Database Authors
Pallavi Subhraveti1, Quang Ong1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 27-Feb-2018 from the annotated genome of Acetobacter pasteurianus IFO 3283, 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 22.0) [Karp16, Karp11] using MetaCyc version 21.5 [Caspi18]. 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 Institutess of Health.
Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NC_0132092,7202,56575802,907,495RefSeq:NC_013209
pAPA01-011193155038191,799RefSeq:NC_013210
pAPA01-020172134038182,940RefSeq:NC_013211
pAPA01-03060550549,961RefSeq:NC_013212
pAPA01-04044003,204RefSeq:NC_013213
pAPA01-05033003,035RefSeq:NC_013214
pAPA01-06011001,815RefSeq:NC_013215
Total:3,1532,917751613,340,249
Ortholog data available?Yes
Database Contents
Genes3,154
Pathways219
Enzymatic Reactions1,132
Transport Reactions62
Polypeptides2,917
Protein Complexes37
Enzymes697
Transporters268
Compounds905
Transcription Units2,057
tRNAs57
Protein Features3,416
GO Terms12,991
Database Version29.0
Sequence SourceAPAS634452
Synonyms Acetobacter pasteurianus IFO 3283-01
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acetobacter
Acetobacter pasteurianus
Acetobacter pasteurianus pasteurianus
Acetobacter pasteurianus 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

References

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

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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