Database Authors
Pallavi Subhraveti1, Peter Midford, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2019 from the annotated genome of Salmonella enterica CVM 19447, 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 23.0 [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
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_AHTP01000020387368415359,142RefSeq:NZ_AHTP01000020
NZ_AHTP01000019372348915352,268RefSeq:NZ_AHTP01000019
NZ_AHTP01000005327307416338,549RefSeq:NZ_AHTP01000005
NZ_AHTP01000011326312212317,554RefSeq:NZ_AHTP01000011
NZ_AHTP01000029289276310295,987RefSeq:NZ_AHTP01000029
NZ_AHTP0100003821420833242,920RefSeq:NZ_AHTP01000038
NZ_AHTP01000043235221410239,410RefSeq:NZ_AHTP01000043
NZ_AHTP0100001325223949226,449RefSeq:NZ_AHTP01000013
NZ_AHTP0100003720319427217,173RefSeq:NZ_AHTP01000037
NZ_AHTP01000008188175211183,616RefSeq:NZ_AHTP01000008
NZ_AHTP0100000617316751175,551RefSeq:NZ_AHTP01000006
NZ_AHTP01000018160150010146,753RefSeq:NZ_AHTP01000018
NZ_AHTP0100000114013613145,616RefSeq:NZ_AHTP01000001
NZ_AHTP0100001215314337139,488RefSeq:NZ_AHTP01000012
NZ_AHTP0100002611110614121,183RefSeq:NZ_AHTP01000026
NZ_AHTP0100001411911135116,928RefSeq:NZ_AHTP01000014
NZ_AHTP0100000712411833108,878RefSeq:NZ_AHTP01000007
NZ_AHTP01000034938724100,240RefSeq:NZ_AHTP01000034
NZ_AHTP0100004496876390,622RefSeq:NZ_AHTP01000044
NZ_AHTP0100003694841988,808RefSeq:NZ_AHTP01000036
NZ_AHTP0100000383820188,414RefSeq:NZ_AHTP01000003
NZ_AHTP0100003189862187,087RefSeq:NZ_AHTP01000031
NZ_AHTP0100003275711375,618RefSeq:NZ_AHTP01000032
NZ_AHTP0100000267640375,432RefSeq:NZ_AHTP01000002
NZ_AHTP0100003369661269,599RefSeq:NZ_AHTP01000033
NZ_AHTP0100001763582362,951RefSeq:NZ_AHTP01000017
NZ_AHTP0100001552520051,951RefSeq:NZ_AHTP01000015
NZ_AHTP0100002531300131,622RefSeq:NZ_AHTP01000025
NZ_AHTP0100000434330130,202RefSeq:NZ_AHTP01000004
NZ_AHTP0100002449480126,310RefSeq:NZ_AHTP01000024
NZ_AHTP0100000921200120,653RefSeq:NZ_AHTP01000009
13 Undisplayed Contigs/Replicons372614336,841
Total:4,7324,473821774,663,815
Ortholog data available?Yes
Database Contents
Genes4,728
Pathways366
Enzymatic Reactions1,881
Transport Reactions211
Polypeptides4,487
Protein Complexes79
Enzymes1,070
Transporters523
Compounds1,395
Transcription Units3,058
tRNAs67
GO Terms2,956
Database Version29.0
Synonyms Salmonella enterica subsp. enterica serovar Newport str. CVM 19447
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Enterobacterales
Enterobacteriaceae
Salmonella
Salmonella enterica
Salmonella enterica enterica
Salmonella enterica enterica serovar Newport
Salmonella enterica enterica serovar Newport str. CVM 19447
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN01816116
NCBI BioProjectPRJNA224116
NCBI-Taxonomy796737
Environmentfrog food
Geographic LocationViet Nam
Annotation ProviderNCBI
Annotation Date2017-11-23
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.3
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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