Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 8-Mar-2022 from the annotated genome of Acinetobacter chinensis WCHAc010005, 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 26.0) [Karp16, Karp11] using MetaCyc version 26.0 [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_CP0321343,4613,308108453,600,635RefSeq:NZ_CP032134
pOXA58_01000562530966,715RefSeq:NZ_CP032133
pNDM1_01000544410339,357RefSeq:NZ_CP032132
p1_01000519190018,155RefSeq:NZ_CP032127
p2_01000566005,433RefSeq:NZ_CP032128
p3_01000555004,353RefSeq:NZ_CP032129
p4_01000511001,398RefSeq:NZ_CP032130
p5_01000511001,243RefSeq:NZ_CP032131
Total:3,5993,434108573,737,289
Ortholog data available?Yes
Database Contents
Genes3,599
Pathways252
Enzymatic Reactions1,277
Transport Reactions55
Polypeptides3,434
Protein Complexes6
Enzymes737
Transporters327
Compounds932
Transcription Units2,555
tRNAs83
Protein Features4,036
GO Terms254
Database Version29.0
Sequence SourceGCF_002165375.2
Synonyms Acinetobacter sp. WCHAc010005
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter chinensis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN07138949
NCBI BioProjectPRJNA224116
NCBI-Taxonomy2004650
EnvironmentSewage
Geographic LocationChina
Collection Date2015-10-31
Annotation ProviderNCBI RefSeq
Annotation Date2021-11-1
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
Annotation CommentBest-placed reference protein set; GeneMarkS-2+
NCBI Genome Typerepresentative

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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