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 Acinetobacter baumannii IS-251, 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_AMEJ01000055500480173518,082RefSeq:NZ_AMEJ01000055
NZ_AMEJ0100001432531348365,086RefSeq:NZ_AMEJ01000014
NZ_AMEJ0100006331130812324,676RefSeq:NZ_AMEJ01000063
NZ_AMEJ0100007128127164304,694RefSeq:NZ_AMEJ01000071
NZ_AMEJ0100001126826413288,822RefSeq:NZ_AMEJ01000011
NZ_AMEJ0100004921621321244,064RefSeq:NZ_AMEJ01000049
NZ_AMEJ01000070193177115196,743RefSeq:NZ_AMEJ01000070
NZ_AMEJ01000059183170211178,927RefSeq:NZ_AMEJ01000059
NZ_AMEJ0100000116816206177,731RefSeq:NZ_AMEJ01000001
NZ_AMEJ0100002610710601112,930RefSeq:NZ_AMEJ01000026
NZ_AMEJ0100003510910342108,552RefSeq:NZ_AMEJ01000035
NZ_AMEJ0100006710710340101,032RefSeq:NZ_AMEJ01000067
NZ_AMEJ0100001982802086,366RefSeq:NZ_AMEJ01000019
NZ_AMEJ0100004779751382,386RefSeq:NZ_AMEJ01000047
NZ_AMEJ0100002794891478,546RefSeq:NZ_AMEJ01000027
NZ_AMEJ0100001063630071,274RefSeq:NZ_AMEJ01000010
NZ_AMEJ0100006868616168,461RefSeq:NZ_AMEJ01000068
NZ_AMEJ0100000265630266,524RefSeq:NZ_AMEJ01000002
NZ_AMEJ0100005063580564,365RefSeq:NZ_AMEJ01000050
NZ_AMEJ0100002549453163,189RefSeq:NZ_AMEJ01000025
NZ_AMEJ0100005656550158,768RefSeq:NZ_AMEJ01000056
NZ_AMEJ0100001656542048,496RefSeq:NZ_AMEJ01000016
NZ_AMEJ0100007238380043,927RefSeq:NZ_AMEJ01000072
NZ_AMEJ0100002148461139,268RefSeq:NZ_AMEJ01000021
NZ_AMEJ0100003852510139,128RefSeq:NZ_AMEJ01000038
NZ_AMEJ0100002031283037,001RefSeq:NZ_AMEJ01000020
NZ_AMEJ0100002933320129,576RefSeq:NZ_AMEJ01000029
NZ_AMEJ0100000542401128,417RefSeq:NZ_AMEJ01000005
NZ_AMEJ0100005122201127,829RefSeq:NZ_AMEJ01000051
NZ_AMEJ0100002828280026,864RefSeq:NZ_AMEJ01000028
NZ_AMEJ0100006628280017,146RefSeq:NZ_AMEJ01000066
NZ_AMEJ0100001819150412,111RefSeq:NZ_AMEJ01000018
NZ_AMEJ0100000812100211,524RefSeq:NZ_AMEJ01000008
NZ_AMEJ0100000917170011,483RefSeq:NZ_AMEJ01000009
NZ_AMEJ0100004413130011,402RefSeq:NZ_AMEJ01000044
NZ_AMEJ0100005713130011,255RefSeq:NZ_AMEJ01000057
36 Undisplayed Contigs/Replicons515102250,641
Total:3,9123,74373964,007,286
Ortholog data available?Yes
Database Contents
Genes3,912
Pathways271
Enzymatic Reactions1,363
Transport Reactions110
Polypeptides3,764
Protein Complexes52
Enzymes797
Transporters356
Compounds1,056
Transcription Units2,682
tRNAs66
GO Terms2,620
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii IS-251
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00761222
NCBI BioProjectPRJNA224116
NCBI-Taxonomy903906
Environmentrespiratory tract
Geographic LocationIraq
Collection Date2008-09-20
HostHomo sapiens
Annotation ProviderNCBI
Annotation Date2017-03-15
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.1
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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