Difference between revisions of "Rs121907974"

From Bioinformatikpedia
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=== Pysicochemical Properities ===
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{| border="1" style="text-align:center; border-spacing:0;"
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|Phe
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|Ser
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|consequences
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|-
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|polar, tiny, hydrophilic, neutral
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|aliphatic, hydrophobic, neutral
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|Ile is much bigger than Ser and also is branched, because it is an aliphatic amino acid. Therefore the structure of both amino acids is really different and Ile is to big for the position where Ser was. Therefore, there has to be a big change in the 3D structure of the protein and the protein probably will loose its function.
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|-
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|}
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----
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=== Visualisation of the mutation ===
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{| 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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|-
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|[[Image:F211.png|thumb|150px|Amino acid Phenylalanine]]
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|[[Image:211S.png|thumb|150px|Amino acid Serine]]
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|[[Image:F211S.png|thumb|150px|Picture which visualize the mutation]]
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|-
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|}
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----
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=== Subsitution Matrices values ===
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{| 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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|-
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|value aa
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|most frequent substitution
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|rarest substitution
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|value aa
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|most frequent substitution
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|rarest substitution
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|value aa
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|most frequent substitution
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|rarest substitution
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|-
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|2
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|28 (Tyr)
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|0 (Asp, Cys, Glu, Lys, Pro, Val)
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|2
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|20 (Tyr)
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|1 (Arg, Asp, Cys, Gln, Glu, Gly, Lys, Pro)
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| -2
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|3 (Tyr)
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| -4 (Pro)
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|-
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|}
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----
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=== Conservation analysis with multiple alignments ===
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[[Image:mut_4.png|thumb|center|600px|Mutation in the multiple alignment]]
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----
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=== Secondary structure mutation analysis ===
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JPred:
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...EEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEEEECCCCC<font color="red">C</font>CCC...
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PsiPred:
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...EEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCEEEEEECCCCCC<font color="red">C</font>EEC...
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Comparison with the real structure:
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{|
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| [[Image:211_mut.png|thumb|250px|Mutation at position 211]]
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| [[Image:211_mut_detail.png|thumb|250px|Mutation at position 211 - detailed view]]
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|}
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----
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=== SNAP Prediction ===
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{| border="1" style="text-align:center; border-spacing:0;"
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|Substitution
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|Prediction
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|Reliability Index
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|Expected Accuracy
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|-
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|S
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|Non-neutral
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|5
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|87%
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|-
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|}
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A detailed list of all possible substitutions can be found [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/rs121907974 here]]
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----
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=== SIFT Prediction ===
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SIFT Matrix:<br>
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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.
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{|
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| [[Image:sift_legend.png|center]]
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|-
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| [[Image:211_sift.png.png|center]]
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|}
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SIFT Table<br>
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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>
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<tr><td><font color=gray> </font></td><td><font color=green>y</font></td><td><font color=black>w</font></td><td><font color=black>v</font></td><td><font color=green>t</font></td><td><font color=green>s</font></td><td><font color=red>r</font></td><td><font color=green>q</font></td><td><font color=black>p</font></td><td><font color=green>n</font></td><td><font color=black>m</font></td><td><font color=black>l</font></td><td><font color=red>k</font></td><td><font color=black>i</font></td><td><font color=red>h</font></td><td><font color=black>g</font></td><td><font color=blue>e</font></td><td><font color=blue>d</font></td><td><font color=green>c</font></td><td><font color=black>a</font></td><th>211F</th><td>1.00</td><td><font color=black>F</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=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>
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|}
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<br><br>
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----
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=== PolyPhen2 Prediction ===
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{|
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| [[Image:mut_4_humdiv.png|thumb|450px|HumDiv prediction]]
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| [[Image:mut_4_humvar.png|thumb|450px|HumVar prediction]]
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|}

Revision as of 16:26, 23 June 2011

Pysicochemical Properities

Phe Ser consequences
polar, tiny, hydrophilic, neutral aliphatic, hydrophobic, neutral Ile is much bigger than Ser and also is branched, because it is an aliphatic amino acid. Therefore the structure of both amino acids is really different and Ile is to big for the position where Ser was. Therefore, there has to be a big change in the 3D structure of the protein and the protein probably will loose its function.

Visualisation of the mutation

picture original aa picture mutated aa combined picture
Amino acid Phenylalanine
Amino acid Serine
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
2 28 (Tyr) 0 (Asp, Cys, Glu, Lys, Pro, Val) 2 20 (Tyr) 1 (Arg, Asp, Cys, Gln, Glu, Gly, Lys, Pro) -2 3 (Tyr) -4 (Pro)

Conservation analysis with multiple alignments

Mutation in the multiple alignment

Secondary structure mutation analysis

JPred:
...EEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCC...
PsiPred:
...EEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCEEEEEECCCCCCCEEC...

Comparison with the real structure:

Mutation at position 211
Mutation at position 211 - detailed view

SNAP Prediction

Substitution Prediction Reliability Index Expected Accuracy
S Non-neutral 5 87%

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
211 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
ywvtsrqpnmlkihgedca211F1.00F



PolyPhen2 Prediction

HumDiv prediction
HumVar prediction
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