Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2022 from the annotated genome of Acidipropionibacterium jensenii FAM 19038, 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_CP0406352,6962,531621032,999,408RefSeq:NZ_CP040635
Ortholog data available?Yes
Database Contents
Genes2,696
Pathways205
Enzymatic Reactions1,043
Transport Reactions59
Polypeptides2,531
Protein Complexes93
Enzymes589
Transporters225
Compounds795
Transcription Units1,862
tRNAs50
Protein Features3,165
GO Terms220
Database Version29.0
Sequence SourceGCF_005890135.1
Synonyms Bacterium acidi propionici b
Propionibacterium jensenii
Propionibacterium jensenii var. raffinosaceum
Propionibacterium peterssonii
Propionibacterium raffinosaceum
Propionibacterium technicum
Propionibacterium zeae
Propionicibacterium jensenii
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Propionibacteriales
Propionibacteriaceae
Acidipropionibacterium
Acidipropionibacterium jensenii
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN11653934
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1749
Environmentcow milk
Geographic LocationSwitzerland
Collection Date2007
Annotation ProviderNCBI RefSeq
Annotation Date2022-04-14
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.1
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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