Summary This Pathway/Genome Database (PGDB) was generated on 27-May-2018 from the annotated genome of Actinomyces sp. HMSC062G12 HMSC062G12, 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_KV814495407388145451,342RefSeq:NZ_KV814495
NZ_KV814513366347118410,846RefSeq:NZ_KV814513
NZ_KV81451129327887327,348RefSeq:NZ_KV814511
NZ_KV814503233214811267,377RefSeq:NZ_KV814503
NZ_KV81450017817323194,969RefSeq:NZ_KV814500
NZ_KV81451011411211127,300RefSeq:NZ_KV814510
NZ_KV81450170652381,488RefSeq:NZ_KV814501
NZ_KV81451462590371,305RefSeq:NZ_KV814514
NZ_KV81449251490256,754RefSeq:NZ_KV814492
NZ_KV81450946423151,096RefSeq:NZ_KV814509
NZ_KV81449930300034,344RefSeq:NZ_KV814499
12 Undisplayed Contigs/Replicons633611,765
Total:1,8621,76052502,085,934
Ortholog data available?Yes
Database Contents
Genes1,863
Pathways129
Enzymatic Reactions687
Transport Reactions35
Polypeptides1,768
Protein Complexes17
Enzymes384
Transporters200
Compounds591
Transcription Units1,168
tRNAs47
Protein Features2,138
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces sp. HMSC062G12
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04480372
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1739450
Environmentabscess l neck
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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