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 15-Oct-2019 from the annotated genome of Acidipropionibacterium acidipropionici FAM 19036, 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 23.0) [Karp16, Karp11] using MetaCyc version 23.1 [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_CP0406343,3243,117701373,622,795RefSeq:NZ_CP040634
Ortholog data available?Yes
Database Contents
Genes3,324
Pathways247
Enzymatic Reactions1,336
Transport Reactions62
Polypeptides3,119
Protein Complexes27
Enzymes670
Transporters357
Compounds1,069
Transcription Units2,236
tRNAs55
Protein Features3,715
GO Terms2
Database Version29.0
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)
BIOSAMPLESAMN11653933
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1748
Environmentcow milk
Geographic LocationSwitzerland
Collection Date2007
Annotation ProviderNCBI RefSeq
Annotation Date2019-05-30
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.8
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 (2019). "The MetaCyc database of metabolic pathways and enzymes-a 2019 update." Nucleic Acids Res. 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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