Database Authors
Jonathan Wagg, SRI International
Summary The primary data source for this dataset was the annotated genome sequence of Shigella flexneri 2a str. 2457T [Wei03], accession number AE014073. This dataset does not include the sequences of four plasmids that are present in the organism, since their sequence was not available at the time. Strain 2457T was selected because it has been the subject of extensive molecular pathogenesis and genetics research.

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

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
Chromosome4,2044,07313104,599,354RefSeq:AE014073
Genes without a physical map position:3
Ortholog data available?Yes
Database Contents
Genes4,206
Pathways341
Enzymatic Reactions1,467
Transport Reactions141
Polypeptides4,086
Protein Complexes59
Enzymes908
Transporters426
Compounds1,089
Transcription Units2,929
tRNAs101
Growth Media19
Transcriptional Regulation561
Protein Features5,813
GO Terms2
Database Version29.0 [History of Updates]
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Enterobacterales
Enterobacteriaceae
Shigella
Shigella flexneri
Shigella flexneri 2a
Shigella flexneri 2a str. 2457T
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
GOLD0007206
NCBI-Taxonomy198215
Relationship to Oxygenfacultative
Trophic Levelheterotroph
Temperature Rangemesophile
Biotic Relationshipfree-living
Pathogenicityhuman
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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

Wei03: Wei J, Goldberg MB, Burland V, Venkatesan MM, Deng W, Fournier G, Mayhew GF, Plunkett G, Rose DJ, Darling A, Mau B, Perna NT, Payne SM, Runyen-Janecky LJ, Zhou S, Schwartz DC, Blattner FR (2003). "Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T." Infect Immun 71(5);2775-86. PMID: 12704152

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