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 sp. DUT-2 DUT-2, 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_CP0146513,6933,203963943,844,171RefSeq:NZ_CP014651
unnamed1160131029141,965RefSeq:NZ_CP014652
unnamed2503501550,047RefSeq:NZ_CP014653
unnamed3342001419,820RefSeq:NZ_CP014654
unnamed413130011,158RefSeq:NZ_CP014655
unnamed575025,511RefSeq:NZ_CP014656
Total:3,9573,407964544,072,672
Ortholog data available?Yes
Database Contents
Genes3,957
Pathways231
Enzymatic Reactions1,305
Transport Reactions7
Polypeptides3,409
Protein Complexes21
Enzymes630
Transporters349
Compounds1,103
Transcription Units2,811
tRNAs73
Protein Features4,122
GO Terms178
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter sp. DUT-2
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04525297
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1809055
Environmentmarine sediments
Geographic LocationChina
Collection Date2015-12-20
Annotation ProviderNCBI RefSeq
Annotation Date2019-04-2
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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