Summary This Pathway/Genome Database (PGDB) was generated on 27-May-2018 from the annotated genome of Actinomyces sp. HMSC072A03 HMSC072A03, 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_KV80766341239967444,372RefSeq:NZ_KV807663
NZ_KV80765335734539381,767RefSeq:NZ_KV807653
NZ_KV80765125724476298,922RefSeq:NZ_KV807651
NZ_KV80757221821161231,910RefSeq:NZ_KV807572
NZ_KV80762116915964199,364RefSeq:NZ_KV807621
NZ_KV80758713613033152,890RefSeq:NZ_KV807587
NZ_KV80759213012343137,928RefSeq:NZ_KV807592
NZ_KV80764362610187,767RefSeq:NZ_KV807643
NZ_KV80762773711182,972RefSeq:NZ_KV807627
NZ_KV80765947470057,904RefSeq:NZ_KV807659
NZ_KV80759748444048,957RefSeq:NZ_KV807597
NZ_KV80757435340138,616RefSeq:NZ_KV807574
NZ_KV80764929244134,606RefSeq:NZ_KV807649
NZ_KV80757916150126,942RefSeq:NZ_KV807579
NZ_KV80760532283126,536RefSeq:NZ_KV807605
NZ_KV80763923210224,641RefSeq:NZ_KV807639
NZ_KV80766212110117,641RefSeq:NZ_KV807662
NZ_KV80756919180111,444RefSeq:NZ_KV807569
81 Undisplayed Contigs/Replicons8582352100,112
Total:2,2122,06750952,405,291
Ortholog data available?Yes
Database Contents
Genes2,213
Pathways152
Enzymatic Reactions768
Transport Reactions50
Polypeptides2,090
Protein Complexes28
Enzymes410
Transporters227
Compounds643
Transcription Units1,319
tRNAs45
Protein Features2,432
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces sp. HMSC072A03
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04477647
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1739339
Environmenturine
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

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