ConSurf

Introduction

ConSurf is a bioinformatics tool for estimating the evolutionary conservation of amino/nucleic acid positions in a protein/DNA/RNA molecule based on the phylogenetic relations between homologous sequences. The degree to which an amino (or nucleic) acid position is evolutionarily conserved is strongly dependent on its structural and functional importance; rapidly evolving positions are variable while slowly evolving positions are conserved. Thus, conservation analysis of positions among members from the same family can often reveal the importance of each position for the protein (or nucleic acid)'s structure or function.In ConSurf, the evolutionary rate is estimated based on the evolutionary relatedness between the protein (DNA/RNA) and its homologues and considering the similarity between amino (nucleic) acids as reflected in the substitutions matrix. One of the advantages of ConSurf in comparison to other methods is the accurate computation of the evolutionary rate by using either an empirical Bayesian method or a maximum likelihood (ML) method.

Methodology

Given the amino or nucleic acid sequence (can be extracted from the 3D structure), ConSurf carries out a search for close homologous sequences using BLAST (or PSI-BLAST) . The user may select one of several databases and specify criteria for defining homologues. The user may also select the desired sequences from the BLAST results. The sequences are clustered and highly similar sequences are removed using CD-HIT. A multiple sequence alignment (MSA) of the homologous sequences is constructed using MAFFT,PRANK, T-COFFEE, MUSCLE(default) or CLUSTALW. The MSA is then used to build a phylogenetic tree using the neighbor-joining algorithm as implemented in the Rate4Site program. Position-specific conservation scores are computed using the empirical Bayesian or ML algorithms. The continuous conservation scores are divided into a discrete scale of nine grades for visualization, from the most variable positions (grade 1) colored turquoise, through intermediately conserved positions (grade 5) colored white, to the most conserved positions (grade 9) colored maroon. The conservation scores are projected onto the protein/nucleotide sequence and on the MSA

Potassium Channel (Kcsa, chains: A, B, C, D) Potassium Channel (Kcsa, chains: A, B, C, D)