Database Authors
Carol A Fulcher1, Pallavi Subhraveti1, Anamika Kothari1, Suzanne Paley1, Ron Caspi1, Ingrid Keseler1, 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. LT2, as obtained from RefSeq (annotation date: 28-SEP-2017).

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]. The initial development of this PGDB was supported by grant GM080746 from the National Institute of Health.

UniProt links, gene and protein names, Protein Data Bank links, InterPro links, protein features, and Gene Ontology annotations were imported from UniProt [UniProt18]. Protein sequence features were imported from Pfam [Finn16]. A number of gene functions with experimental evidence were integrated from [Thiele11, Seif18]. A curation effort at SRI updated a number of genes, proteins, and metabolic pathways based on information from the biomedical literature.

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NC_0031974,6044,446117414,857,450RefSeq:NC_003197
pSLT1031021093,933RefSeq:NC_003277
Total:4,7074,548118414,951,383
Ortholog data available?Yes
Database Contents
Genes4,714
Pathways481
Enzymatic Reactions1,941
Transport Reactions194
Polypeptides4,554
Protein Complexes195
Enzymes1,407
Transporters542
Compounds1,340
Transcription Units2,961
tRNAs85
Growth Media22
Transcriptional Regulation9
Protein Features6,388
GO Terms70,742
Gene Essentiality Datasets1
Database Version29.0
Image of Salmonella Typhimurium cells
Image of Salmonella Typhimurium cells, provided by the National Institute of Allergy and Infectious Diseases (NIAID). Used under creative commons license.
Synonyms Salmonella enterica subsp. enterica str. serovar Typhimurium str. LT2
Salmonella enterica subsp. enterica serovar Typhimurium strain LT2
Salmonella enterica subsp. enterica serovar Typhimurium strain LT2-LTL2
Salmonella typhimurium LT2
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
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. LT2
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02604315
NCBI BioProjectPRJNA57799
NCBI-Taxonomy99287
Relationship to Oxygenfacultative
Temperature Rangemesophile
Pathogenicityanimal
NCBI Genome Typereference
Copyright 2019, SRI International. All Rights Reserved.

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

Finn16: Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, Salazar GA, Tate J, Bateman A (2016). "The Pfam protein families database: towards a more sustainable future." Nucleic Acids Res 44(D1);D279-85. PMID: 26673716

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

Seif18: Seif Y, Kavvas E, Lachance JC, Yurkovich JT, Nuccio SP, Fang X, Catoiu E, Raffatellu M, Palsson BO, Monk JM (2018). "Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits." Nat Commun 9(1);3771. PMID: 30218022

Thiele11: Thiele I, Hyduke DR, Steeb B, Fankam G, Allen DK, Bazzani S, Charusanti P, Chen FC, Fleming RM, Hsiung CA, De Keersmaecker SC, Liao YC, Marchal K, Mo ML, Ozdemir E, Raghunathan A, Reed JL, Shin SI, Sigurbjornsdottir S, Steinmann J, Sudarsan S, Swainston N, Thijs IM, Zengler K, Palsson BO, Adkins JN, Bumann D (2011). "A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2." BMC Syst Biol 5;8. PMID: 21244678

UniProt18: UniProt Consortium T (2018). "UniProt: the universal protein knowledgebase." Nucleic Acids Res 46(5);2699. PMID: 29425356

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