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. HMSC075C01 HMSC075C01, 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_KV81098716516014188,633RefSeq:NZ_KV810987
NZ_KV811040145130411188,343RefSeq:NZ_KV811040
NZ_KV81103114213138186,494RefSeq:NZ_KV811031
NZ_KV81101016816404175,056RefSeq:NZ_KV811010
NZ_KV81102813513104165,060RefSeq:NZ_KV811028
NZ_KV811009999342128,006RefSeq:NZ_KV811009
NZ_KV81093011010118118,236RefSeq:NZ_KV810930
NZ_KV811036918524104,146RefSeq:NZ_KV811036
NZ_KV810997848301103,974RefSeq:NZ_KV810997
NZ_KV810969847563101,574RefSeq:NZ_KV810969
NZ_KV81096475713195,915RefSeq:NZ_KV810964
NZ_KV81098475722194,164RefSeq:NZ_KV810984
NZ_KV81099674720290,851RefSeq:NZ_KV810996
NZ_KV81099283820190,376RefSeq:NZ_KV810992
NZ_KV81092873711184,948RefSeq:NZ_KV810928
NZ_KV81098664610381,048RefSeq:NZ_KV810986
NZ_KV81097261582178,798RefSeq:NZ_KV810972
NZ_KV81097456492574,096RefSeq:NZ_KV810974
NZ_KV81102056504268,576RefSeq:NZ_KV811020
NZ_KV81103752461562,440RefSeq:NZ_KV811037
NZ_KV81097056511461,625RefSeq:NZ_KV810970
NZ_KV81103840363158,899RefSeq:NZ_KV811038
NZ_KV81097843411153,914RefSeq:NZ_KV810978
NZ_KV81097949424350,557RefSeq:NZ_KV810979
NZ_KV81093748470150,495RefSeq:NZ_KV810937
NZ_KV81102921210044,362RefSeq:NZ_KV811029
NZ_KV81093130262240,246RefSeq:NZ_KV810931
NZ_KV81098326240238,372RefSeq:NZ_KV810983
NZ_KV81101128250336,937RefSeq:NZ_KV811011
NZ_KV81100335320335,871RefSeq:NZ_KV811003
NZ_KV81104130260434,335RefSeq:NZ_KV811041
NZ_KV81102534273433,765RefSeq:NZ_KV811025
NZ_KV81096325230231,816RefSeq:NZ_KV810963
NZ_KV81095224240031,064RefSeq:NZ_KV810952
NZ_KV81094230231628,860RefSeq:NZ_KV810942
NZ_KV81096024240028,412RefSeq:NZ_KV810960
NZ_KV81100421200127,943RefSeq:NZ_KV811004
NZ_KV81095331263226,573RefSeq:NZ_KV810953
NZ_KV81102319190023,797RefSeq:NZ_KV811023
NZ_KV81091920190121,863RefSeq:NZ_KV810919
NZ_KV81093217160120,655RefSeq:NZ_KV810932
NZ_KV81097315131119,224RefSeq:NZ_KV810973
NZ_KV81099817160112,287RefSeq:NZ_KV810998
NZ_KV8109511060412,259RefSeq:NZ_KV810951
98 Undisplayed Contigs/Replicons9392746167,255
Total:2,7302,504621643,272,120
Ortholog data available?No
Database Contents
Genes2,723
Pathways176
Enzymatic Reactions906
Transport Reactions46
Polypeptides2,604
Protein Complexes88
Enzymes530
Transporters204
Compounds687
Transcription Units2,054
tRNAs49
Protein Features2,919
GO Terms188
Database Version29.0
Sequence SourceGCF_001812965.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
unclassified Actinomyces
Actinomyces sp. HMSC075C01
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04480050
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1739387
Environmentabscess l cheek
HostHomo sapiens
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2021-07-13
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

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