Similar protocols

Pipeline publication

[…] eing compared and all non-redundant domains in CATH at the 95% sequence identity level. The Z-score helps in evaluating whether an SSAP score obtained between two domains is likely to be due to chance structural similarity., The boundaries of TBP domains used in this study were defined manually from PDB entries. The following boundaries were used: for TBP, we used residues 15–97 of chain A of PDB structure 1mp9; for DNA glycosylase, we used residues 1–84 of chain A of PDB structure 1 mpg; finally, for the N-terminal domain of RNase HIII, we considered residues 2–67 of chain A in PDB structure 2d0a., Structural predictions of the putatively single TBP-domain proteins were performed using the Phyre2 server (http://www.sbg.bio.ic.ac.uk/phyre2/) ()., All multiple sequence alignments were performed with the Kalign software version 2.04 () and default settings. Alignments were subsequently manually inspected for alignment errors., Bayesian trees were inferred using PhyloBayes 3.2e () using two parallel chains with the CAT + Gamma + I model () until sufficient convergence was achieved, corresponding to ∼10 million generations with sampling every 100 generations and 2.5 million generations discarded as burn-in., Cluster analysis of TBP domain-containing proteins was performed using CLANS v. 2 (). A data set comprising the full complement of sequences as of 2011-11-07 for the Alka-N, OGG_N and TBP families was downloaded from PFAM (http://pfam.sanger.ac.uk/) (). A representative selection of RNase HIII TBP-domain sequences and putative single TBP-domain proteins were then added to that data set. Accession information for the sequences present in the analy […]

Pipeline specifications

Software tools Phyre, Kalign, PhyloBayes