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 sp. oral taxon 848 F0332, 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_CP0405032,1142,00259532,526,493RefSeq:NZ_CP040503
Ortholog data available?Yes
Database Contents
Genes2,114
Pathways145
Enzymatic Reactions816
Transport Reactions45
Polypeptides2,002
Protein Complexes21
Enzymes399
Transporters177
Compounds703
Transcription Units1,486
tRNAs47
Protein Features2,344
Database Version29.0
Synonyms Actinomyces sp. oral taxon 848 strain F0332
Actinomyces sp. oral taxon 848 str. F0332
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces sp. oral taxon 848
Actinomyces sp. oral taxon 848 F0332
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00008757
NCBI BioProjectPRJNA224116
NCBI-Taxonomy649743
Environmentoral
HostHomo sapiens
Human Microbiome Body Siteoral
Annotation ProviderNCBI RefSeq
Annotation Date2019-05-30
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

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