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 13-Mar-2021 from the annotated genome of Acidipropionibacterium acidipropionici ATCC 4875, 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 25.0) [Karp16, Karp11] using MetaCyc version 24.5 [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
NC_0193953,3813,24269703,656,170RefSeq:NC_019395
Ortholog data available?Yes
Database Contents
Genes3,381
Pathways239
Enzymatic Reactions1,083
Transport Reactions72
Polypeptides3,242
Protein Complexes57
Enzymes712
Transporters368
Compounds805
Transcription Units2,237
tRNAs54
Protein Features3,813
GO Terms2
Database Version29.0
Sequence SourceGCF_000310065.1
Synonyms Acidipropionibacterium acidipropionici DSM 20272
Acidipropionibacterium acidipropionici JCM 6432
Propionibacterium acidipropionici ATCC 4875
Propionibacterium acidipropionici DSM 20272
Propionibacterium acidipropionici JCM 6432
Acidipropionibacterium acidipropionici ATCC 4875
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Propionibacteriales
Propionibacteriaceae
Acidipropionibacterium
Acidipropionibacterium acidipropionici
Acidipropionibacterium acidipropionici ATCC 4875
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02603885
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1171373
Annotation ProviderNCBI RefSeq
Annotation Date2021-01-17
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.0
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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