Database Authors
Pallavi Subhraveti1, Anamika Kothari1, Peter Midford1, Ron Caspi1, Lisa Moore1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 30-Oct-2024 from the annotated genome of Acetobacter pasteurianus SRCM101342, as obtained from RefSeq (annotation date: 05-JUN-2024). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 28.5) [Karp11, Karp16] using MetaCyc version 28.1 [Caspi20]. It has not undergone any manual curation or review, and may contain errors.
Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_CP0215092,6252,49076592,754,755RefSeq:NZ_CP021509
pAP1342-3256231025256,755RefSeq:NZ_CP021512
pAP1342-2189158031190,983RefSeq:NZ_CP021511
pAP1342-549490043,021RefSeq:NZ_CP021514
pAP1342-1291901022,563RefSeq:NZ_CP021510
pAP1342-422200219,899RefSeq:NZ_CP021513
Total:3,1702,967761273,287,976
Ortholog data available?No
Database Contents
Genes3,170
Pathways267
Enzymatic Reactions1,471
Transport Reactions56
Polypeptides2,967
Protein Complexes60
Enzymes694
Transporters227
Compounds1,272
Transcription Units2,156
tRNAs57
Protein Features3,554
GO Terms3,797
Database Version29.0
Sequence SourceGCF_002173735.1
Synonyms Acetobacter pasteurianus subsp. pasteurianus
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acetobacter
Acetobacter pasteurianus
Acetobacter pasteurianus pasteurianus
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN07125916
NCBI BioProjectPRJNA224116
NCBI-Taxonomy481145
Environmentfood
Geographic LocationSouth Korea
Collection Date2017-01-9
Annotation ProviderNCBI RefSeq
Annotation Date2024-06-5
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.7
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, BIOCYC17.