typereference
Copyright 2004-2016 SRI International.

References

Caspi20: Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2020). "The MetaCyc database of metabolic pathways and enzymes - a 2019 update." Nucleic Acids Res 48(D1);D445-D453. PMID: 31586394

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

Karp19: Karp PD, Midford PE, Billington R, Kothari A, Krummenacker M, Latendresse M, Ong WK, Subhraveti P, Caspi R, Fulcher C, Keseler IM, Paley SM (2019). "Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform. PMID: 31813964

Read03: Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA, Gill SR, Holtzapple EK, Okstad OA, Helgason E, Rilstone J, Wu M, Kolonay JF, Beanan MJ, Dodson RJ, Brinkac LM, Gwinn M, DeBoy RT, Madpu R, Daugherty SC, Durkin AS, Haft DH, Nelson WC, Peterson JD, Pop M, Khouri HM, Radune D, Benton JL, Mahamoud Y, Jiang L, Hance IR, Weidman JF, Berry KJ, Plaut RD, Wolf AM, Watkins KL, Nierman WC, Hazen A, Cline R, Redmond C, Thwaite JE, White O, Salzberg SL, Thomason B, Friedlander AM, Koehler TM, Hanna PC, Kolsto AB, Fraser CM (2003). "The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria." Nature 423(6935);81-6. PMID: 12721629

Report Errors or Provide Feedback
Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC14.