Database Authors
Pallavi Subhraveti1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2020 from the annotated genome of Acidipropionibacterium jensenii DSM 20535, 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 24.0) [Karp16, Karp11] using MetaCyc version 23.5 [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
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_AUDD0100000123422455256,499RefSeq:NZ_AUDD01000001
NZ_AUDD0100000218518023207,295RefSeq:NZ_AUDD01000002
NZ_AUDD0100000318317742197,439RefSeq:NZ_AUDD01000003
NZ_AUDD0100000418217615196,263RefSeq:NZ_AUDD01000004
NZ_AUDD0100000517316643187,959RefSeq:NZ_AUDD01000005
NZ_AUDD0100000616916216180,851RefSeq:NZ_AUDD01000006
NZ_AUDD0100000717116038161,716RefSeq:NZ_AUDD01000007
NZ_AUDD0100000813512753155,416RefSeq:NZ_AUDD01000008
NZ_AUDD0100000911811035125,513RefSeq:NZ_AUDD01000009
NZ_AUDD01000010989800114,438RefSeq:NZ_AUDD01000010
NZ_AUDD01000011838102101,850RefSeq:NZ_AUDD01000011
NZ_AUDD0100001275703296,307RefSeq:NZ_AUDD01000012
NZ_AUDD0100001384794195,228RefSeq:NZ_AUDD01000013
NZ_AUDD0100001474720283,421RefSeq:NZ_AUDD01000014
NZ_AUDD0100001564582466,466RefSeq:NZ_AUDD01000015
NZ_AUDD0100001660534360,162RefSeq:NZ_AUDD01000016
NZ_KE38434557524157,610RefSeq:NZ_KE384345
NZ_AUDD0100001939370252,601RefSeq:NZ_AUDD01000019
NZ_AUDD0100002037360149,948RefSeq:NZ_AUDD01000020
NZ_AUDD0100002146441149,396RefSeq:NZ_AUDD01000021
NZ_AUDD0100002242410149,046RefSeq:NZ_AUDD01000022
NZ_AUDD0100002340336140,798RefSeq:NZ_AUDD01000023
NZ_AUDD0100002430281134,081RefSeq:NZ_AUDD01000024
NZ_AUDD0100002534310333,758RefSeq:NZ_AUDD01000025
NZ_AUDD0100002613110227,229RefSeq:NZ_AUDD01000026
NZ_AUDD0100002723201227,183RefSeq:NZ_AUDD01000027
NZ_AUDD0100002819170223,666RefSeq:NZ_AUDD01000028
NZ_AUDD0100003023221021,639RefSeq:NZ_AUDD01000030
NZ_AUDD0100002920190121,601RefSeq:NZ_AUDD01000029
NZ_AUDD0100003116150121,364RefSeq:NZ_AUDD01000031
NZ_AUDD0100003215150020,094RefSeq:NZ_AUDD01000032
NZ_AUDD0100003313110216,975RefSeq:NZ_AUDD01000033
NZ_AUDD0100003415130216,901RefSeq:NZ_AUDD01000034
NZ_AUDD0100003516150116,504RefSeq:NZ_AUDD01000035
NZ_AUDD0100003612100214,715RefSeq:NZ_AUDD01000036
NZ_AUDD0100003812120014,373RefSeq:NZ_AUDD01000038
NZ_AUDD0100003912111013,493RefSeq:NZ_AUDD01000039
NZ_AUDD01000043119119,848RefSeq:NZ_AUDD01000043
18 Undisplayed Contigs/Replicons7170120108,708
Total:2,7242,565581013,028,354
Ortholog data available?Yes
Database Contents
Genes2,722
Pathways231
Enzymatic Reactions1,074
Transport Reactions51
Polypeptides2,590
Protein Complexes43
Enzymes615
Transporters297
Compounds818
Transcription Units1,887
tRNAs51
Protein Features3,167
GO Terms5
Database Version29.0
Sequence SourceGCF_000425285.1
Synonyms Propionibacterium jensenii DSM 20535
Acidipropionibacterium jensenii DSM 20535
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Propionibacteriales
Propionibacteriaceae
Acidipropionibacterium
Acidipropionibacterium jensenii
Acidipropionibacterium jensenii DSM 20535
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02441538
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1122997
EnvironmentButtermilk
Relationship to Oxygenanaerobe
Annotation ProviderNCBI RefSeq
Annotation Date2019-11-25
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.10
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

Report Errors or Provide Feedback
Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC17A.