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 CMC-CR-MDR-Ab66, 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_CP0163003,8163,64897713,990,003RefSeq:NZ_CP016300
pCMCVTAb1-Ab6611911612110,967RefSeq:NZ_CP016301
pCMCVTAb2-Ab6694870773,188RefSeq:NZ_CP016302
Total:4,0293,85198804,174,158
Ortholog data available?Yes
Database Contents
Genes4,029
Pathways291
Enzymatic Reactions1,469
Transport Reactions101
Polypeptides3,851
Protein Complexes53
Enzymes853
Transporters380
Compounds1,070
Transcription Units2,717
tRNAs76
Protein Features4,605
GO Terms2,527
Database Version29.0
Sequence SourceGCF_001922245.1
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)
BIOSAMPLESAMN04096370
NCBI BioProjectPRJNA224116
NCBI-Taxonomy470
EnvironmentTA
Geographic LocationUSA
Latitude/Longitude37.2667 N 79.9333 W
HostHomo sapiens
Annotation ProviderNCBI RefSeq
Annotation Date2021-02-1
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.0
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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