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 ascendens LMG 1591, 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
NZ_CP0151682,7002,380752452,810,721RefSeq:NZ_CP015168
unnamed1258215043259,464RefSeq:NZ_CP015169
unnamed211084026117,661RefSeq:NZ_CP015170
unnamed331270428,186RefSeq:NZ_CP015171
Total:3,0992,706753183,216,032
Ortholog data available?No
Database Contents
Genes3,099
Pathways246
Enzymatic Reactions1,269
Transport Reactions42
Polypeptides2,706
Protein Complexes4
Enzymes688
Transporters232
Compounds933
Transcription Units2,044
tRNAs56
Protein Features3,390
GO Terms153
Database Version29.0
Sequence SourceGCF_001766255.1
Synonyms Acetobacter pasteurianus subsp. ascendens
Acetobacter pasteurianus subsp. paradoxus
Bacterium ascendans
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acetobacter
Acetobacter ascendens
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04605655
NCBI BioProjectPRJNA224116
NCBI-Taxonomy481146
Geographic LocationNetherlands
Collection Date1975
Annotation ProviderNCBI RefSeq
Annotation Date2021-05-5
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.1
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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