Identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments-0

Nd (2, 3) would be predicted as possessing a strong coupling signal. Columns 4 – 6 illustrate the computation of frequencies for . All sequences containing a gap at position or were removed. In the case of columns = 4, = 5 it is one sequence (labelled red). For the determination of frequencies in columns = 5 and = 6, four sequences have to be removed (labelled green).<p><b>Copyright information:</b></p><p>Taken from ": Identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments"</p><p>http://www.biomedcentral.com/1471-2105/9/151</p><p>BMC Bioinformatics 2008;9():151-151.</p><p>Published online 18 Mar 2008</p><p>PMCID:PMC2323388.</p><p></p

Identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments-3

<p><b>Copyright information:</b></p><p>Taken from ": Identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments"</p><p>http://www.biomedcentral.com/1471-2105/9/151</p><p>BMC Bioinformatics 2008;9():151-151.</p><p>Published online 18 Mar 2008</p><p>PMCID:PMC2323388.</p><p></p

Additional file 1: of AGeNNT: annotation of enzyme families by means of refined neighborhood networks

Usage of AGeNNT. A tutorial guiding through the process of generating SSNs, rGNNs by means of AGeNNT and their visualisation by means of Cytoscape. (PDF 3996 kb

Additional file 5: of Assessing in silico the recruitment and functional spectrum of bacterial enzymes from secondary metabolism

1005 multiple Fasta files (one per BGC that comprises enzymes) containing the sequences of the data set enzymes SM* . The BGC are named according to MIBiG nomenclature. (ZIP 6333 kb

Additional file 3: Figure S1. of Assessing in silico the recruitment and functional spectrum of bacterial enzymes from secondary metabolism

Figure in PDF format showing the analysis of neofunctionalization based on the BLAST cutoff 1E-10. (PDF 146 kb

Additional file 2: Table S2. of Assessing in silico the recruitment and functional spectrum of bacterial enzymes from secondary metabolism

Table in Excel format listing the number of homologous BLAST hits found in enzymes PM* for all enzymes represented in enzymes SM* . Hits are added according to EC numbers and EC subdivisions. (XLSX 29 kb

Additional file 1: of An assessment of catalytic residue 3D ensembles for the prediction of enzyme function

Composition of data set ENZ_SITES. (PDF 84 kb

<i>In vivo</i> complementation of auxotrophic <i>E</i>. <i>coli</i> strains by PriA, HisA, HisA ancestors, and TrpF.

<p><i>In vivo</i> complementation of auxotrophic <i>E</i>. <i>coli</i> strains by PriA, HisA, HisA ancestors, and TrpF.</p

Additional file 1: Table S1. of Assessing in silico the recruitment and functional spectrum of bacterial enzymes from secondary metabolism

Table in Excel format listing the occurrence of EC numbers, EC subclasses, and of EC subdivisions in enzymes PM* and enzymes SM* . (XLSX 114 kb