Sandbox6 Eric Martz: Difference between revisions
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===Homology Model for 83-341=== | ===Homology Model for 83-341=== | ||
<Structure size='450' frame='true' align='right' scene='Sandbox6_Eric_Martz/83-341/1' /> | <Structure size='450' frame='true' align='right' scene='Sandbox6_Eric_Martz/83-341/1' /> | ||
*Homology model of 83-341 on template chain A of [[3e4c]], 52% sequence identity (<scene name='Sandbox6_Eric_Martz/83-341/1'>restore initial scene</scene>). | *Homology model of 83-341 on template chain A of [[3e4c]], 52% sequence identity (<scene name='Sandbox6_Eric_Martz/83-341/1'>restore initial scene</scene>). Confidence in this model is high because of the 52% sequence identity and sequence alignment with only one 10-residue gap. | ||
{{Template:ColorKey_Amino2CarboxyRainbow}} | {{Template:ColorKey_Amino2CarboxyRainbow}} | ||
*<scene name='Sandbox6_Eric_Martz/83-341/2'>Segment 83-140</scene>. | *<scene name='Sandbox6_Eric_Martz/83-341/2'>Segment 83-140</scene>. | ||
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* 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 <scene name='Sandbox6_Eric_Martz/83-341_conservation/3'>few on the outside face are highly conserved</scene>, namely Asn130, Val135, Val136, Glu139, Asn140. <scene name='Sandbox6_Eric_Martz/83-341_conservation/4'>Hide 141-341</scene>. | * 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 <scene name='Sandbox6_Eric_Martz/83-341_conservation/3'>few on the outside face are highly conserved</scene>, namely Asn130, Val135, Val136, Glu139, Asn140. <scene name='Sandbox6_Eric_Martz/83-341_conservation/4'>Hide 141-341</scene>. | ||
The homology model can be downloaded from [[:Image:Caspase12-homology-model-83-341-on-3e4c-a.pdb|homology-model-83-341]]. | *The homology model can be downloaded from [[:Image:Caspase12-homology-model-83-341-on-3e4c-a.pdb|homology-model-83-341]]. | ||
===Homology Model for 2-88=== | |||
===Notes=== | ===Notes=== | ||
<references /> | <references /> | ||
Revision as of 22:55, 7 February 2011
Please do not edit this page. Eric Martz, February 2011.
Homology Model for 83-341Homology Model for 83-341
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- 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.
| Amino Terminus | Carboxy Terminus |
- .
- The seems unremarkable. Bear in mind that sidechain positions are incorrect in a homology model.
- The inner face of 95-140 is . Bear in mind that sidechain 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 2-88Homology Model for 2-88
NotesNotes
- ↑ ConSurf run using 80 sequences from the Uniref-90 sequence database. MSA average pairwise distance (APD) 0.94.