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 175 F0384, 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_AFUR010000011,3881,33338171,635,528RefSeq:NZ_AFUR01000001
NZ_AFUR01000006586565813746,000RefSeq:NZ_AFUR01000006
NZ_AFUR0100000723121777286,340RefSeq:NZ_AFUR01000007
NZ_AFUR0100000520018965250,280RefSeq:NZ_AFUR01000005
NZ_AFUR0100000213512933151,281RefSeq:NZ_AFUR01000002
NZ_AFUR0100000450471261,225RefSeq:NZ_AFUR01000004
NZ_AFUR0100000354012,676RefSeq:NZ_AFUR01000003
Total:2,5952,48463483,133,330
Ortholog data available?No
Database Contents
Genes2,595
Pathways181
Enzymatic Reactions916
Transport Reactions55
Polypeptides2,487
Protein Complexes89
Enzymes521
Transporters202
Compounds700
Transcription Units1,830
tRNAs51
Protein Features2,999
GO Terms192
Database Version29.0
Sequence SourceGCF_000223355.1
Synonyms Actinomyces sp. oral taxon 175 strain F0384
Actinomyces sp. oral taxon 175 str. F0384
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
unclassified Actinomyces
Actinomyces sp. oral taxon 175
Actinomyces sp. oral taxon 175 F0384
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00195309
NCBI BioProjectPRJNA224116
NCBI-Taxonomy944560
Environmentbiological product [ENVO:02000043]
HostHomo sapiens
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2021-07-4
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.2
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.