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 Actinomyces sp. oral taxon 181 F0379, 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
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_KB291553766734284829,725RefSeq:NZ_KB291553
NZ_KB29155125924892303,095RefSeq:NZ_KB291551
NZ_KB29154119919531222,099RefSeq:NZ_KB291541
NZ_KB29154317616556190,372RefSeq:NZ_KB291543
NZ_KB29155014414121186,670RefSeq:NZ_KB291550
NZ_KB29154070673099,490RefSeq:NZ_KB291540
NZ_KB29154842411055,948RefSeq:NZ_KB291548
7 Undisplayed Contigs/Replicons993013,907
Total:1,6681,60054141,901,306
Ortholog data available?No
Database Contents
Genes1,665
Pathways146
Enzymatic Reactions747
Transport Reactions32
Polypeptides1,613
Protein Complexes65
Enzymes396
Transporters138
Compounds555
Transcription Units1,024
tRNAs48
Protein Features2,120
GO Terms147
Database Version29.0
Sequence SourceGCF_000318335.2
Synonyms Actinomyces sp. oral taxon 181 str. F0379
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
unclassified Actinomyces
Actinomyces sp. oral taxon 181
Actinomyces sp. oral taxon 181 F0379
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02436933
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1127690
Environmentoral cavity
HostHomo sapiens
Human Microbiome Body Siteoral
Annotation ProviderNCBI RefSeq
Annotation Date2022-01-13
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
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, BIOCYC18A.