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 849 F0330, 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_JH470348417385527532,981RefSeq:NZ_JH470348
NZ_JH470349354322725460,856RefSeq:NZ_JH470349
NZ_JH4703503803551510439,981RefSeq:NZ_JH470350
NZ_JH470351321309210348,756RefSeq:NZ_JH470351
NZ_JH4703522412181310279,883RefSeq:NZ_JH470352
NZ_JH470353179160217205,633RefSeq:NZ_JH470353
NZ_JH470354147126318191,106RefSeq:NZ_JH470354
NZ_JH470355148135310175,749RefSeq:NZ_JH470355
NZ_JH470356978917136,726RefSeq:NZ_JH470356
NZ_JH47035711110326136,089RefSeq:NZ_JH470357
NZ_JH470358978935124,469RefSeq:NZ_JH470358
NZ_JH47035957512471,629RefSeq:NZ_JH470359
NZ_JH47036051490262,259RefSeq:NZ_JH470360
NZ_JH47036132291254,828RefSeq:NZ_JH470361
NZ_JH47036223180535,687RefSeq:NZ_JH470362
NZ_JH47036326250133,575RefSeq:NZ_JH470363
NZ_JH47036428250328,264RefSeq:NZ_JH470364
NZ_JH47036523200327,673RefSeq:NZ_JH470365
NZ_JH4703661290314,511RefSeq:NZ_JH470366
57 Undisplayed Contigs/Replicons353054898,719
Total:2,8272,547642163,459,374
Ortholog data available?No
Database Contents
Genes2,823
Pathways184
Enzymatic Reactions923
Transport Reactions54
Polypeptides2,744
Protein Complexes95
Enzymes514
Transporters224
Compounds700
Transcription Units2,250
tRNAs50
Protein Features2,894
GO Terms202
Database Version29.0
Sequence SourceGCF_000239715.1
Synonyms Actinomyces sp. oral taxon 849 str. F0330
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
unclassified Actinomyces
Actinomyces sp. oral taxon 849
Actinomyces sp. oral taxon 849 F0330
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02463764
NCBI BioProjectPRJNA224116
NCBI-Taxonomy653386
Environmentbiological product [ENVO:02000043]
HostHomo sapiens
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2021-12-18
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

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Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC18A.