Difference between revisions of "Rs121907967"

From Bioinformatikpedia
(Created page with "{| border="1" style="text-align:center; border-spacing:0;" |Substitution |Prediction |Reliability Index |Expected Accuracy |- |A |Non-neutral |5 |87% |- |C |Non-neutral |5 |87% …")
 
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=== Pysicochemical Properities ===
  +
 
{| border="1" style="text-align:center; border-spacing:0;"
  
{| border="1" style="text-align:center; border-spacing:0;"
  +
|Trp
−
|Substitution
  
  +
|TER
−
|Prediction
  
  +
|consequences
−
|Reliability Index
 
−
|Expected Accuracy
  
 
|-
  
|-
  +
|aromatic, polar, hydrophobic
−
|A
  
  +
|TER
−
|Non-neutral
  
  +
|By this change, the protein is not complete, therefore it is not possible for the protein to fold and to function.
−
|5
  
−
|87%
  
 
|-
  
|-
−
|C
 +
|}
  +
−
|Non-neutral
  
  +
----
−
|5
  
  +
−
|87%
  
  +
=== 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
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|combined picture
 
|-
  
|-
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|[[Image:W329.png|thumb|150px|Amino acid Tryptophan]]
−
|D
  
  +
|
−
|Non-neutral
  
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|[[Image:prot_ter.png|thumb|150px|Visualization of the mutated protein]]
−
|5
  
−
|87%
  
 
|-
  
|-
−
|E
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|}
  +
−
|Non-neutral
  
  +
----
−
|6
  
  +
−
|93%
  
  +
=== 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
−
|5
  
  +
|value aa
−
|87%
  
  +
|most frequent substitution
  +
|rarest substitution
  +
|value aa
  +
|most frequent substitution
  +
|rarest substitution
 
|-
  
|-
−
|G
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|X
  +
|2 (Arg)
−
|Non-neutral
  
  +
|0 (all, except Arg, Phe, Ser, Tyr)
−
|6
  
−
|93%
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|X
  +
|2 (Arg)
  +
|0 (all, except Arg, His, Leu, Phe, Ser, Tyr)
  +
|X
  +
|2 (Tyr)
  +
| -4 (Asn, Asp, Pro)
 
|-
  
|-
−
|H
 +
|}
  +
−
|Non-neutral
  
  +
----
−
|6
  
  +
−
|93%
  
  +
=== Conservation Analysis with Multiple Alignments ===
−
|-
  
  +
[[Image:mut_6.png|thumb|center|600px|Mutation in the multiple alignment]]
−
|I
  
  +
−
|Non-neutral
  
  +
----
−
|5
  
  +
−
|87%
  
  +
=== Secondary Structure Mutation Analysis'''
−
|-
  
  +
−
|K
  
  +
JPred:
−
|Non-neutral
  
  +
...CCCCCCCCC<font color="red">C</font>CCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEECC...
−
|6
  
  +
PsiPred:
−
|93%
  
  +
...CCCCCCCCC<font color="red">C</font>CCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEECC...
−
|-
  
  +
−
|L
  
  +
Comparison with the real structure:
−
|Non-neutral
  
−
|5
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{|
  +
| [[Image:329_mut.png|thumb|250px|Mutation at position 329]]
−
|87%
  
  +
| [[Image:329_mut_detail.png|thumb|250px|Mutation at position 329 - detailed view]]
−
|-
  
−
|M
 +
|}
  +
−
|Non-neutral
  
  +
----
−
|5
  
  +
−
|87%
  
  +
=== SNAP Prediction ===
−
|-
  
  +
−
|N
  
  +
No prediction available, because the protein ends here.
−
|Non-neutral
  
  +
−
|5
  
  +
A detailed list of all possible substitutions can be found [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/rs121907967_SNAP here]]
−
|87%
  
  +
−
|-
  
  +
----
−
|P
  
  +
−
|Non-neutral
  
  +
=== SIFT Prediction ===
−
|5
  
  +
−
|87%
  
  +
SIFT Matrix:<br>
−
|-
  
  +
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.
−
|Q
  
  +
−
|Non-neutral
  
−
|5
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{|
  +
| [[Image:sift_legend.png|center]]
−
|87%
  
−
|-
  
−
|R
  
−
|Non-neutral
  
−
|5
  
−
|87%
  
−
|-
  
−
|T
  
−
|Non-neutral
  
−
|5
  
−
|87%
  
−
|-
  
−
|V
  
−
|Non-neutral
  
−
|5
  
−
|87%
  
−
|-
  
−
|Y
  
−
|Non-neutral
  
−
|4
  
−
|82%
  
−
|-
  
−
|S
  
−
|Non-neutral
  
−
|5
  
−
|87%
  
 
|-
  
|-
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| [[Image:329_sift.png.png|center]]
 
|}
  
|}
  +
<br><br>
   
  +
----
−
Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_mutation_analysis_HEXA sequence-based mutation analysis]]
  
  +
  +
=== PolyPhen2 Prediction ===
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  +
{|
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| [[Image:mut_7_humdiv.png|thumb|450px|HumDiv prediction]]
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| [[Image:mut_7_humvar.png|thumb|450px|HumVar prediction]]
  +
|}

Revision as of 17:39, 23 June 2011

Pysicochemical Properities

Trp TER consequences
aromatic, polar, hydrophobic TER By this change, the protein is not complete, therefore it is not possible for the protein to fold and to function.

Visualisation of the Mutation

picture original aa picture mutated aa combined picture
Amino acid Tryptophan
Visualization of the mutated protein

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
X 2 (Arg) 0 (all, except Arg, Phe, Ser, Tyr) X 2 (Arg) 0 (all, except Arg, His, Leu, Phe, Ser, Tyr) X 2 (Tyr) -4 (Asn, Asp, Pro)

Conservation Analysis with Multiple Alignments

Mutation in the multiple alignment

=== Secondary Structure Mutation Analysis 

JPred:
...CCCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEECC...
PsiPred:
...CCCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEECC...

Comparison with the real structure:

Mutation at position 329
Mutation at position 329 - detailed view

SNAP Prediction

No prediction available, because the protein ends here.

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
329 sift.png.png



PolyPhen2 Prediction

HumDiv prediction
HumVar prediction
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