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 OIFC143, 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_AFDL010000022,8632,71568802,952,924RefSeq:NZ_AFDL01000002
NZ_AFDL010000041,2661,19626441,281,499RefSeq:NZ_AFDL01000004
pOIFC143-128145134011127,633RefSeq:NZ_AFDL01000008
pOIFC143-7095910469,518RefSeq:NZ_AFDL01000006
pOIFC143-6.21110016,241RefSeq:NZ_AFDL01000007
pOIFC143-2.311002,277RefSeq:NZ_AFDL01000005
NZ_AFDL010000031100782RefSeq:NZ_AFDL01000003
NZ_AFDL010000011001453RefSeq:NZ_AFDL01000001
Total:4,3834,148941414,441,327
Ortholog data available?Yes
Database Contents
Genes4,383
Pathways276
Enzymatic Reactions1,333
Transport Reactions117
Polypeptides4,149
Protein Complexes56
Enzymes836
Transporters396
Compounds1,103
Transcription Units2,935
tRNAs72
GO Terms1,390
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii OIFC143
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02436631
NCBI BioProjectPRJNA224116
NCBI-Taxonomy903893
Geographic LocationUSA
Collection Date2003-07-31
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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