Database Authors
Pallavi Subhraveti1, Peter Midford1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 13-Mar-2021 from the annotated genome of Acinetobacter baumannii AF-401, 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 25.0) [Karp16, Karp11] using MetaCyc version 24.5 [Caspi20]. 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
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_CP0182544,1223,94397824,250,048RefSeq:NZ_CP018254
pAF-40117170017,583RefSeq:NZ_CP018255
Total:4,1393,96097824,267,631
Ortholog data available?Yes
Database Contents
Genes4,139
Pathways292
Enzymatic Reactions1,404
Transport Reactions100
Polypeptides3,960
Protein Complexes53
Enzymes845
Transporters379
Compounds1,073
Transcription Units2,723
tRNAs73
Protein Features4,712
GO Terms2,163
Database Version29.0
Sequence SourceGCF_001896005.1
Synonyms Acinetobacter genomosp. 2
Acinetobacter genomospecies 2
Acinetobacter sp. NCTC 7422
Bacterium anitratum
bacterium SPL81
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN06077191
NCBI BioProjectPRJNA224116
NCBI-Taxonomy470
EnvironmentSmall Colon
Geographic LocationMexico
Collection Date2009-07-1
HostHomo sapiens
Annotation ProviderNCBI RefSeq
Annotation Date2020-05-18
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

References

Caspi20: Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2020). "The MetaCyc database of metabolic pathways and enzymes - a 2019 update." Nucleic Acids Res 48(D1);D445-D453. PMID: 31586394

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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