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 OIFC189, 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_AFDM010000091,5791,49061281,626,953RefSeq:NZ_AFDM01000009
NZ_AFDM010000081,03698027291,089,698RefSeq:NZ_AFDM01000008
NZ_AFDM010000041,0159834281,054,250RefSeq:NZ_AFDM01000004
NZ_AFDM01000001143127313116,434RefSeq:NZ_AFDM01000001
pOIFC189-11112111911110,967RefSeq:NZ_AFDM01000010
NZ_AFDM0100000350470336,787RefSeq:NZ_AFDM01000003
NZ_AFDM010000061111006,109RefSeq:NZ_AFDM01000006
NZ_AFDM010000023102835RefSeq:NZ_AFDM01000002
NZ_AFDM010000073102708RefSeq:NZ_AFDM01000007
NZ_AFDM010000052002374RefSeq:NZ_AFDM01000005
Total:3,9633,759961084,043,115
Ortholog data available?Yes
Database Contents
Genes3,963
Pathways261
Enzymatic Reactions1,299
Transport Reactions113
Polypeptides3,761
Protein Complexes53
Enzymes808
Transporters367
Compounds1,060
Transcription Units2,721
tRNAs74
GO Terms2,383
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii OIFC189
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00114925
NCBI BioProjectPRJNA224116
NCBI-Taxonomy903894
Geographic LocationUSA
Collection Date2003-10-4
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

Report Errors or Provide Feedback
Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC18A.