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 ATCC 10720, 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
NZ_CP0191814,9864,6951191724,865,682RefSeq:NZ_CP019181
pATCC10720141113028124,201RefSeq:NZ_CP019182
Total:5,1274,8081192004,989,883
Ortholog data available?Yes
Database Contents
Genes5,128
Pathways328
Enzymatic Reactions1,664
Transport Reactions220
Polypeptides4,809
Protein Complexes39
Enzymes1,088
Transporters539
Compounds1,268
Transcription Units3,232
tRNAs87
Protein Features6,133
GO Terms2,264
Database Version29.0
Synonyms Salmonella enterica subsp. enterica serovar Inverness strain ATCC 10720
Salmonella enterica subsp. enterica serovar Inverness str. ATCC 10720
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Enterobacterales
Enterobacteriaceae
Salmonella
Salmonella enterica
Salmonella enterica enterica
Salmonella enterica enterica serovar Inverness
Salmonella enterica enterica serovar Inverness str. ATCC 10720
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN01823716
NCBI BioProjectPRJNA224116
NCBI-Taxonomy941187

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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