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 42N, 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_AESX01000067251235610239,562RefSeq:NZ_AESX01000067
NZ_AESX01000056270242820225,716RefSeq:NZ_AESX01000056
NZ_AESX0100004620519348221,533RefSeq:NZ_AESX01000046
NZ_AESX0100007117917702208,457RefSeq:NZ_AESX01000071
NZ_AESX01000041228215112207,092RefSeq:NZ_AESX01000041
NZ_AESX0100007818717809204,098RefSeq:NZ_AESX01000078
NZ_AESX01000057208194410194,389RefSeq:NZ_AESX01000057
NZ_AESX0100001219218624191,433RefSeq:NZ_AESX01000012
NZ_AESX0100005517016721175,445RefSeq:NZ_AESX01000055
NZ_AESX0100001114413815147,756RefSeq:NZ_AESX01000011
NZ_AESX0100004914113614143,723RefSeq:NZ_AESX01000049
NZ_AESX0100005816315526142,470RefSeq:NZ_AESX01000058
NZ_AESX0100003015314319140,622RefSeq:NZ_AESX01000030
NZ_AESX01000025137126011138,297RefSeq:NZ_AESX01000025
NZ_AESX0100004313713205134,064RefSeq:NZ_AESX01000043
NZ_AESX01000019153139212121,552RefSeq:NZ_AESX01000019
NZ_AESX0100001310810314110,692RefSeq:NZ_AESX01000013
NZ_AESX010000231029615105,399RefSeq:NZ_AESX01000023
NZ_AESX010000591059924103,821RefSeq:NZ_AESX01000059
NZ_AESX010000381061020497,441RefSeq:NZ_AESX01000038
NZ_AESX0100003688812595,989RefSeq:NZ_AESX01000036
NZ_AESX0100005397916092,913RefSeq:NZ_AESX01000053
NZ_AESX0100003764640084,245RefSeq:NZ_AESX01000037
NZ_AESX0100000774720281,836RefSeq:NZ_AESX01000007
NZ_AESX0100002975671777,574RefSeq:NZ_AESX01000029
NZ_AESX0100007279761276,280RefSeq:NZ_AESX01000072
NZ_AESX0100002183771574,918RefSeq:NZ_AESX01000021
NZ_AESX0100003375700566,784RefSeq:NZ_AESX01000033
NZ_AESX0100002660552363,814RefSeq:NZ_AESX01000026
NZ_AESX0100001566632161,515RefSeq:NZ_AESX01000015
NZ_AESX0100003458570161,514RefSeq:NZ_AESX01000034
NZ_AESX0100001660561356,532RefSeq:NZ_AESX01000016
NZ_AESX0100002855540156,266RefSeq:NZ_AESX01000028
NZ_AESX0100005255493354,607RefSeq:NZ_AESX01000052
NZ_AESX0100002457550249,598RefSeq:NZ_AESX01000024
NZ_AESX0100007643410246,798RefSeq:NZ_AESX01000076
NZ_AESX0100006438370139,558RefSeq:NZ_AESX01000064
NZ_AESX0100006228280034,117RefSeq:NZ_AESX01000062
NZ_AESX0100004737322331,019RefSeq:NZ_AESX01000047
NZ_AESX0100003928223327,735RefSeq:NZ_AESX01000039
NZ_AESX0100003548480026,097RefSeq:NZ_AESX01000035
NZ_AESX0100006328260223,521RefSeq:NZ_AESX01000063
NZ_AESX0100007031280322,546RefSeq:NZ_AESX01000070
NZ_AESX0100005121210022,462RefSeq:NZ_AESX01000051
NZ_AESX0100004221180318,481RefSeq:NZ_AESX01000042
NZ_AESX0100001813130015,722RefSeq:NZ_AESX01000018
NZ_AESX0100007512100214,259RefSeq:NZ_AESX01000075
NZ_AESX0100005415121211,580RefSeq:NZ_AESX01000054
NZ_AESX010000601311209,635RefSeq:NZ_AESX01000060
31 Undisplayed Contigs/Replicons342972858,373
Total:4,8254,519722344,709,850
Ortholog data available?Yes
Database Contents
Genes4,823
Pathways355
Enzymatic Reactions1,842
Transport Reactions215
Polypeptides4,549
Protein Complexes81
Enzymes1,053
Transporters524
Compounds1,406
Transcription Units3,119
tRNAs60
GO Terms2,638
Database Version29.0
Synonyms Salmonella enterica subsp. enterica serovar Montevideo strain 42N
Salmonella enterica subsp. enterica serovar Montevideo str. 42N
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Enterobacterales
Enterobacteriaceae
Salmonella
Salmonella enterica
Salmonella enterica enterica
Salmonella enterica enterica serovar Montevideo
Salmonella enterica enterica serovar Montevideo str. 42N
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00754299
NCBI BioProjectPRJNA224116
NCBI-Taxonomy763921
Annotation ProviderNCBI
Annotation Date2017-11-22
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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