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 AB_TG2631, 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_AMIM01000079315302112312,311RefSeq:NZ_AMIM01000079
NZ_AMIM0100004020220101208,534RefSeq:NZ_AMIM01000040
NZ_AMIM0100006315915504169,422RefSeq:NZ_AMIM01000063
NZ_AMIM0100004115514564166,291RefSeq:NZ_AMIM01000041
NZ_AMIM0100002915314913155,941RefSeq:NZ_AMIM01000029
NZ_AMIM0100004414213552150,472RefSeq:NZ_AMIM01000044
NZ_AMIM0100004612512041135,011RefSeq:NZ_AMIM01000046
NZ_AMIM0100002312011703129,095RefSeq:NZ_AMIM01000023
NZ_AMIM0100000511811305127,733RefSeq:NZ_AMIM01000005
NZ_AMIM0100001411110731118,977RefSeq:NZ_AMIM01000014
NZ_AMIM0100006711410923116,837RefSeq:NZ_AMIM01000067
NZ_AMIM0100007310810512114,168RefSeq:NZ_AMIM01000073
NZ_AMIM010000721009901107,953RefSeq:NZ_AMIM01000072
NZ_AMIM01000088807343107,736RefSeq:NZ_AMIM01000088
NZ_AMIM01000051969303104,524RefSeq:NZ_AMIM01000051
NZ_AMIM0100001990900096,876RefSeq:NZ_AMIM01000019
NZ_AMIM0100003986840296,148RefSeq:NZ_AMIM01000039
NZ_AMIM0100004582762475,917RefSeq:NZ_AMIM01000045
NZ_AMIM0100007572680467,692RefSeq:NZ_AMIM01000075
NZ_AMIM0100009468634165,509RefSeq:NZ_AMIM01000094
NZ_AMIM0100004977741264,722RefSeq:NZ_AMIM01000049
NZ_AMIM0100001857540364,454RefSeq:NZ_AMIM01000018
NZ_AMIM0100005656551057,321RefSeq:NZ_AMIM01000056
NZ_AMIM0100008652474155,367RefSeq:NZ_AMIM01000086
NZ_AMIM0100002447443053,798RefSeq:NZ_AMIM01000024
NZ_AMIM0100000641381248,844RefSeq:NZ_AMIM01000006
NZ_AMIM0100003044440048,319RefSeq:NZ_AMIM01000030
NZ_AMIM0100009546450147,225RefSeq:NZ_AMIM01000095
NZ_AMIM0100003651490247,166RefSeq:NZ_AMIM01000036
NZ_AMIM0100008246450144,079RefSeq:NZ_AMIM01000082
NZ_AMIM0100000240390143,275RefSeq:NZ_AMIM01000002
NZ_AMIM0100002838380043,201RefSeq:NZ_AMIM01000028
NZ_AMIM0100005739390042,702RefSeq:NZ_AMIM01000057
NZ_AMIM0100006543411142,600RefSeq:NZ_AMIM01000065
NZ_AMIM0100006141410042,237RefSeq:NZ_AMIM01000061
NZ_AMIM0100005537370041,270RefSeq:NZ_AMIM01000055
NZ_AMIM0100007137350237,331RefSeq:NZ_AMIM01000071
NZ_AMIM0100003829290031,814RefSeq:NZ_AMIM01000038
NZ_AMIM0100000324230128,565RefSeq:NZ_AMIM01000003
NZ_AMIM0100009225240127,807RefSeq:NZ_AMIM01000092
NZ_AMIM0100003328280026,659RefSeq:NZ_AMIM01000033
NZ_AMIM0100004826260024,765RefSeq:NZ_AMIM01000048
NZ_AMIM0100000926241123,980RefSeq:NZ_AMIM01000009
NZ_AMIM0100006422200222,735RefSeq:NZ_AMIM01000064
NZ_AMIM0100004317160119,040RefSeq:NZ_AMIM01000043
NZ_AMIM0100001331310018,588RefSeq:NZ_AMIM01000013
NZ_AMIM0100008930300018,522RefSeq:NZ_AMIM01000089
NZ_AMIM0100005917160118,313RefSeq:NZ_AMIM01000059
NZ_AMIM0100006819150417,533RefSeq:NZ_AMIM01000068
NZ_AMIM0100008110100014,265RefSeq:NZ_AMIM01000081
NZ_AMIM0100004712110113,990RefSeq:NZ_AMIM01000047
NZ_AMIM0100002712120013,242RefSeq:NZ_AMIM01000027
NZ_AMIM0100002024230111,567RefSeq:NZ_AMIM01000020
NZ_AMIM0100001520190110,017RefSeq:NZ_AMIM01000015
41 Undisplayed Contigs/Replicons747061988,842
Total:3,7553,59661983,881,302
Ortholog data available?Yes
Database Contents
Genes3,753
Pathways261
Enzymatic Reactions1,298
Transport Reactions111
Polypeptides3,624
Protein Complexes52
Enzymes796
Transporters365
Compounds1,057
Transcription Units2,638
tRNAs53
GO Terms2,346
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii AB_TG2631
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471230
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1221282
Environmentblood
HostHomo sapiens
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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