Database Authors
Pallavi Subhraveti1, Quang Ong1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 27-Feb-2018 from the annotated genome of Salmonella enterica ERL12960, 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 22.0) [Karp16, Karp11] using MetaCyc version 21.5 [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 Institutess of Health.
Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
Chromosome 15,0114,5741103274,807,646RefSeq:NZ_LT904894
213612916106,704RefSeq:NZ_LT904895
Total:5,1474,7031113334,914,350
Ortholog data available?Yes
Database Contents
Genes5,148
Pathways328
Enzymatic Reactions1,663
Transport Reactions213
Polypeptides4,704
Protein Complexes33
Enzymes1,060
Transporters518
Compounds1,264
Transcription Units3,212
tRNAs80
Protein Features8,374
GO Terms14,261
Database Version29.0
Synonyms ATCC 19430 [[Salmonella typhi]]
ATCC 19430 [[Salmonella typhi]]
Bacillus typhi
Bacterium (subgen. Eberthella) typhi
CUETM 79.394 [[Salmonella typhi]]
CUETM 79.394 [[Salmonella typhi]]
HAMBI 1306 [[Salmonella typhi]]
HAMBI 1306 [[Salmonella typhi]]
NCTC 8385 [[Salmonella typhi]]
NCTC 8385 [[Salmonella typhi]]
SGSC 2666 [[Salmonella typhi]]
Salmonella choleraesuis serovar Typhi
Salmonella choleraesuis typhi
Salmonella enterica ser. typhi
Salmonella enterica serotype Typhi
Salmonella enterica serovar Typhi
strain Felix Ty 2 [[Salmonella typhi]]
strain Ty 2 [[Salmonella typhi]]
strain Ty2 [[Salmonella typhi]]
Salmonella enterica subsp. enterica serovar Typhi
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Enterobacterales
Enterobacteriaceae
Salmonella
Salmonella enterica
Salmonella enterica enterica
Salmonella enterica enterica serovar Typhi
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMEA2072792
NCBI BioProjectPRJNA224116
NCBI-Taxonomy90370
EnvironmentNot known
Geographic LocationIndia
Collection Date2012

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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