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 13-Mar-2021 from the annotated genome of Acetobacter pasteurianus IFO 3283 substr. IFO 3283-12, 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 25.0) [Karp16, Karp11] using MetaCyc version 24.5 [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
NC_0171082,7032,57376542,904,624RefSeq:NC_017108
pAPA12-014182151031191,411RefSeq:NC_017136
pAPA12-020162133029182,940RefSeq:NC_017113
pAPA12-03061600149,961RefSeq:NC_017114
pAPA12-04044003,204RefSeq:NC_017115
pAPA12-05033003,035RefSeq:NC_017116
pAPA12-06022001,815RefSeq:NC_017137
Total:3,1172,926761153,336,990
Ortholog data available?Yes
Database Contents
Genes3,117
Pathways246
Enzymatic Reactions1,196
Transport Reactions53
Polypeptides2,926
Protein Complexes40
Enzymes683
Transporters272
Compounds901
Transcription Units2,009
tRNAs57
Protein Features3,551
GO Terms2
Database Version29.0
Sequence SourceGCF_000010965.1
Synonyms Acetobacter pasteurianus NBRC 3283-12
Acetobacter pasteurianus IFO 3283-12
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acetobacter
Acetobacter pasteurianus
Acetobacter pasteurianus pasteurianus
Acetobacter pasteurianus pasteurianus IFO 3283-12
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00061107
NCBI BioProjectPRJNA224116
NCBI-Taxonomy634459
Annotation ProviderNCBI RefSeq
Annotation Date2020-12-20
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.0
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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