Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 8-Mar-2022 from the annotated genome of Actinomyces oris UMB0183, 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_PKKL01000001642614235768,471RefSeq:NZ_PKKL01000001
NZ_PKKL0100000237036055479,114RefSeq:NZ_PKKL01000002
NZ_PKKL010000033853631210450,256RefSeq:NZ_PKKL01000003
NZ_PKKL0100000429829440369,768RefSeq:NZ_PKKL01000004
NZ_PKKL0100000529629312306,882RefSeq:NZ_PKKL01000005
NZ_PKKL0100000624123830293,901RefSeq:NZ_PKKL01000006
NZ_PKKL0100000717116083229,912RefSeq:NZ_PKKL01000007
NZ_PKKL0100000859570275,017RefSeq:NZ_PKKL01000008
NZ_PKKL0100000941382137,178RefSeq:NZ_PKKL01000009
6 Undisplayed Contigs/Replicons11104,523
Total:2,5052,41859283,015,022
Ortholog data available?No
Database Contents
Genes2,502
Pathways187
Enzymatic Reactions931
Transport Reactions54
Polypeptides2,437
Protein Complexes3
Enzymes566
Transporters309
Compounds702
Transcription Units1,781
tRNAs49
Protein Features2,928
GO Terms193
Database Version29.0
Sequence SourceGCF_002847555.1
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)
BIOSAMPLESAMN08193633
NCBI BioProjectPRJNA224116
NCBI-Taxonomy544580
Geographic LocationUSA
Collection Date2015
HostHomo sapiens
Annotation ProviderNCBI RefSeq
Annotation Date2022-01-5
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
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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