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 172 F0311, 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_KE95220670682074,163RefSeq:NZ_KE952206
NZ_KE95223559590068,801RefSeq:NZ_KE952235
NZ_KE95219553512063,213RefSeq:NZ_KE952195
NZ_KE95222446441157,266RefSeq:NZ_KE952224
NZ_KE95226155541057,265RefSeq:NZ_KE952261
NZ_KE95215742411053,042RefSeq:NZ_KE952157
NZ_KE95214448480042,281RefSeq:NZ_KE952144
NZ_KE95209944421140,457RefSeq:NZ_KE952099
NZ_KE95212634312139,584RefSeq:NZ_KE952126
NZ_KE95227139335138,257RefSeq:NZ_KE952271
NZ_KE95217638360237,943RefSeq:NZ_KE952176
NZ_KE95228335350037,132RefSeq:NZ_KE952283
NZ_KE95229129290036,598RefSeq:NZ_KE952291
NZ_KE95218629270235,569RefSeq:NZ_KE952186
NZ_KE95220523221035,305RefSeq:NZ_KE952205
NZ_KE95214128280034,240RefSeq:NZ_KE952141
NZ_KE95212331300133,948RefSeq:NZ_KE952123
NZ_KE95216134321133,815RefSeq:NZ_KE952161
NZ_KE95226631300133,769RefSeq:NZ_KE952266
NZ_KE95229325250033,546RefSeq:NZ_KE952293
NZ_KE95226812120031,918RefSeq:NZ_KE952268
NZ_KE95225721210030,241RefSeq:NZ_KE952257
NZ_KE95213823210228,316RefSeq:NZ_KE952138
NZ_KE95223616140227,916RefSeq:NZ_KE952236
NZ_KE95212924231027,350RefSeq:NZ_KE952129
NZ_KE95224818180027,075RefSeq:NZ_KE952248
NZ_KE95210226231227,060RefSeq:NZ_KE952102
NZ_KE95214916160026,732RefSeq:NZ_KE952149
NZ_KE95220721181226,552RefSeq:NZ_KE952207
NZ_KE95213529281026,470RefSeq:NZ_KE952135
NZ_KE95210721191125,408RefSeq:NZ_KE952107
NZ_KE95210415140123,268RefSeq:NZ_KE952104
NZ_KE95215015150023,155RefSeq:NZ_KE952150
NZ_KE95217420200021,023RefSeq:NZ_KE952174
NZ_KE95222819181020,950RefSeq:NZ_KE952228
NZ_KE95215613130020,778RefSeq:NZ_KE952156
NZ_KE95214015132020,572RefSeq:NZ_KE952140
NZ_KE95215322193020,545RefSeq:NZ_KE952153
NZ_KE95216220155019,443RefSeq:NZ_KE952162
NZ_KE95216817140319,347RefSeq:NZ_KE952168
NZ_KE95217817160119,045RefSeq:NZ_KE952178
NZ_KE95226318180018,779RefSeq:NZ_KE952263
NZ_KE95218917170017,473RefSeq:NZ_KE952189
NZ_KE95224617140316,562RefSeq:NZ_KE952246
NZ_KE95225014140016,243RefSeq:NZ_KE952250
NZ_KE95221517170016,135RefSeq:NZ_KE952215
NZ_KE95213017170015,931RefSeq:NZ_KE952130
NZ_KE95215513130015,884RefSeq:NZ_KE952155
NZ_KE95216013110215,194RefSeq:NZ_KE952160
NZ_KE952285750214,799RefSeq:NZ_KE952285
NZ_KE95227713130014,549RefSeq:NZ_KE952277
NZ_KE95212712120014,474RefSeq:NZ_KE952127
NZ_KE95218513112014,442RefSeq:NZ_KE952185
NZ_KE95217112120012,398RefSeq:NZ_KE952171
NZ_KE95216412120010,726RefSeq:NZ_KE952164
NZ_KE9522251211019,532RefSeq:NZ_KE952225
NZ_KE952298109019,024RefSeq:NZ_KE952298
158 Undisplayed Contigs/Replicons5305151644838,487
Total:1,9851,85651782,469,990
Ortholog data available?No
Database Contents
Genes1,984
Pathways166
Enzymatic Reactions803
Transport Reactions32
Polypeptides2,043
Protein Complexes63
Enzymes440
Transporters137
Compounds570
Transcription Units1,429
tRNAs46
Protein Features2,304
GO Terms135
Database Version29.0
Sequence SourceGCF_000466265.1
Synonyms Actinomyces sp. oral taxon 172 str. F0311
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
unclassified Actinomyces
Actinomyces sp. oral taxon 172
Actinomyces sp. oral taxon 172 F0311
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02436818
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1321775
Environmentoral cavity- mouth
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

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