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 25-Oct-2020 from the annotated genome of Actinomyces oris T14V, 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 24.5) [Karp16, Karp11] using MetaCyc version 24.1 [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_CP0142322,5152,38663663,042,917RefSeq:NZ_CP014232
Ortholog data available?Yes
Database Contents
Genes2,515
Pathways186
Enzymatic Reactions869
Transport Reactions75
Polypeptides2,386
Protein Complexes34
Enzymes521
Transporters265
Compounds685
Transcription Units1,799
tRNAs51
Protein Features2,864
Database Version29.0
Sequence SourceGCF_001553935.1
Synonyms Actinomyces naeslundii genospecies 2
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces oris
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04435864
NCBI BioProjectPRJNA224116
NCBI-Taxonomy544580
Environmentcurette
Geographic LocationUSA
Latitude/Longitude42.34 N 71.09 W
Relationship to Oxygenanaerobe
HostHomo sapiens
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2020-04-5
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
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

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