Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2022 from the annotated genome of Acinetobacter cumulans WCHAc060092, 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_CP0359343,2353,050112733,427,709RefSeq:NZ_CP035934
p1_060092168154104177,151RefSeq:NZ_CP035936
pNDM1_06009254510348,560RefSeq:NZ_CP035935
p2_06009223210218,761RefSeq:NZ_CP035937
p3_060092660012,247RefSeq:NZ_CP035938
p4_06009299009,699RefSeq:NZ_CP035939
p5_06009277008,138RefSeq:NZ_CP035940
p6_06009266004,692RefSeq:NZ_CP035941
p7_06009222002,123RefSeq:NZ_CP035942
p8_06009222001,791RefSeq:NZ_CP035943
Total:3,5123,308122823,710,871
Ortholog data available?Yes
Database Contents
Genes3,512
Pathways246
Enzymatic Reactions1,278
Transport Reactions55
Polypeptides3,308
Protein Complexes66
Enzymes723
Transporters289
Compounds942
Transcription Units2,521
tRNAs96
Protein Features4,051
GO Terms274
Database Version29.0
Sequence SourceGCF_003024525.3
Synonyms Acinetobacter sp. WCHAc060001
Acinetobacter sp. WCHAc060002
Acinetobacter sp. WCHAc060003
Acinetobacter sp. WCHAc060004
Acinetobacter sp. WCHAc060008
Acinetobacter sp. WCHAc060092
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter cumulans
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN08772519
NCBI BioProjectPRJNA224116
NCBI-Taxonomy2136182
EnvironmentSewage
Geographic LocationChina
Collection Date2018
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+

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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Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC18A.