Difference between revisions of "Rs1800430"

From Bioinformatikpedia
(Created page with "{| border="1" style="text-align:center; border-spacing:0;" |Substitution |Prediction |Reliability Index |Expected Accuracy |- |A |Non-neutral |0 |58% |- |C |Non-neutral |2 |70% …")
 
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=== Pysicochemical Properities ===
  +
 
{| border="1" style="text-align:center; border-spacing:0;"
  
{| border="1" style="text-align:center; border-spacing:0;"
  +
|Asn
−
|Substitution
  
  +
|Asp
−
|Prediction
  
  +
|consequences
−
|Reliability Index
 
−
|Expected Accuracy
  
 
|-
  
|-
  +
|polar, small, hydrophilic, negatively charged
−
|A
  
  +
|polar, small, hydrophilic, negatively charged
−
|Non-neutral
  
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|Both amino acids have the same properities and therefore we suggest that an exchange of these two amino acids do not destroy the protein structure and function
−
|0
  
−
|58%
  
 
|-
  
|-
−
|C
 +
|}
  +
−
|Non-neutral
  
  +
----
−
|2
  
  +
−
|70%
  
  +
=== Visualisation of the Mutation ===
  +
  +
{| border="1" style="text-align:center; border-spacing:0;"
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|picture original aa
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|picture mutated aa
  +
|combined picture
 
|-
  
|-
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|[[Image:N399.png|thumb|150px|Amino acid Asparagine]]
−
|D
  
  +
|[[Image:399D.png|thumb|150px|Amino acid Aspartic acid]]
−
|Neutral
  
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|[[Image:N399D.png|thumb|150px|Picture which visualize the mutation]]
−
|1
  
−
|60%
  
 
|-
  
|-
−
|E
 +
|}
  +
−
|Neutral
  
  +
----
−
|1
  
  +
−
|60%
  
  +
=== Subsitution Matrices Values ===
  +
{| border="1" style="text-align:center; border-spacing:0;"
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|colspan="3" | PAM 1
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|colspan="3" | Pam 250
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|colspan="3" | BLOSOUM 62
 
|-
  
|-
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|value aa
−
|F
  
  +
|most frequent substitution
−
|Non-neutral
  
  +
|rarest substitution
−
|1
  
  +
|value aa
−
|63%
  
  +
|most frequent substitution
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|rarest substitution
  +
|value aa
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|most frequent substitution
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|rarest substitution
 
|-
  
|-
−
|G
 +
|36
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|36 (Asp)
−
|Non-neutral
  
  +
|0 (Cys, Met)
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|7
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|7 (Asp)
  +
|2 (Cys, Leu, Phe, Trp)
 
|1
  
|1
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|1 (Asp, His, Ser)
−
|63%
  
  +
| -4 (Trp)
 
|-
  
|-
−
|S
 +
|}
  +
−
|Neutral
  
  +
----
−
|0
  
  +
−
|53%
  
  +
=== Conservation Analysis with Multiple Alignments ===
−
|-
  
  +
−
|I
  
  +
[[Image:mut_8.png|thumb|center|600px|Mutation in the multiple alignment]]
−
|Non-neutral
  
  +
−
|1
  
  +
----
−
|63%
  
  +
−
|-
  
  +
=== Secondary Structure Mutation Analysis ===
−
|K
  
  +
−
|Non-neutral
  
  +
JPred:
−
|0
  
  +
...CCCCCCCEEEEEECCCCCCC<font color="red">C</font>HHHHHHHHHCCCCEEECCCCCCCCCCCCCCCCCC...
−
|58%
  
  +
PsiPred:
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...CCCCCCCCEEEEECCCCCCC<font color="red">H</font>HHHHHHHHHCCCEEEECCCCCCCCCCCCCCCCCC...
  +
  +
Comparison with the real structure:
  +
{|
  +
| [[Image:399_mut.png|thumb|250px|Mutation at position 399]]
  +
| [[Image:399_mut_detail.png|thumb|250px|Mutation at position 399 - detailed view]]
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|}
  +
  +
----
  +
  +
=== SNAP Prediction ===
  +
  +
{| border="1" style="text-align:center; border-spacing:0;"
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|Substitution
  +
|Prediction
  +
|Reliability Index
  +
|Expected Accuracy
 
|-
  
|-
−
|L
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|D
−
|Non-neutral
  
−
|0
  
−
|58%
  
−
|-
  
−
|M
  
−
|Non-neutral
  
−
|0
  
−
|58%
  
−
|-
  
−
|H
  
−
|Non-neutral
  
−
|0
  
−
|58%
  
−
|-
  
−
|P
  
−
|Non-neutral
  
−
|1
  
−
|63%
  
−
|-
  
−
|Q
  
 
|Neutral
  
|Neutral
−
|2
  
−
|69%
  
−
|-
  
−
|R
  
−
|Non-neutral
  
−
|0
  
−
|58%
  
−
|-
  
−
|T
  
−
|Non-neutral
  
−
|0
  
−
|58%
  
−
|-
  
−
|V
  
−
|Non-neutral
  
 
|1
  
|1
−
|63%
 +
|60%
 
|-
  
|-
−
|Y
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|}
  +
−
|Non-neutral
  
