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 wuhouensis WCHA60, 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_CP0317163,6683,500106623,851,088RefSeq:NZ_CP031716
p1_01006041410038,671RefSeq:NZ_CP031709
p2_01006040390130,787RefSeq:NZ_CP031710
p4_01006014140012,273RefSeq:NZ_CP031712
p3_01006013130012,086RefSeq:NZ_CP031711
p5_01006099005,424RefSeq:NZ_CP031713
p6_01006066005,113RefSeq:NZ_CP031714
p7_01006077005,009RefSeq:NZ_CP031715
Total:3,7983,629106633,960,451
Ortholog data available?Yes
Database Contents
Genes3,798
Pathways263
Enzymatic Reactions1,315
Transport Reactions61
Polypeptides3,629
Protein Complexes7
Enzymes758
Transporters349
Compounds958
Transcription Units2,760
tRNAs81
Protein Features4,321
GO Terms264
Database Version29.0
Sequence SourceGCF_001696605.3
Synonyms Acinetobacter sp. WCHA60
Acinetobacter sp. WCHA62
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter wuhouensis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN05356836
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1879050
Environmenthospital sewage
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+

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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