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 EC, 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_CP0382623,6233,370951583,708,164RefSeq:NZ_CP038262
pEC_gr13138112026128,013RefSeq:NZ_CP038263
pEC_gr689840576,956RefSeq:NZ_CP038264
pEC_mcr4.341370443,093RefSeq:NZ_CP038265
Total:3,8913,603951933,956,226
Ortholog data available?Yes
Database Contents
Genes3,891
Pathways269
Enzymatic Reactions1,320
Transport Reactions112
Polypeptides3,605
Protein Complexes46
Enzymes779
Transporters341
Compounds1,081
Transcription Units2,719
tRNAs73
Protein Features4,493
GO Terms1,223
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)
BIOSAMPLESAMN10386510
NCBI BioProjectPRJNA224116
NCBI-Taxonomy470
Geographic LocationCzech Republic
Latitude/Longitude49.19 N 16.6 E
Collection Date2018-12-31/2017-12-31
Annotation ProviderNCBI RefSeq
Annotation Date2019-04-3
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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