Database Authors
Georgia Isom1, Vincent Poon1, Veronica Armendarez2, Govind Chandra2, Mervyn Bibb2, Gregory L Challis1, Christophe Corre1, David Hodgson1, Jonathan Moore1
1University of Warwick, 2John Innes Centre
Summary This Pathway/Genome Database (PGDB) for Streptomyces coelicolor A3(2) was created by a team from the John Innes Center and the University of Warwick from the annotated genome [Bentley02] using the PathoLogic component of the Pathway Tools software [Karp11, Karp19] and the MetaCyc reference database [Caspi20]. The PGDB, which integrates the biochemical reaction network and metabolic pathways of the organism with its genome, was improved by limited manual curation.

Citations: [Kanehisa97, Kanehisa00, Bentley04, SRI05, Borodina05]

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
Chromosome7,9087,8500588,667,507
SCP135635105356,073
SCP234340031,317
Total:8,2988,2350639,054,897
Ortholog data available?Yes
Database Contents
Genes8,299
Pathways403
Enzymatic Reactions1,742
Transport Reactions34
Polypeptides8,198
Protein Complexes49
Enzymes1,203
Transporters643
Compounds1,243
Transcription Units6,086
tRNAs63
Transcriptional Regulation118
Protein Features21
GO Terms25,101
Database Version29.0
Synonyms Streptomyces coelicolor A3(2)
"Cladothrix coelicolor" (Muller 1908) Mace 1913
"Corynebacterium coelicolor" (Muller 1908) Muller 1950
"Nocardia coelicolor" (Muller 1908) Chalmers and Christopherson 1916
"Streptothrix coelicolor" Muller 1908
Actinomyces coelicolor
Cladothrix coelicolor
Nocardia coelicolor
Streptomyces coelicolor (Muller 1908) Waksman and Henrici 1948
Streptomyces coelicolor subspecies coelicolor
Streptothrix coelicolor
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Kitasatosporales
Streptomycetaceae
Streptomyces
Streptomyces albidoflavus group
Streptomyces coelicolor
Streptomyces coelicolor A3(2)
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
GOLD0000692
NCBI-Taxonomy100226
NCBI Genome Typereference
Copyright University of Warwick, 2013

References

Bentley02: Bentley SD, Chater KF, Cerdeno-Tarraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D, Bateman A, Brown S, Chandra G, Chen CW, Collins M, Cronin A, Fraser A, Goble A, Hidalgo J, Hornsby T, Howarth S, Huang CH, Kieser T, Larke L, Murphy L, Oliver K, O'Neil S, Rabbinowitsch E, Rajandream MA, Rutherford K, Rutter S, Seeger K, Saunders D, Sharp S, Squares R, Squares S, Taylor K, Warren T, Wietzorrek A, Woodward J, Barrell BG, Parkhill J, Hopwood DA (2002). "Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)." Nature 417(6885);141-7. PMID: 12000953

Bentley04: Bentley SD, Brown S, Murphy LD, Harris DE, Quail MA, Parkhill J, Barrell BG, McCormick JR, Santamaria RI, Losick R, Yamasaki M, Kinashi H, Chen CW, Chandra G, Jakimowicz D, Kieser HM, Kieser T, Chater KF (2004). "SCP1, a 356,023 bp linear plasmid adapted to the ecology and developmental biology of its host, Streptomyces coelicolor A3(2)." Mol Microbiol 51(6);1615-28. PMID: 15009889

Borodina05: Borodina I, Krabben P, Nielsen J (2005). "Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism." Genome Res 15(6);820-9. PMID: 15930493

Caspi20: Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2020). "The MetaCyc database of metabolic pathways and enzymes - a 2019 update." Nucleic Acids Res 48(D1);D445-D453. PMID: 31586394

Kanehisa00: Kanehisa M, Goto S (2000). "KEGG: kyoto encyclopedia of genes and genomes." Nucleic Acids Res 28(1);27-30. PMID: 10592173

Kanehisa97: Kanehisa M (1997). "A database for post-genome analysis." Trends Genet 13(9);375-6. PMID: 9287494

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

Karp19: Karp PD, Midford PE, Billington R, Kothari A, Krummenacker M, Latendresse M, Ong WK, Subhraveti P, Caspi R, Fulcher C, Keseler IM, Paley SM (2019). "Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform. PMID: 31813964

SRI05: SRI International (2005). "BioCyc and Pathway Tools Publications." BioCyc Database Collection.

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of this database: Nature, 417(6885):141 2002
Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC14.