Alignment between the mature region of CaclXIP, Hevamine [GenBank: DQ873889], Concanavalin B [Swiss-P49347]49347], and XIP-I [Swiss-Prot: Q8L5C6 ], was performed using the structural alignment tool of Jalview 2.4 software [ 32] and improved by hand until a satisfactory placement of conserved blocks and amino acid identities was obtained.
The alignment of the actin/Hsp70 superfamily proteins was manually edited using the structural alignment of the following representative proteins: 3DAW_A (alpha-actin), 2BTF_A (beta-actin), 1NM1_A (Dictyostelium actin), 1K8K_B (Arp2), 1K8K_A (Arp3), 2ZGY_A (StbA), 2FSN_A (Ta0583), 1JCF_A (MreB), and 2E8A_A (Hsp70).
The effect of amino acid substitutions on the local structural alterations in the homologous protein structures could also be studied using the structural alignments provided in DoSA.
We conducted similar comparisons using the structural mtr alignment, and found no evidence of Numts [although these might not always be detectable through structural analysis, see Olson & Yoder (2002)].
Since cGSTs protein structure is quite conserved, we have overcome the problems of nucleotide homoplasy by using the structural information when building sequence alignments for cGSTs from multiple classes, which increased confidence in the phylogenetic analyses relative to previous studies (see [ 6, 23] and references therein).
To determine the extent of structural similarity between these two domains, we analyzed structural neighbours of the NC4 domain using the VAST structural alignment algorithm [ 32].
The structural variability between 100 models computed from the structural alignment using MODELLER and energy minimized using CHARMM is illustrated for the 1flp helix 1 test case, using the per residue backbone RMSD after optimal superimposition of the entire structure (Figure 4).
[Refer to Hasegawa and Holm (2009) for references of these scores/aligners.] Due to lack of space, we restrict our results herein to those obtained when comparing the DALI Score, TM-Score, and I-value measures, using TM-Align and DALI as the structural alignment generators.
We used this structural alignment as a basis for the sequence alignments shown in Fig. 1f and Additional file 1: Figure S1, S4, as well as for superposition of multiple structures in Additional file 1: Figure S5.
In the structural alignment used for modeling of UNC-8 to 3HGC, the only non-proline cis-peptide in 3HGC which aligns to the sequence of UNC-8, aligns to a proline in the UNC-8 sequence and was maintained.
7 structural entries of odorant-binding proteins (OBPs; PDB ID: 1dqe, 2wcj, 2gte, 2erb, 3k1e, 3bfh, 1ow4), available then, were used for the construction of the structural alignment.
