Database Authors
Pallavi Subhraveti1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 12-Dec-2018 from the annotated genome of Salmonella enterica enterica serovar Typhimurium str. SL1344, as obtained from RefSeq (annotation date: 12-JAN-2018).

The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 23.0) [Karp16, Karp11] using MetaCyc version 22.6 [Caspi18]. 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 Institute of Health.

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NC_0168105,0054,7341221494,878,012RefSeq:NC_016810
pSLT_SL134412010901193,842RefSeq:NC_017720
pCol1B9_SL13441191140586,908RefSeq:NC_017718
pRSF1010_SL13441210028,688RefSeq:NC_017719
Total:5,2564,9671221675,067,450
Ortholog data available?Yes
Database Contents
Genes5,256
Pathways372
Enzymatic Reactions1,619
Transport Reactions152
Polypeptides4,972
Protein Complexes82
Enzymes1,099
Transporters529
Compounds1,154
Transcription Units3,318
tRNAs85
Growth Media7
Protein Features6,499
GO Terms43,766
Gene Essentiality Datasets7
Database Version29.0
Synonyms Salmonella enterica subsp. enterica str. serovar Typhimurium str. SL1344
Salmonella enterica subsp. enterica serovar Typhimurium strain SL1344
Salmonella typhimurium SL1344
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Enterobacterales
Enterobacteriaceae
Salmonella
Salmonella enterica
Salmonella enterica enterica
Salmonella enterica enterica serovar Typhimurium
Salmonella enterica enterica serovar Typhimurium str. SL1344
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMEA3138382
NCBI BioProjectPRJNA224116
NCBI-Taxonomy216597
Annotation ProviderNCBI
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.4
Annotation CommentBest-placed reference protein set; GeneMarkS+

References

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

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