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 thoenii DSM 20276, 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_KE3840184634371115505,097RefSeq:NZ_KE384018
NZ_KE38401936234976389,403RefSeq:NZ_KE384019
NZ_AUHZ01000005236222212276,911RefSeq:NZ_AUHZ01000005
NZ_AUHZ0100000621120245228,745RefSeq:NZ_AUHZ01000006
NZ_AUHZ0100000715815350168,662RefSeq:NZ_AUHZ01000007
NZ_AUHZ0100000812011721130,955RefSeq:NZ_AUHZ01000008
NZ_AUHZ01000009989413123,381RefSeq:NZ_AUHZ01000009
NZ_AUHZ01000010938913122,103RefSeq:NZ_AUHZ01000010
NZ_AUHZ01000011878241103,083RefSeq:NZ_AUHZ01000011
NZ_AUHZ01000012878232100,655RefSeq:NZ_AUHZ01000012
NZ_AUHZ0100001397940398,733RefSeq:NZ_AUHZ01000013
NZ_AUHZ0100001474720296,090RefSeq:NZ_AUHZ01000014
NZ_AUHZ0100001565584365,473RefSeq:NZ_AUHZ01000015
NZ_AUHZ0100001664536561,611RefSeq:NZ_AUHZ01000016
NZ_AUHZ0100001747440357,208RefSeq:NZ_AUHZ01000017
NZ_AUHZ0100001831280342,685RefSeq:NZ_AUHZ01000018
NZ_AUHZ0100001935330241,757RefSeq:NZ_AUHZ01000019
NZ_AUHZ0100002036350138,546RefSeq:NZ_AUHZ01000020
NZ_AUHZ0100002140380237,537RefSeq:NZ_AUHZ01000021
NZ_AUHZ0100002225220324,626RefSeq:NZ_AUHZ01000022
NZ_AUHZ0100002319160323,335RefSeq:NZ_AUHZ01000023
NZ_AUHZ0100002412120022,719RefSeq:NZ_AUHZ01000024
NZ_AUHZ0100002521172220,423RefSeq:NZ_AUHZ01000025
NZ_AUHZ0100002618161115,647RefSeq:NZ_AUHZ01000026
NZ_AUHZ0100002711100114,909RefSeq:NZ_AUHZ01000027
NZ_AUHZ0100002816140214,617RefSeq:NZ_AUHZ01000028
NZ_AUHZ0100002913112013,436RefSeq:NZ_AUHZ01000029
NZ_AUHZ01000034129218,869RefSeq:NZ_AUHZ01000034
17 Undisplayed Contigs/Replicons726941290,856
Total:2,6362,47861972,938,072
Ortholog data available?Yes
Database Contents
Genes2,632
Pathways214
Enzymatic Reactions1,053
Transport Reactions52
Polypeptides2,509
Protein Complexes40
Enzymes602
Transporters278
Compounds784
Transcription Units1,860
tRNAs50
Protein Features3,103
GO Terms8
Database Version29.0
Sequence SourceGCF_000423445.1
Synonyms Propionibacterium thoenii DSM 20276
Acidipropionibacterium thoenii DSM 20276
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Propionibacteriales
Propionibacteriaceae
Acidipropionibacterium
Acidipropionibacterium thoenii
Acidipropionibacterium thoenii DSM 20276
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02440839
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1122998
EnvironmentCheese
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+
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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