Deciphering structure and topology of conserved COG2042 orphan proteins-0

Copyright information:

Taken from "Deciphering structure and topology of conserved COG2042 orphan proteins"

BMC Structural Biology 2005;5():3-3.

Published online 8 Feb 2005

PMCID:PMC549553.

Copyright © 2005 Armengaud et al; licensee BioMed Central Ltd.

Archaeal and eukaryal homologs were obtained from public databases [54] by PSI-BLAST searches. To get the most conserved alignment between COG2042 polypeptide sequences, most probable start codons should be considered as atg at nucleotide 500978 on Crick strand for MTH554 from str. DeltaH (NC_000916), gtg at nucleotide 1526308 on Watson strand for Vng2075c from sp. NRC-1 (NC_002607), atg at nucleotide 8398 on Watson strand for Mbur141901 from DSM6242 (NZ_AADH01000008) and atg at nucleotide 484790 on Crick strand for SSO0551 from (NC_002754). Asterisks indicate modified protein sequences according to this new proposed annotation. Multiple alignments were performed by ClustalW. Following removal of a few ambiguously aligned regions, a data set was assembled comprising 40 sequences over 162 amino acid positions. An unrooted evolutionary distance tree was constructed based on Kimura distances and neighbor joining tree reconstruction algorithm. Bootstrap confidence levels at nodes were computed by the Phylips package with 400 replicates. Scale bar represents unit of amino acid substitutions per position. Accession numbers (gi) are indicated beside the organism. B – Conserved sequence blocks in the alignment of COG2042 members. Based on the phylogenetic analysis (Panel A), eight representative sequences were selected out of 40 COG2042 sequences. Four first sequences are from Archaea while last four sequences are from Eukaryota. SSO0551 sequence (gi38605619) from , labeled with an asterisk, has been numbered according to the new annotation proposed in RESULTS section. Invariant residues in the eight sequences are shown in red and conserved residues in blue. Two conserved motifs commented in the results section are indicated with grey boxes.