Note_GeneOrthology – GeneOrthology

WID Note_GeneOrthology
Name GeneOrthology
Comments Gene orthology to the organisms listed below was determined by bidirectional best BLAST as computed by KEGG [PUB_0113]. E. coli K-12 MG1655 M. pneumoniae M129 M. hyopneumoniae 232 M. mobile 163K B. subtilis 168 S. oneidensis MR-1 S. coelicolor A3(2) It has been shown that all of the smaller M. genitalium genome is contained in the larger M. pneumoniae genome [PUB_0605]. M. pneumoniae is the closest phylogenetic relative of M. genitalium. M. pneumoniae and E. coli orthology were refined based on a number of criteria. First we searched for common names of genes between the two species. Second we searched for matching gene descriptions. Finally we used the BioCyc ‘Align Multi-Genome Browser’ [PUB_0006] function to determine orthologs. After refinement we were able to map all but 6 M. genitalium genes to M. pneumoniae and 283 M. genitalium genes to E. coli .
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  2. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y. KEGG for linking genomes to life and the environment. Nucleic Acids Res 36, D480-4 (2008). WholeCell: PUB_0113, PubMed: 18077471, URL:

  3. Keseler IM, Bonavides-Martínez C, Collado-Vides J, Gama-Castro S, Gunsalus RP, Johnson DA, Krummenacker M, Nolan LM, Paley S, Paulsen IT, Peralta-Gil M, Santos-Zavaleta A, Shearer AG, Karp PD. EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Res 37, D464-70 (2009). WholeCell: PUB_0006, PubMed: 18974181

Created 2012-10-01 15:07:34
Last updated 2012-10-01 15:13:57