Summary This Pathway/Genome Database (PGDB) was generated on 27-May-2018 from the annotated genome of Actinomyces sp. HMSC064C12 HMSC064C12, 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_KV80866445945045479,873RefSeq:NZ_KV808664
NZ_KV80866541440167444,424RefSeq:NZ_KV808665
NZ_KV80867125824873298,284RefSeq:NZ_KV808671
NZ_KV80866321821161231,651RefSeq:NZ_KV808663
NZ_KV80867316715764198,549RefSeq:NZ_KV808673
NZ_KV80866118217372179,351RefSeq:NZ_KV808661
NZ_KV80864213513131152,851RefSeq:NZ_KV808642
NZ_KV80866963590488,374RefSeq:NZ_KV808669
NZ_KV80866873711182,832RefSeq:NZ_KV808668
NZ_KV80863648444048,959RefSeq:NZ_KV808636
NZ_KV80865436340238,485RefSeq:NZ_KV808654
NZ_KV80867229244134,509RefSeq:NZ_KV808672
NZ_KV80863216150126,942RefSeq:NZ_KV808632
NZ_KV80865723220124,529RefSeq:NZ_KV808657
NZ_KV80865612110117,420RefSeq:NZ_KV808656
NZ_KV80862614140012,472RefSeq:NZ_KV808626
NZ_KV8086281211016,731RefSeq:NZ_KV808628
33 Undisplayed Contigs/Replicons242342136,240
Total:2,2072,09952562,402,476
Ortholog data available?Yes
Database Contents
Genes2,205
Pathways152
Enzymatic Reactions771
Transport Reactions50
Polypeptides2,106
Protein Complexes28
Enzymes415
Transporters228
Compounds648
Transcription Units1,278
tRNAs46
Protein Features2,455
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces sp. HMSC064C12
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04477660
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1739355
Environmentwound r ear
HostHomo sapiens
Human Microbiome Body Sitenot-specified

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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