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 25-Oct-2020 from the annotated genome of Acetobacter oryzifermentans SLV-7, 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 24.5) [Karp16, Karp11] using MetaCyc version 24.1 [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_CP0111202,6742,52877692,799,488RefSeq:NZ_CP011120
unnamed1172148024165,374RefSeq:NZ_CP011121
unnamed2126106020116,245RefSeq:NZ_CP011122
unnamed335300525,290RefSeq:NZ_CP011123
Total:3,0072,812771183,106,397
Ortholog data available?No
Database Contents
Genes3,007
Pathways240
Enzymatic Reactions1,128
Transport Reactions57
Polypeptides2,812
Protein Complexes39
Enzymes654
Transporters241
Compounds860
Transcription Units1,882
tRNAs58
Protein Features3,332
GO Terms1
Database Version29.0
Sequence SourceGCF_001628715.1
Synonyms Acetobacter sp. SLV-7
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acetobacter
Acetobacter oryzifermentans
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN03437041
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1633874
EnvironmentVinegar
Geographic LocationSouth Korea
Collection Date2014-03-2
Annotation ProviderNCBI RefSeq
Annotation Date2020-04-9
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
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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