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 bereziniae CIP 70.12, 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 Institutes of Health.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_KB8497562,7032,57066672,895,014RefSeq:NZ_KB849756
NZ_KB8497551,7131,62437521,791,452RefSeq:NZ_KB849755
NZ_KB849754365336029340,066RefSeq:NZ_KB849754
Total:4,7814,5301031485,026,532
Ortholog data available?Yes
Database Contents
Genes4,781
Pathways227
Enzymatic Reactions1,350
Transport Reactions82
Polypeptides4,541
Protein Complexes41
Enzymes768
Transporters350
Compounds1,103
Transcription Units3,442
tRNAs77
GO Terms15,837
Database Version29.0
Synonyms Acinetobacter bereziniae CIP 70.12
Acinetobacter bereziniae CIP 70.12 = LMG 1003
Acinetobacter bereziniae LMG 1003
Acinetobacter bereziniae LMG 1003 = CIP 70.12
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter bereziniae
Acinetobacter bereziniae LMG 1003 = CIP 70.12
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN01087834
NCBI BioProjectPRJNA224116
NCBI-Taxonomy981324
Environmentwound
Collection Date1960
HostHomo sapiens
Annotation ProviderNCBI
Annotation Date2017-11-24
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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