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_2008-15-69, 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_AMHN0100001025324634279,082RefSeq:NZ_AMHN01000010
NZ_AMHN0100000423723403251,225RefSeq:NZ_AMHN01000004
NZ_AMHN0100002623322076247,682RefSeq:NZ_AMHN01000026
NZ_AMHN0100000818418103193,028RefSeq:NZ_AMHN01000008
NZ_AMHN0100007318917892191,410RefSeq:NZ_AMHN01000073
NZ_AMHN0100000916716052176,116RefSeq:NZ_AMHN01000009
NZ_AMHN0100005013713133172,979RefSeq:NZ_AMHN01000050
NZ_AMHN0100001413613042143,965RefSeq:NZ_AMHN01000014
NZ_AMHN0100001214414112138,593RefSeq:NZ_AMHN01000012
NZ_AMHN0100006912011352131,485RefSeq:NZ_AMHN01000069
NZ_AMHN0100000511911702128,122RefSeq:NZ_AMHN01000005
NZ_AMHN0100006612212101127,651RefSeq:NZ_AMHN01000066
NZ_AMHN0100003813713502126,987RefSeq:NZ_AMHN01000038
NZ_AMHN0100000112211804125,504RefSeq:NZ_AMHN01000001
NZ_AMHN0100002912612600107,016RefSeq:NZ_AMHN01000029
NZ_AMHN01000011938832106,116RefSeq:NZ_AMHN01000011
NZ_AMHN0100001710810512103,745RefSeq:NZ_AMHN01000017
NZ_AMHN0100002187830499,340RefSeq:NZ_AMHN01000021
NZ_AMHN01000028103952697,837RefSeq:NZ_AMHN01000028
NZ_AMHN0100001988860295,769RefSeq:NZ_AMHN01000019
NZ_AMHN0100001691874092,732RefSeq:NZ_AMHN01000016
NZ_AMHN0100003389872090,262RefSeq:NZ_AMHN01000033
NZ_AMHN0100005275740186,160RefSeq:NZ_AMHN01000052
NZ_AMHN0100007471670475,788RefSeq:NZ_AMHN01000074
NZ_AMHN0100003771710065,987RefSeq:NZ_AMHN01000037
NZ_AMHN0100004155531159,544RefSeq:NZ_AMHN01000041
NZ_AMHN0100003555541055,418RefSeq:NZ_AMHN01000035
NZ_AMHN0100000653530055,093RefSeq:NZ_AMHN01000006
NZ_AMHN0100002353521052,832RefSeq:NZ_AMHN01000023
NZ_AMHN0100003948470150,390RefSeq:NZ_AMHN01000039
NZ_AMHN0100001348442243,620RefSeq:NZ_AMHN01000013
NZ_AMHN0100001535321234,659RefSeq:NZ_AMHN01000015
NZ_AMHN0100004030300034,654RefSeq:NZ_AMHN01000040
NZ_AMHN0100002030280233,098RefSeq:NZ_AMHN01000020
NZ_AMHN0100004226260028,356RefSeq:NZ_AMHN01000042
NZ_AMHN0100003428280026,436RefSeq:NZ_AMHN01000034
NZ_AMHN0100006425231123,602RefSeq:NZ_AMHN01000064
NZ_AMHN0100002224220221,838RefSeq:NZ_AMHN01000022
NZ_AMHN0100007019150420,585RefSeq:NZ_AMHN01000070
NZ_AMHN0100002716160016,843RefSeq:NZ_AMHN01000027
NZ_AMHN0100005120200015,213RefSeq:NZ_AMHN01000051
NZ_AMHN0100000715150012,518RefSeq:NZ_AMHN01000007
NZ_AMHN010000621283112,218RefSeq:NZ_AMHN01000062
NZ_AMHN0100006013120111,103RefSeq:NZ_AMHN01000060
NZ_AMHN010000361414009,132RefSeq:NZ_AMHN01000036
NZ_AMHN010000551413016,301RefSeq:NZ_AMHN01000055
29 Undisplayed Contigs/Replicons494362058,873
Total:4,0043,84265974,136,907
Ortholog data available?Yes
Database Contents
Genes4,004
Pathways275
Enzymatic Reactions1,329
Transport Reactions117
Polypeptides3,856
Protein Complexes55
Enzymes804
Transporters390
Compounds1,093
Transcription Units2,736
tRNAs57
GO Terms1,279
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii AB_2008-15-69
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471249
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1221258
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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