  +
A detailed list of all possible substitutions can be found [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/rs1800430_SNAP here]]
−
|2
  
  +
−
|70%
  
−
|-
 +
----
  +
−
|W
  
  +
=== SIFT Prediction ===
−
|Non-neutral
  
  +
−
|3
  
  +
SIFT Matrix:<br>
−
|78%
  
  +
Each entry contains the score at a particular position (row) for an amino acid substitution (column). Substitutions predicted to be intolerant are highlighted in red.
  +
  +
{|
  +
| [[Image:sift_legend.png|center]]
 
|-
  
|-
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| [[Image:399_sift.png.png|center]]
 
|}
  
|}
   
  +
SIFT Table<br>
−
Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_mutation_analysis_HEXA sequence-based mutation analysis]]
  
  +
Threshold for intolerance is 0.05.<BR>Amino acid color code: nonpolar, <font color=green>uncharged polar</font>, <font color=red>basic</font>, <font color=blue>acidic</font>. <BR>Capital letters indicate amino acids appearing in the alignment, lower case letters result from prediction.
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<br>
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{| class="wikitable centered"
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|<table cellspacing=0 border=0 width=0 cols=41><th colspan=20 align=center>Predict Not Tolerated</th><BR><th>Position</th><th>Seq Rep</th><BR><th colspan=20 align=center>Predict Tolerated</th>
  +
<tr><td><font color=gray> </font></td><td><font color=gray> </font></td><td><font color=gray> </font></td><td><font color=gray> </font></td><td><font color=gray> </font></td><td><font color=gray> </font></td><td><font color=gray> </font></td><td><font color=gray> </font></td><td><font color=gray> </font></td><td><font color=gray> </font></td><td><font color=gray> </font></td><td><font color=gray> </font></td><td><font color=gray> </font></td><td><font color=gray> </font></td><td><font color=gray> </font></td><td><font color=black>w</font></td><td><font color=green>y</font></td><td><font color=black>f</font></td><td><font color=green>c</font></td><td><font color=black>m</font></td><th>399N</th><td>0.72</td><td><font color=black>i</font></td><td><font color=red>H</font></td><td><font color=black>v</font></td><td><font color=black>l</font></td><td><font color=black>g</font></td><td><font color=black>P</font></td><td><font color=green>t</font></td><td><font color=red>R</font></td><td><font color=blue>D</font></td><td><font color=blue>E</font></td><td><font color=green>Q</font></td><td><font color=black>A</font></td><td><font color=green>S</font></td><td><font color=red>K</font></td><td><font color=green>N</font></td><td><font color=gray> </font></td><td><font color=gray> </font></td><td><font color=gray> </font></td><td><font color=gray> </font></td><td><font color=gray> </font></td></tr></table>
  +
|}
  +
<br><br>
  +
  +
----
  +
  +
=== PolyPhen2 Prediction ===
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  +
{|
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| [[Image:mut_8_humdiv.png|thumb|450px|HumDiv prediction]]
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| [[Image:mut_8_humvar.png|thumb|450px|HumVar prediction]]
  +
|}

Revision as of 16:43, 23 June 2011

Pysicochemical Properities

Asn Asp consequences
polar, small, hydrophilic, negatively charged polar, small, hydrophilic, negatively charged Both amino acids have the same properities and therefore we suggest that an exchange of these two amino acids do not destroy the protein structure and function

Visualisation of the Mutation

picture original aa picture mutated aa combined picture
Amino acid Asparagine
Amino acid Aspartic acid
Picture which visualize the mutation

Subsitution Matrices Values

PAM 1 Pam 250 BLOSOUM 62
value aa most frequent substitution rarest substitution value aa most frequent substitution rarest substitution value aa most frequent substitution rarest substitution
36 36 (Asp) 0 (Cys, Met) 7 7 (Asp) 2 (Cys, Leu, Phe, Trp) 1 1 (Asp, His, Ser) -4 (Trp)

Conservation Analysis with Multiple Alignments

Mutation in the multiple alignment

Secondary Structure Mutation Analysis

JPred:
...CCCCCCCEEEEEECCCCCCCCHHHHHHHHHCCCCEEECCCCCCCCCCCCCCCCCC...
PsiPred:
...CCCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCCCC...

Comparison with the real structure:

Mutation at position 399
Mutation at position 399 - detailed view

SNAP Prediction

Substitution Prediction Reliability Index Expected Accuracy
D Neutral 1 60%

A detailed list of all possible substitutions can be found [here]

SIFT Prediction

SIFT Matrix:
Each entry contains the score at a particular position (row) for an amino acid substitution (column). Substitutions predicted to be intolerant are highlighted in red.

Sift legend.png
399 sift.png.png

SIFT Table
Threshold for intolerance is 0.05.
Amino acid color code: nonpolar, uncharged polar, basic, acidic.
Capital letters indicate amino acids appearing in the alignment, lower case letters result from prediction.



Predict Not ToleratedPositionSeq RepPredict Tolerated
wyfcm399N0.72iHvlgPtRDEQASKN



PolyPhen2 Prediction

HumDiv prediction
HumVar prediction
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