Sandbox6 Eric Martz: Difference between revisions
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{{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>. | ||
*The <scene name='Sandbox6_Eric_Martz/83-341_charge/1'>distribution of charges</scene> seems unremarkable. Bear in mind that sidechain positions are incorrect in a homology model. | *The <scene name='Sandbox6_Eric_Martz/83-341_charge/1'>distribution of charges</scene> seems unremarkable. Bear in mind that sidechain rotamer positions are incorrect in a homology model. | ||
<center>{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}</center> | <center>{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}</center> | ||
*The inner face of 95-140 is <scene name='Sandbox6_Eric_Martz/83-341_hydrophobic/1'>partially hydrophobic</scene>. Bear in mind that sidechain positions are incorrect in a homology model. <scene name='Sandbox6_Eric_Martz/83-341_hydrophobic/2'>Hide 141-341</scene>. The distribution of hydrophobic residues in 83-140 of the homology model is similar to that in the <scene name='Sandbox6_Eric_Martz/3e4c_147-205_hydrophobic/1'>corresponding residues 147-205 in the template 3e4c</scene>. | *The inner face of 95-140 is <scene name='Sandbox6_Eric_Martz/83-341_hydrophobic/1'>partially hydrophobic</scene>. Bear in mind that sidechain rotamer positions are incorrect in a homology model. <scene name='Sandbox6_Eric_Martz/83-341_hydrophobic/2'>Hide 141-341</scene>. The distribution of hydrophobic residues in 83-140 of the homology model is similar to that in the <scene name='Sandbox6_Eric_Martz/3e4c_147-205_hydrophobic/1'>corresponding residues 147-205 in the template 3e4c</scene>. | ||
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* This model shows a <scene name='Sandbox6_Eric_Martz/2-88_charge/1'>noteworthy separation of charges</scene>, with a large region containing only negative charges. | * This model shows a <scene name='Sandbox6_Eric_Martz/2-88_charge/1'>noteworthy separation of charges</scene>, with a large region containing only negative charges. | ||
<center>{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}</center> | <center>{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}</center> | ||
*Analysis of evolutionary conservation | *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 <scene name='Sandbox6_Eric_Martz/2-88_conservation/1'>conserved patch</scene> that may be of interest<ref>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.</ref> (To identify the conserved residues, toggle spinning off, then touch each residue with the mouse, and observe the popup "hover" report.) | ||
**<scene name='Sandbox6_Eric_Martz/2-88_conservation/2'>Cartoon</scene><table align="right"><tr><td>{{Template:ColorKey_ConSurf_NoGray}}</td></tr></table> | |||
**<scene name='Sandbox6_Eric_Martz/2-88_conservation/3'>Cartoon decorated with conserved residues</scene> | |||
**<scene name='Sandbox6_Eric_Martz/2-88_conservation/1'>Spacefilling</scene> | |||
*This model can be downloaded from [[:Image:Caspase12-homology-model-2-88-on-1dgn-a.pdb|model-2-88]]. | *This model can be downloaded from [[:Image:Caspase12-homology-model-2-88-on-1dgn-a.pdb|model-2-88]]. | ||
===Notes=== | ===Notes=== | ||
<references /> | <references /> | ||
Latest revision as of 23:47, 9 February 2011
Please do not edit this page. Eric Martz, February 2011.
Homology Model for 83-341Homology 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.
| Amino Terminus | Carboxy Terminus |
- .
- 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 2-88Homology 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.
NotesNotes
- ↑ ConSurf run using 80 sequences from the Uniref-90 sequence database. MSA average pairwise distance (APD) 0.94.
- ↑ 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.