Difference between revisions of "Sequence-Based Mutation Analysis Hemochromatosis"
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PsiPred (wt): CCCEECCCCC<font color="red">H</font>HHHHHHHHHH |
PsiPred (wt): CCCEECCCCC<font color="red">H</font>HHHHHHHHHH |
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PsiPred (mt): CCCEECCCCC<font color="red">H</font>HHHHHHHHHH |
PsiPred (mt): CCCEECCCCC<font color="red">H</font>HHHHHHHHHH |
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| + | <figtable id="A162S_pymol"> |
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| + | | align="right" | [[File:hemo_A162S_wt.png|thumb|200px|Wildtype.]] |
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| + | | align="right" | [[File:hemo_A162S_mt.png|thumb|200px|Mutant.]] |
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| + | |+ style="caption-side: bottom; text-align: left" |<font size=1>'''Table TODO:''' ... |
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Revision as of 14:06, 16 June 2012
Hemochromatosis>>Task 6: Sequence-based mutation analysis
Contents
Riddle of the Task
Coming soon... or later...
Short task description
Detailed description: Sequence-based mutation analysis
Protocol
A protocol with a description of the data acquisition and other scripts used for this task is available here.
SNPs
From MSUD: M35T V53M G93R Q127H A162S L183P T217I R224W E277K C282S
Amino acid features
<figtable id="TODO_ID">
| Mutation | Hydrophobicity (wt) | Hydrophobicity (mt) | Polarity (wt) | Polarity (mt) | pI (wt) | pI (mt) | v.d.W. volume (wt) | v.d.W. volume (mt) |
|---|---|---|---|---|---|---|---|---|
| M35T | 1.9 | -0.7 | nonpolar | polar | 5.74 | 5.60 | 124 | 93 |
| V53M | 4.2 | 1.9 | nonpolar | nonpolar | 6.00 | 5.74 | 105 | 124 |
| G93R | -0.4 | -4.5 | nonpolar | polar | 6.06 | 10.76 | 48 | 148 |
| Q127H | -3.5 | -3.2 | polar | polar | 5.65 | 7.60 | 114 | 118 |
| A162S | 1.8 | -0.8 | nonpolar | polar | 6.01 | 5.68 | 67 | 73 |
| L183P | 3.8 | -1.6 | nonpolar | nonpolar | 6.01 | 6.30 | 124 | 90 |
| T217I | -0.7 | 4.5 | polar | nonpolar | 5.60 | 6.05 | 93 | 124 |
| R224W | -4.5 | -0.9 | polar | nonpolar | 10.76 | 5.89 | 148 | 163 |
| E277K | -3.5 | -3.9 | polar | polar | 3.15 | 9.60 | 109 | 135 |
| C282S | 2.5 | -0.8 | polar | polar | 5.05 | 5.68 | 86 | 73 |
</figtable>
Evolutionary analysis
BLOSUM62/PAM1/PAM250
<figtable id="TODO_ID">
| Mutation | BLOSUM62 | PAM1 | PAM250 |
|---|---|---|---|
| M35T | -1 | 6 | 500 |
| V53M | 1 | 4 | 200 |
| G93R | -2 | 0 | 200 |
| Q127H | 0 | 20 | 700 |
| A162S | 1 | 28 | 900 |
| L183P | -3 | 2 | 300 |
| T217I | -1 | 7 | 400 |
| R224W | -3 | 2 | 200 |
| E277K | 1 | 7 | 800 |
| C282S | -1 | 11 | 700 |
</figtable>
PSSM
Tables for the mutations can be found here.
MSA conservation
M35T
- Secondary structure assignment: sheet
SEQ (mt): LRSHSLHYLFTGASEQDLGLS DSSP (wt): CCEEEEEEEEEEECCCCCCE PsiPred (wt): CCCCCCCEEEEEEECCCCCCC PsiPred (mt): CCCCCCCEEEEEEECCCCCCC
<figtable id="M35T_pymol">
</figtable>
V53M
- Secondary structure assignment: sheet
SEQ (mt): GLSLFEALGYMDDQLFVFYDH DSSP (wt): CCECCEEEEEECCEEEEEEEC PsiPred (wt): CCCEEEEEEEECCEEEEEEEC PsiPred (mt): CCCEEEEEEEECCEEEEEEEC
<figtable id="V53M_pymol">
</figtable>
G93R
- Secondary structure assignment: helix
SEQ (mt): MWLQLSQSLKRWDHMFTVDFW DSSP (wt): HHHHHHHHHHHHHHHHHHHHH PsiPred (wt): HHHHHHHHHHHHHHHHHHHHH PsiPred (mt): HHHHHHHHHHHHHHHHHHHHH
<figtable id="G93R_pymol">
</figtable>
Q127H
- Secondary structure assignment: coil
SEQ (mt): TLQVILGCEMHEDNSTEGYWK DSSP (wt): EEEEEEEEEECCCCCEEEEEE PsiPred (wt): EEEEECCCCCCCCCCCCCEEE PsiPred (mt): CEEEECCCEECCCCCCCCCCE
<figtable id="Q127H_pymol">
</figtable>
A162S
- Secondary structure assignment: helix
SEQ (mt): TLDWRAAEPRSWPTKLEWERH DSSP (wt): HCEEEECCHHHHHHHHHHHCC PsiPred (wt): CCCEECCCCCHHHHHHHHHHH PsiPred (mt): CCCEECCCCCHHHHHHHHHHH
<figtable id="A162S_pymol">
</figtable>
L183P
- Secondary structure assignment: helix (trusting DSSP)
SEQ (mt): KIRARQNRAYPERDCPAQLQQ DSSP (wt): CHHHHHHHHHHHHHHHHHHHH PsiPred (wt): HHHHHHHHCCCCCCHHHHHHH PsiPred (mt): HHHHHHHHCCCCCCHHHHHHH
T217I
- Secondary structure assignment: coil
SEQ (mt): PPLVKVTHHVISSVTTLRCRA DSSP (wt): CCEEEEEEEECCCCEEEEEEE PsiPred (wt): CCCEEEECCCCCCCCEEEEEE PsiPred (mt): CCCEEEECCCCCCCCEEEEEE
R224W
- Secondary structure assignment: sheet
SEQ (mt): HHVTSSVTTLWCRALNYYPQN DSSP (wt): EEECCCCEEEEEEEEEEECCC PsiPred (wt): CCCCCCCCEEEEEECCCCCCC PsiPred (mt): CCCCCCCCEEEEEECCCCCCC
E277K
- Secondary structure assignment: helix (trusting DSSP)
SEQ (mt): WITLAVPPGEKQRYTCQVEHP DSSP (wt): EEEEEECCCHHHHEEEEEECC PsiPred (wt): EEEEEECCCCCCCEEEEEECC PsiPred (mt): EEEEEECCCCCCCEEEEEECC
C282S
- Secondary structure assignment: sheet
SEQ (mt): VPPGEEQRYTSQVEHPGLDQP DSSP (wt): ECCCHHHHEEEEEECCCCCCC PsiPred (wt): ECCCCCCCEEEEEECCCCCCC PsiPred (mt): ECCCCCCCCEEEEECCCCCCC
References
<references/>
