Database Authors
Pallavi Subhraveti1, Quang Ong1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated by the PathoLogic program [Karp10, Karp11, Caspi14] using Pathway Tools software version 20.5 and MetaCyc version 20.1 on 16-Oct-2016 18:43:19 from the annotated genome of Actinomyces sp. SD1 as obtained from RefSeq.

This BioCyc Tier 3 PGDB was computationally generated. It has not undergone any manual curation nor manual review, and thus may contain errors. Development of this PGDB was supported by grant GM080746 from the NIH.

Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_CZPX010000051,1751,10232411,390,721RefSeq:NZ_CZPX01000005
NZ_CZPX010000047176732519803,507RefSeq:NZ_CZPX01000004
NZ_CZPX01000003231213810257,756RefSeq:NZ_CZPX01000003
NZ_CZPX0100000244005,462RefSeq:NZ_CZPX01000002
NZ_CZPX010000012020904RefSeq:NZ_CZPX01000001
Total:2,1291,99267702,458,350
Ortholog data available?Yes
Database Contents
Genes2,128
Pathways145
Enzymatic Reactions765
Transport Reactions39
Polypeptides1,992
Protein Complexes17
Enzymes441
Transporters181
Compounds607
Transcription Units1,364
tRNAs50
Protein Features2,367
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces sp. SD1
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1673722

References

Caspi14: Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA, Holland TA, Keseler IM, Kothari A, Kubo A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Weerasinghe D, Zhang P, Karp PD (2014). "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases." Nucleic Acids Res. 42(1):D459-D471. PMID: 24225315

Karp10: Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee TJ, Kaipa P, Gilham F, Spaulding A, Popescu L, Altman T, Paulsen I, Keseler IM, Caspi R (2010). "Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology." Brief Bioinform 11(1);40-79. PMID: 19955237

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

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