Difference between revisions of "Sequence-Based Mutation Analysis Hemochromatosis"

From Bioinformatikpedia
(→‎L183P)
Line 251: Line 251:
 
* Secondary structure assignment: sheet
  
* Secondary structure assignment: sheet
   
−
SEQ: LRSHSLHYLF<font color="red">T</font>GASEQDLGLS
 +
SEQ (mt): LRSHSLHYLF<font color="red">T</font>GASEQDLGLS
 
DSSP (wt): CCEEEEEEE<font color="red">E</font>EEECCCCCCE
  
DSSP (wt): CCEEEEEEE<font color="red">E</font>EEECCCCCCE
 
PsiPred (wt): CCCCCCCEEE<font color="red">E</font>EEECCCCCCC
  
PsiPred (wt): CCCCCCCEEE<font color="red">E</font>EEECCCCCCC
Line 267: Line 267:
 
* Secondary structure assignment: sheet
  
* Secondary structure assignment: sheet
   
−
SEQ: GLSLFEALGY<font color="red">M</font>DDQLFVFYDH
 +
SEQ (mt): GLSLFEALGY<font color="red">M</font>DDQLFVFYDH
 
DSSP (wt): CCECCEEEEE<font color="red">E</font>CCEEEEEEEC
  
DSSP (wt): CCECCEEEEE<font color="red">E</font>CCEEEEEEEC
 
PsiPred (wt): CCCEEEEEEE<font color="red">E</font>CCEEEEEEEC
  
PsiPred (wt): CCCEEEEEEE<font color="red">E</font>CCEEEEEEEC
Line 279: Line 279:
 
* Secondary structure assignment: helix
  
* Secondary structure assignment: helix
   
−
SEQ: MWLQLSQSLK<font color="red">R</font>WDHMFTVDFW
 +
SEQ (mt): MWLQLSQSLK<font color="red">R</font>WDHMFTVDFW
 
DSSP (wt): HHHHHHHHHH<font color="red">H</font>HHHHHHHHHH
  
DSSP (wt): HHHHHHHHHH<font color="red">H</font>HHHHHHHHHH
 
PsiPred (wt): HHHHHHHHHH<font color="red">H</font>HHHHHHHHHH
  
PsiPred (wt): HHHHHHHHHH<font color="red">H</font>HHHHHHHHHH
Line 291: Line 291:
 
* Secondary structure assignment: coil
  
* Secondary structure assignment: coil
   
−
SEQ: TLQVILGCEM<font color="red">H</font>EDNSTEGYWK
 +
SEQ (mt): TLQVILGCEM<font color="red">H</font>EDNSTEGYWK
 
DSSP (wt): EEEEEEEEEE<font color="red">C</font>CCCCEEEEEE
  
DSSP (wt): EEEEEEEEEE<font color="red">C</font>CCCCEEEEEE
 
PsiPred (wt): EEEEECCCCC<font color="red">C</font>CCCCCCCEEE
  
PsiPred (wt): EEEEECCCCC<font color="red">C</font>CCCCCCCEEE
Line 303: Line 303:
 
* Secondary structure assignment: helix
  
* Secondary structure assignment: helix
   
−
SEQ: TLDWRAAEPR<font color="red">S</font>WPTKLEWERH
 +
SEQ (mt): TLDWRAAEPR<font color="red">S</font>WPTKLEWERH
 
DSSP (wt): HCEEEECCHH<font color="red">H</font>HHHHHHHHCC
  
DSSP (wt): HCEEEECCHH<font color="red">H</font>HHHHHHHHCC
 
PsiPred (wt): CCCEECCCCC<font color="red">H</font>HHHHHHHHHH
  
PsiPred (wt): CCCEECCCCC<font color="red">H</font>HHHHHHHHHH
Line 315: Line 315:
 
* Secondary structure assignment: helix (trusting DSSP)
  
* Secondary structure assignment: helix (trusting DSSP)
   
−
SEQ: KIRARQNRAY<font color="red">P</font>ERDCPAQLQQ
 +
SEQ (mt): KIRARQNRAY<font color="red">P</font>ERDCPAQLQQ
 
DSSP (wt): CHHHHHHHHH<font color="red">H</font>HHHHHHHHHH
  
DSSP (wt): CHHHHHHHHH<font color="red">H</font>HHHHHHHHHH
 
PsiPred (wt): HHHHHHHHCC<font color="red">C</font>CCCHHHHHHH
  
PsiPred (wt): HHHHHHHHCC<font color="red">C</font>CCCHHHHHHH
Line 327: Line 327:
 
* Secondary structure assignment: coil
  
* Secondary structure assignment: coil
   
−
SEQ: PPLVKVTHHV<font color="red">I</font>SSVTTLRCRA
 +
SEQ (mt): PPLVKVTHHV<font color="red">I</font>SSVTTLRCRA
 
