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 15-Oct-2019 from the annotated genome of Actinomyces odontolyticus XH001, 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 23.0) [Karp16, Karp11] using MetaCyc version 23.1 [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_CP0400062,0891,97461542,360,133RefSeq:NZ_CP040006
Ortholog data available?Yes
Database Contents
Genes2,089
Pathways145
Enzymatic Reactions827
Transport Reactions50
Polypeptides1,974
Protein Complexes26
Enzymes412
Transporters200
Compounds720
Transcription Units1,329
tRNAs49
Protein Features2,475
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces odontolyticus
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN11483329
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1660
Environmenthuman oral cavity UCLA1
Geographic LocationUSA
Latitude/Longitude34.07 N 118.45 W
Collection Date2013-05
HostHomo sapiens
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2019-05-26
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.8
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 (2019). "The MetaCyc database of metabolic pathways and enzymes-a 2019 update." Nucleic Acids Res. 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.