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 Acidipropionibacterium acidipropionici ATCC 55737, 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_CP0143523,4233,26268933,704,826RefSeq:NZ_CP014352
unnamed22002,365RefSeq:NZ_CP014353
Total:3,4253,26468933,707,191
Ortholog data available?Yes
Database Contents
Genes3,425
Pathways243
Enzymatic Reactions1,089
Transport Reactions67
Polypeptides3,266
Protein Complexes57
Enzymes689
Transporters357
Compounds827
Transcription Units2,249
tRNAs53
Protein Features3,822
GO Terms1
Database Version29.0
Sequence SourceGCF_001602115.1
Synonyms Bacillus acidi propionici
Propionibacterium acidi-propionici
Propionibacterium acidipropionici
Propionibacterium arabinosum
Propionibacterium pentosaceum
Propionicibacterium acidipropionici
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Propionibacteriales
Propionibacteriaceae
Acidipropionibacterium
Acidipropionibacterium acidipropionici
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04455717
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1748
EnvironmentCorn
Geographic LocationUSA
Collection Date1996-01-31
Annotation ProviderNCBI RefSeq
Annotation Date2019-12-20
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.10
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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