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 on 27-Feb-2018 from the annotated genome of Rhodococcus sp. YL-1 YL-1, 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 21.5 [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
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_CP0172995,9125,77267736,367,154RefSeq:NZ_CP017299
pYLC1426411015423,076RefSeq:NZ_CP017300
pYLL1390345045393,079RefSeq:NZ_CP017303
pYLL2310290020339,489RefSeq:NZ_CP017304
pYLC258570164,544RefSeq:NZ_CP017301
pYLC31212007,616RefSeq:NZ_CP017302
Total:7,1086,887671547,594,958
Ortholog data available?Yes
Database Contents
Genes7,109
Pathways279
Enzymatic Reactions1,530
Transport Reactions87
Polypeptides6,888
Protein Complexes22
Enzymes1,229
Transporters700
Compounds1,322
Transcription Units4,689
tRNAs53
Protein Features7,788
GO Terms19
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Mycobacteriales
Nocardiaceae
Rhodococcus <high G+C Gram-positive bacteria>
Rhodococcus sp. YL-1
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN05786337
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1045808
Environmentsoil

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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