Additional file 1.
Structure-based sequence alignment of the H. salinarum LrpA1 (OE2621R) with other archaeal and bacterial Lrp-homologues. The percentages in parenthesis represent a sequence comparison between LrpA1 and the aligned sequences. The alignment includes P. furiosus LrpA (PF1601; 38%), M. jannaschii Ptr2 (MJ0723; 30%), H. walsbyi Lrp-like protein (HQ3354A; 76%), H. salinarum Lrp (OE3923F; 25%), S. solfataricus LysM (SSO0157; 21%), B. subtilis LrpC (BSU04250; 24%), E. coli AsnC (APECO1_2720; 26%), and E. coli Lrp (b0889; 23%). The HTH DNA-binding motif (αB-αC) and the RAM-domain (β2αDβ3β4αEβ5) are boxed, including the asparagine binding site of E. coli AsnC. Amino acids are shaded in grey according to sequence conservation. Conserved methionine/prolines of the LrpA1-subgroup are shaded in blue. LrpA1 shares highest sequence identity (76%) with the Lrp-like regulator (HQ3354A) from Haloquadratum walsbyi. A comparison between LrpA1 and other Lrp-homologues revealed 38% identity with LrpA (PF1601) from P. furiosus, 30% identity with Ptr2 (MJ0723) from M. jannaschii, 21% identity with S. solfataricus LysM (SSO0157) and 24% identity with LrpC (BSU04250) from Bacillus subtilis. E. coli Lrp (b0889) showed 23% and E. coli AsnC (APECO1_2720) 26% identity. Secondary structure elements are indicated as red α-helices and green β-strands. In both H. salinarum Lrp proteins the N-terminal helix-turn-helix (HTH) motif and the C-terminal regulation of amino acid metabolism (RAM)-domain were identified based on the structure of cristallized Lrp/AsnC homologues. The figure was made by using the INDONESIA alignment package (D. Madsen, P. Johansson and G.J. Kleywegt manuscript in preparation).
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Schwaiger et al. BMC Molecular Biology 2010 11:40 doi:10.1186/1471-2199-11-40