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 01-June-2020 from the annotated genome of Acetobacter aceti TMW2.1153, 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_CP0146923,4123,154631953,725,037RefSeq:NZ_CP014692
Ortholog data available?Yes
Database Contents
Genes3,412
Pathways245
Enzymatic Reactions1,220
Transport Reactions64
Polypeptides3,155
Protein Complexes40
Enzymes695
Transporters283
Compounds946
Transcription Units2,275
tRNAs50
Protein Features3,800
GO Terms1
Database Version29.0
Sequence SourceGCF_002005445.1
Synonyms Acetimonas aceti
Acetobacter aceti aceti
Acetobacter aceti orleanensis
Acetobacter aceti subsp. aceti
Acetobacter aceti var. muciparum
Acetobacter ketogenum
Acetobacter lafarianum
Acetobacter sp. LMG 1496
Acetobacter sp. LMG 1512
Acetobacter (subgen. Acetobacter) aceti
Bacillus aceticus
Bacteriopsis aceti
Bacterium acetigenoidum
Bacterium aceti
Bacterium hansenianum
Micrococcus aceti
Mycoderma aceti souches non visqueuses (membraneuses)
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acetobacter
Acetobacter subgen. Acetobacter
Acetobacter aceti
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04396917
NCBI BioProjectPRJNA224116
NCBI-Taxonomy435
Environmentwater kefir
Geographic LocationGermany
Annotation ProviderNCBI RefSeq
Annotation Date2019-09-7
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.9
Annotation CommentBest-placed reference protein set; GeneMarkS-2+
NCBI Genome Typerepresentative

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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