DSSP (wt): CCEEEEEEEE<font color="red">C</font>CCCEEEEEEE
  
DSSP (wt): CCEEEEEEEE<font color="red">C</font>CCCEEEEEEE
 
PsiPred (wt): CCCEEEECCC<font color="red">C</font>CCCCEEEEEE
  
PsiPred (wt): CCCEEEECCC<font color="red">C</font>CCCCEEEEEE
Line 339: Line 339:
 
* Secondary structure assignment: sheet
  
* Secondary structure assignment: sheet
   
−
SEQ: HHVTSSVTTL<font color="red">W</font>CRALNYYPQN
 +
SEQ (mt): HHVTSSVTTL<font color="red">W</font>CRALNYYPQN
 
DSSP (wt): EEECCCCEEE<font color="red">E</font>EEEEEEECCC
  
DSSP (wt): EEECCCCEEE<font color="red">E</font>EEEEEEECCC
 
PsiPred (wt): CCCCCCCCEE<font color="red">E</font>EEECCCCCCC
  
PsiPred (wt): CCCCCCCCEE<font color="red">E</font>EEECCCCCCC
Line 351: Line 351:
 
* Secondary structure assignment: helix (trusting DSSP)
  
* Secondary structure assignment: helix (trusting DSSP)
   
−
SEQ: WITLAVPPGE<font color="red">K</font>QRYTCQVEHP
 +
SEQ (mt): WITLAVPPGE<font color="red">K</font>QRYTCQVEHP
 
DSSP (wt): EEEEEECCCH<font color="red">H</font>HHEEEEEECC
  
DSSP (wt): EEEEEECCCH<font color="red">H</font>HHEEEEEECC
 
PsiPred (wt): EEEEEECCCC<font color="red">C</font>CCEEEEEECC
  
PsiPred (wt): EEEEEECCCC<font color="red">C</font>CCEEEEEECC
Line 363: Line 363:
 
* Secondary structure assignment: sheet
  
* Secondary structure assignment: sheet
   
−
SEQ: VPPGEEQRYT<font color="red">S</font>QVEHPGLDQP
 +
SEQ (mt): VPPGEEQRYT<font color="red">S</font>QVEHPGLDQP
 
DSSP (wt): ECCCHHHHEE<font color="red">E</font>EEECCCCCCC
  
DSSP (wt): ECCCHHHHEE<font color="red">E</font>EEECCCCCCC
 
PsiPred (wt): ECCCCCCCEE<font color="red">E</font>EEECCCCCCC
  
PsiPred (wt): ECCCCCCCEE<font color="red">E</font>EEECCCCCCC

Revision as of 23:00, 14 June 2012

Hemochromatosis>>Task 6: Sequence-based mutation analysis


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
TODO: description.

</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
TODO: description.

</figtable>



PSSM


MSA conservation


M35T

  • Secondary structure assignment: sheet
SEQ (mt):     LRSHSLHYLFTGASEQDLGLS
DSSP (wt):     CCEEEEEEEEEEECCCCCCE
PsiPred (wt): CCCCCCCEEEEEEECCCCCCC
PsiPred (mt): CCCCCCCEEEEEEECCCCCCC
  • SIFT prediction:
  • SNAP prediction:
  • Polyphen2 prediction:


V53M

  • Secondary structure assignment: sheet
SEQ (mt):     GLSLFEALGYMDDQLFVFYDH
DSSP (wt):    CCECCEEEEEECCEEEEEEEC
PsiPred (wt): CCCEEEEEEEECCEEEEEEEC
PsiPred (mt): CCCEEEEEEEECCEEEEEEEC


G93R

  • Secondary structure assignment: helix
SEQ (mt):     MWLQLSQSLKRWDHMFTVDFW
DSSP (wt):    HHHHHHHHHHHHHHHHHHHHH
PsiPred (wt): HHHHHHHHHHHHHHHHHHHHH
PsiPred (mt): HHHHHHHHHHHHHHHHHHHHH


Q127H

  • Secondary structure assignment: coil
SEQ (mt):     TLQVILGCEMHEDNSTEGYWK
DSSP (wt):    EEEEEEEEEECCCCCEEEEEE
PsiPred (wt): EEEEECCCCCCCCCCCCCEEE
PsiPred (mt): CEEEECCCEECCCCCCCCCCE


A162S

  • Secondary structure assignment: helix
SEQ (mt):     TLDWRAAEPRSWPTKLEWERH
DSSP (wt):    HCEEEECCHHHHHHHHHHHCC
PsiPred (wt): CCCEECCCCCHHHHHHHHHHH
PsiPred (mt): CCCEECCCCCHHHHHHHHHHH


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/>

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