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 Acetobacter pasteurianus IFO 3283 substr. IFO 3283-01, 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
NC_0132092,7062,57676542,907,495RefSeq:NC_013209
pAPA01-011184152032191,799RefSeq:NC_013210
pAPA01-020162133029182,940RefSeq:NC_013211
pAPA01-03061600149,961RefSeq:NC_013212
pAPA01-04044003,204RefSeq:NC_013213
pAPA01-05033003,035RefSeq:NC_013214
pAPA01-06022001,815RefSeq:NC_013215
Total:3,1222,930761163,340,249
Ortholog data available?Yes
Database Contents
Genes3,122
Pathways257
Enzymatic Reactions1,323
Transport Reactions44
Polypeptides2,930
Protein Complexes6
Enzymes712
Transporters300
Compounds994
Transcription Units2,009
tRNAs57
Protein Features30
GO Terms13,229
Database Version29.0
Sequence SourceGCF_000010825.1
Synonyms Acetobacter pasteurianus IFO 3283-01
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acetobacter
Acetobacter pasteurianus
Acetobacter pasteurianus IFO 3283-01
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00060943
NCBI BioProjectPRJNA224116
NCBI-Taxonomy634452
Annotation ProviderNCBI RefSeq
Annotation Date2021-08-15
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.2
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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