Summary This Pathway/Genome Database (PGDB) was generated on 27-May-2018 from the annotated genome of Actinomyces sp. HMSC06A08 HMSC06A08, 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 22.0) [Karp16, Karp11] using MetaCyc version 22.0 [Caspi18]. 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 Institutess of Health.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_KV78843447345977485,672RefSeq:NZ_KV788434
NZ_KV788445459441414474,864RefSeq:NZ_KV788445
NZ_KV78844725524573298,474RefSeq:NZ_KV788447
NZ_KV78843621921261231,645RefSeq:NZ_KV788436
NZ_KV78842622922072220,750RefSeq:NZ_KV788426
NZ_KV78843016715773198,745RefSeq:NZ_KV788430
NZ_KV78842863610288,453RefSeq:NZ_KV788428
NZ_KV78844076732183,156RefSeq:NZ_KV788440
NZ_KV78843374711282,746RefSeq:NZ_KV788433
NZ_KV78844162601169,626RefSeq:NZ_KV788441
NZ_KV78842748444048,953RefSeq:NZ_KV788427
NZ_KV78844336340238,493RefSeq:NZ_KV788443
NZ_KV78843128244034,435RefSeq:NZ_KV788431
NZ_KV78843916150126,939RefSeq:NZ_KV788439
NZ_KV78844612110117,330RefSeq:NZ_KV788446
10 Undisplayed Contigs/Replicons1293521,967
Total:2,2342,13653452,422,248
Ortholog data available?Yes
Database Contents
Genes2,235
Pathways153
Enzymatic Reactions780
Transport Reactions50
Polypeptides2,141
Protein Complexes28
Enzymes415
Transporters222
Compounds654
Transcription Units1,280
tRNAs48
Protein Features2,464
GO Terms10,879
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces sp. HMSC06A08
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN03433341
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1581120
EnvironmentUrinary Tract
HostHomo sapiens
Human Microbiome Body Siteurogenital-tract

References

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

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.