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 15-Oct-2019 from the annotated genome of Acinetobacter baumannii ACN21, 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 23.1 [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_CP0386443,6733,450941293,827,138RefSeq:NZ_CP038644
unnamed113212219116,047RefSeq:NZ_CP038645
unnamed2644601857,333RefSeq:NZ_CP038646
unnamed392079,909RefSeq:NZ_CP038647
unnamed41111009,205RefSeq:NZ_CP038648
unnamed572057,396RefSeq:NZ_CP038649
unnamed681076,944RefSeq:NZ_CP038650
unnamed764025,844RefSeq:NZ_CP038651
unnamed871065,734RefSeq:NZ_CP038652
Total:3,9173,639951834,045,550
Ortholog data available?Yes
Database Contents
Genes3,917
Pathways262
Enzymatic Reactions1,287
Transport Reactions34
Polypeptides3,641
Protein Complexes36
Enzymes747
Transporters378
Compounds1,046
Transcription Units2,746
tRNAs73
Protein Features4,382
GO Terms1,894
Database Version29.0
Synonyms Acinetobacter genomosp. 2
Acinetobacter genomospecies 2
Bacterium anitratum
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)
BIOSAMPLESAMN11311113
NCBI BioProjectPRJNA224116
NCBI-Taxonomy470
Environmentblood
Geographic LocationIndia
Latitude/Longitude28.402 N 76.826 E
Collection Date2018-12-31/2017-12-31
HostHomo sapiens
Human Microbiome Body Siteblood
Annotation ProviderNCBI RefSeq
Annotation Date2019-04-11
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.8
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 (2019). "The MetaCyc database of metabolic pathways and enzymes-a 2019 update." Nucleic Acids Res. 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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