Difference between revisions of "Sequence-based mutation analysis BCKDHA"

From Bioinformatikpedia
(Subset of mutations)
(Subset of mutations)
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!worst
 
!worst
 
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|29||G/E|| -2 || -4 (I + L)
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|29||G/E|| -2 || -4 (I, L)||7||0 (I, W, Y)||9||2 (W)
 
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|125||Q/E || 2 || -3 (C + F +I)
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|125||Q/E || 2 || -3 (C, F, I)||27 || 0 (F, W, Y)||7||1 (C, F, W)
 
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|166||Y/N || -2 || -3 (D + G + P)
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|166||Y/N || -2 || -3 (D, G, P)||3||0 (R, D, Q, G, K, M, P)||2||1 (A, R, D, Q, E, G, K, P)
 
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|249||G/S || 0 || -4 (I + L)
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|249||G/S || 0 || -4 (I, L)||21||0 (I, W, Y)||11||2 (W)
 
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|264||C/W|| -2 || -4 (E)
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|264||C/W|| -2 || -4 (E)||0 ||0 (N, D, Q, E, G, L, K, M, F, W) ||1||1 (R, N, D, Q, E, L, K, M, F, W)
 
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|265||R/W|| -3 || -3 (W + V + F + I + C)
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|265||R/W|| -3 || -3 (W, V, F, I, C)||8||0 (D, E, G, Y)||7||1 (F)
 
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|326||I/T|| -1 || -4 (G)
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|326||I/T|| -1 || -4 (G)||7||0 (G, A, P, W)||4||1 (W)
 
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|361||I/V|| 3|| -4 (G)
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|361||I/V|| 3|| -4 (G)||33||0 (G, H, P, W)||9||1 (W)
 
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|409||F/C|| -2|| -4 (P)
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|409||F/C|| -2|| -4 (P)||0||0 (D, C, Q, E, K, P, V) ||1||1 (R, D, C, Q, E, G, K, P)
 
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|438||Y/N|| -2 || -3 (D + G + P)
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|438||Y/N|| -2 || -3 (D, G, P)||3||0 (R, D, Q, G, K, M, P)||2||1 (A, R, D, Q, E, G, K, P)
 
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|}
   

Revision as of 23:01, 21 June 2011

Subset of mutations

Reference amino acid Mutated amino acid Secondary Structure
Position Residue Properties Structure Residue Properties Structure
29 G tiny, small E charged, polar C
125 Q acidic, polar E charged, polar C
166 Y hydrophobic, aromatic, polar N acidic, polar, small H
249 G tiny, small S polar, small, tiny, hydroxylic H
264 C sulphur containing, hydrophobic, tiny, small, polar W hydrophobic, aromatic, polar E
265 R charged, positive (basic), polar W E
326 I T E
361 I V H
409 F C C
438 Y N C


Position AA1/AA2 BLOSUM62 PAM1 PAM250
score worst score worst score worst
29 G/E -2 -4 (I, L) 7 0 (I, W, Y) 9 2 (W)
125 Q/E 2 -3 (C, F, I) 27 0 (F, W, Y) 7 1 (C, F, W)
166 Y/N -2 -3 (D, G, P) 3 0 (R, D, Q, G, K, M, P) 2 1 (A, R, D, Q, E, G, K, P)
249 G/S 0 -4 (I, L) 21 0 (I, W, Y) 11 2 (W)
264 C/W -2 -4 (E) 0 0 (N, D, Q, E, G, L, K, M, F, W) 1 1 (R, N, D, Q, E, L, K, M, F, W)
265 R/W -3 -3 (W, V, F, I, C) 8 0 (D, E, G, Y) 7 1 (F)
326 I/T -1 -4 (G) 7 0 (G, A, P, W) 4 1 (W)
361 I/V 3 -4 (G) 33 0 (G, H, P, W) 9 1 (W)
409 F/C -2 -4 (P) 0 0 (D, C, Q, E, K, P, V) 1 1 (R, D, C, Q, E, G, K, P)
438 Y/N -2 -3 (D, G, P) 3 0 (R, D, Q, G, K, M, P) 2 1 (A, R, D, Q, E, G, K, P)

Annotation: H = helix, E = beta-sheet, C = coil

BLOSUM62
PAM1
PAM250

PSSM

PsiBlast was run using the following command: blastpgp -i sequence.fasta -j 5 -d /data/blast/nr/nr -C profile.ckp

SNAP

To run SNAP we used the command:

snapfun -i BCKDHA.fasta -m mutations.txt -o SNAP.out

SIFT

Polyphen2

Position AA1/AA2 HumDiv HumVar
prediction Score Sensitivity Specificity prediction Score Sensitivity Specificity
29 G/E benign 0.025 0.96 0.80 benign 0.018 0.96 0.52
125 Q/E possibly damaging 0.759 0.85 0.93 benign 0.285 0.87 0.75
166 Y/N probably damaging 0.997 0.40 0.98 probably damaging 0.964 0.59 0.93
249 G/S benign 0.145 0.93 0.86 benign 0.292 0.86 0.75
264 C/W probably damaging 1.000 0.00 1.00 probably damaging 1.000 0.00 1.00
265 R/W probably damaging 1.000 0.00 1.00 probably damaging 1.000 0.00 1.00
326 I/T probably damaging 0.997 0.40 0.98 probably damaging 0.998 0.16 0.99
361 I/V benign 0.039 0.95 0.82 benign 0.178 0.89 0.70
409 F/C probably damaging 0.998 0.27 0.99 probably damaging 0.939 0.64 0.92
438 Y/N probably damaging 1.000 0.00 1.00 probably damaging 0.987 0.49 0.96



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