Computational protocol: Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA

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Protocol publication

[…] Orthologs of YcbY were identified from a search of the KEGG database () (http://www.genome.jp/kegg) using the E. coli sequence (accession code b0948) as the query. Candidate sequences were fed into the protein–protein interaction database StringDB () (http://string.embl.de) to detect possible functional relationships. Evidence of gene fusion, as well as cooccurrence and coexpression of orthologs was identified using a high confidence cutoff level of 0.8. Bacterial species with YcbY orthologs possessed either one ORF with similar size and sequence to the E. coli protein or two separate ORFs that correspond to the N- and C-terminal of YcbY (YcbY-N and YcbY-C). These are exemplified here by the S. mutans proteins Smu472 (accession code SMU_472) and Smu776 (SMU_776). Multiple sequence alignments of all YcbY orthologs were made using the CLUSTALX software program (), structural comparisons were carried out using DALI, and conserved domains were found in the COG database (). The likelihood of gene fusion having occurred was tested in the fusion protein database FusionDB (). Alignment graphics were generated using ESPript (). […]

Pipeline specifications

Software tools Clustal W, ESPript
Databases FusionDB KEGG STRING
Application Protein interaction analysis
Organisms Streptococcus mutans, Escherichia coli