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_2007-16-27-01, 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_AMHJ0100005935133984365,734RefSeq:NZ_AMHJ01000059
NZ_AMHJ01000051323305612337,655RefSeq:NZ_AMHJ01000051
NZ_AMHJ0100005329828963336,420RefSeq:NZ_AMHJ01000053
NZ_AMHJ0100003021220615221,430RefSeq:NZ_AMHJ01000030
NZ_AMHJ0100003920119344219,397RefSeq:NZ_AMHJ01000039
NZ_AMHJ0100001819719403212,758RefSeq:NZ_AMHJ01000018
NZ_AMHJ0100004517816693176,488RefSeq:NZ_AMHJ01000045
NZ_AMHJ0100000113913405157,350RefSeq:NZ_AMHJ01000001
NZ_AMHJ0100000412912612129,544RefSeq:NZ_AMHJ01000004
NZ_AMHJ0100002010610222116,149RefSeq:NZ_AMHJ01000020
NZ_AMHJ0100002612211741112,551RefSeq:NZ_AMHJ01000026
NZ_AMHJ0100003412010929110,399RefSeq:NZ_AMHJ01000034
NZ_AMHJ0100000396913294,095RefSeq:NZ_AMHJ01000003
NZ_AMHJ0100001382780490,407RefSeq:NZ_AMHJ01000013
NZ_AMHJ0100007187834088,720RefSeq:NZ_AMHJ01000071
NZ_AMHJ0100004070680283,041RefSeq:NZ_AMHJ01000040
NZ_AMHJ0100001679770281,432RefSeq:NZ_AMHJ01000016
NZ_AMHJ0100002473700378,931RefSeq:NZ_AMHJ01000024
NZ_AMHJ0100006772673274,054RefSeq:NZ_AMHJ01000067
NZ_AMHJ0100002882801172,832RefSeq:NZ_AMHJ01000028
NZ_AMHJ0100006169660372,393RefSeq:NZ_AMHJ01000061
NZ_AMHJ0100004763590471,178RefSeq:NZ_AMHJ01000047
NZ_AMHJ0100000672700268,426RefSeq:NZ_AMHJ01000006
NZ_AMHJ0100006366630367,875RefSeq:NZ_AMHJ01000063
NZ_AMHJ0100002751491158,589RefSeq:NZ_AMHJ01000027
NZ_AMHJ0100002947450257,372RefSeq:NZ_AMHJ01000029
NZ_AMHJ0100004145413150,546RefSeq:NZ_AMHJ01000041
NZ_AMHJ0100001944380640,937RefSeq:NZ_AMHJ01000019
NZ_AMHJ0100003137370037,878RefSeq:NZ_AMHJ01000031
NZ_AMHJ0100000730300034,591RefSeq:NZ_AMHJ01000007
NZ_AMHJ0100003532284032,290RefSeq:NZ_AMHJ01000035
NZ_AMHJ0100002128260229,290RefSeq:NZ_AMHJ01000021
NZ_AMHJ0100002235350025,452RefSeq:NZ_AMHJ01000022
NZ_AMHJ0100004636360021,940RefSeq:NZ_AMHJ01000046
NZ_AMHJ0100000923230021,380RefSeq:NZ_AMHJ01000009
NZ_AMHJ0100001429280121,050RefSeq:NZ_AMHJ01000014
NZ_AMHJ0100003713120113,995RefSeq:NZ_AMHJ01000037
NZ_AMHJ0100005012110112,677RefSeq:NZ_AMHJ01000050
NZ_AMHJ0100002327270011,932RefSeq:NZ_AMHJ01000023
NZ_AMHJ010000361919009,813RefSeq:NZ_AMHJ01000036
NZ_AMHJ010000331414007,338RefSeq:NZ_AMHJ01000033
30 Undisplayed Contigs/Replicons282262143,780
Total:3,8583,673681173,970,109
Ortholog data available?Yes
Database Contents
Genes3,858
Pathways269
Enzymatic Reactions1,293
Transport Reactions96
Polypeptides3,685
Protein Complexes53
Enzymes776
Transporters354
Compounds1,053
Transcription Units2,694
tRNAs60
GO Terms1,277
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii AB_2007-16-27-01
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471276
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1221254
Environmenthospital surface
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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