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

From Bioinformatikpedia
(Subset of mutations)
(Subset of mutations)
Line 78: Line 78:
 
C = coil
 
C = coil
 
{|
 
{|
|[[File:BLOSUM62_BCKDHA.gif| thumb |BLOSUM62]]||[[File:PAM1_BCKDHA.png | thumb | PAM1]]
+
|[[File:BLOSUM62_BCKDHA.gif| thumb |BLOSUM62]]||[[File:PAM1_BCKDHA.png | thumb | PAM1]]||[[File:PAM250_BCKDHA.png | thumb | PAM250]]
 
|}
 
|}
   

Revision as of 21:44, 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)
125 Q/E 2 -3 (C + F +I)
166 Y/N -2 -3 (D + G + P)
249 G/S 0 -4 (I + L)
264 C/W -2 -4 (E)
265 R/W -3 -3 (W + V + F + I + C)
326 I/T -1 -4 (G)
361 I/V 3 -4 (G)
409 F/C -2 -4 (P)
438 Y/N -2 -3 (D + G + 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



back to Maple_syrup_urine_disease main page