Database Authors
Pallavi Subhraveti1, Peter Midford1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Oct-2019 from the annotated genome of Salmonella enterica servovar Typhimurium str. FORC88, as obtained from RefSeq (see the RefSeq entry for the authors of the original genome sequence). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 23.0) [Karp16, Karp11] using MetaCyc version 23.1 [Caspi20]. It has not undergone any manual curation or review, and may contain errors. Development of this PGDB was supported by grant GM080746 from the National Institutes of Health.
Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_CP0290294,5174,305122904,634,278RefSeq:NZ_CP029029
Ortholog data available?Yes
Database Contents
Genes4,517
Pathways402
Enzymatic Reactions1,983
Transport Reactions224
Polypeptides4,307
Protein Complexes81
Enzymes1,080
Transporters535
Compounds1,520
Transcription Units2,911
tRNAs84
Protein Features5,928
GO Terms2,322
Database Version29.0
Synonyms Bacillus typhimurium
Salmonella choleraesuis serotype typhimurium
Salmonella enterica 1,4,[5],12,:i:1,2
Salmonella enterica ser. typhimurium
Salmonella enterica serotype Typhimurium
Salmonella enterica serovar Typhimurium
Salmonella enterica subsp. enterica serovar 1,4,[5],12,:i:1,2
Salmonella typhi-murium
Salmonella enterica subsp. enterica serovar Typhimurium NCTC 74 [[Salmonella typhimurium]]
Salmonella enterica subsp. enterica serovar Typhimurium JCM 1652 [[Salmonella typhimurium]]
Salmonella enterica subsp. enterica serovar Typhimurium CIP 58.58 [[Salmonella typhimurium]]
Salmonella enterica subsp. enterica serovar Typhimurium ATCC 13311 [[Salmonella typhimurium]]
Salmonella enterica subsp. enterica serovar Typhimurium
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Enterobacterales
Enterobacteriaceae
Salmonella
Salmonella enterica
Salmonella enterica enterica
Salmonella enterica enterica serovar Typhimurium
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN08944422
NCBI BioProjectPRJNA224116
NCBI-Taxonomy90371
EnvironmentHuman blood
Geographic LocationSouth Korea
Latitude/Longitude37.57 N 128.98 E
Collection Date2015-01-31/2015-02-1
HostHomo sapiens
Human Microbiome Body Siteblood
Annotation ProviderNCBI RefSeq
Annotation Date2019-05-7
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.8
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

References

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

Karp16: Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A, Fulcher C, Keseler IM, Caspi R (2016). "Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform 17(5);877-90. PMID: 26454094

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