Sandbox6 Eric Martz

From Proteopedia

Please do not edit this page. Eric Martz, February 2011.

Homology Model for 83-341

• Homology model of 83-341 on template chain A of 3e4c, 52% sequence identity (). Confidence in this model is high because of the 52% sequence identity and sequence alignment with only one 10-residue gap.

• .
• The seems unremarkable. Bear in mind that sidechain rotamer positions are incorrect in a homology model.

• The inner face of 95-140 is . Bear in mind that sidechain rotamer positions are incorrect in a homology model. . The distribution of hydrophobic residues in 83-140 of the homology model is similar to that in the .

• The inner face of 95-140 is , even based upon a multiple sequence alignment that includes mostly types other than 12^[1] .

• When the multiple sequence alignment is limited to the 14 type-12 sequences available from Uniprot (APD 0.30), most of the residues have insufficient data, but a , namely Asn130, Val135, Val136, Glu139, Asn140. .

• The homology model can be downloaded from homology-model-83-341.

Homology Model for 2-88

• Swiss-Model produced a using chain A of 1dgn as template. Confidence in this model is low because the sequence alignment had only 19% identity.
• This model shows a , with a large region containing only negative charges.

• Analysis of evolutionary conservation for 2-88 is difficult because not enough related sequences are available in Uniprot. Thus most of the residues have "insufficient data" (yellow). Despite the paucity of information, there appears to be a that may be of interest^[2] (To identify the conserved residues, toggle spinning off, then touch each residue with the mouse, and observe the popup "hover" report.)
• This model can be downloaded from model-2-88.

Notes

1. ↑ ConSurf run using 80 sequences from the Uniref-90 sequence database. MSA average pairwise distance (APD) 0.94.
2. ↑ ConSurf run with E value cutoff rat default 0.001, Uniref-90 database, 2 PSI-BLAST iterations, 18 sequences after filtration (35%/95%), average pairwise distance in the multiple sequence alignment 1.09, 57 yellow residues. Number of yellow residues was not reduced in a separate run with the E value raised to 0.03, Uniprot database, 3 PSI-BLAST iterations, and filtration at 25%/98%. This gave 22 sequences, APD 0.90, but 65 yellow residues.