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

From Bioinformatikpedia
(SNAP)
(Subset of mutations)
Line 6: Line 6:
 
!colspan="3"|Reference amino acid
 
!colspan="3"|Reference amino acid
 
!colspan="3"|Mutated amino acid
 
!colspan="3"|Mutated amino acid
!rowspan="2"|BLOSUM62
 
!rowspan="2"|PAM1
 
!rowspan="2"|PAM250
 
 
!rowspan="2"|Secondary Structure
 
!rowspan="2"|Secondary Structure
 
|-
 
|-
Line 19: Line 16:
 
!Structure
 
!Structure
 
|-
 
|-
|29||G||tiny, small||||E||charged, polar|| || || ||||C
+
|29||G||tiny, small||||E||charged, polar|| ||C
 
|-
 
|-
|125||Q||acidic, polar||||E||charged, polar|| || || ||||C
+
|125||Q||acidic, polar||||E||charged, polar|| ||C
 
|-
 
|-
|166||Y||hydrophobic, aromatic, polar||||N||acidic, polar, small|| || || ||||H
+
|166||Y||hydrophobic, aromatic, polar||||N||acidic, polar, small|| ||H
 
|-
 
|-
|249||G||tiny, small||||S||polar, small, tiny, hydroxylic|| || || ||||H
+
|249||G||tiny, small||||S||polar, small, tiny, hydroxylic|| || H
 
|-
 
|-
|264||C||sulphur containing, hydrophobic, tiny, small, polar||||W||hydrophobic, aromatic, polar|| || || ||||E
+
|264||C||sulphur containing, hydrophobic, tiny, small, polar||||W||hydrophobic, aromatic, polar|| ||E
 
|-
 
|-
|265||R||charged, positive (basic), polar||||W|||| || || ||||E
+
|265||R||charged, positive (basic), polar||||W|||| ||E
 
|-
 
|-
|326||I||||||T|||| || || ||||E
+
|326||I||||||T|||| ||E
 
|-
 
|-
|361||I||||||V|||| || || ||||H
+
|361||I||||||V|||| ||H
 
|-
 
|-
|409||F||||||C|||| || || ||||C
+
|409||F||||||C||||||C
 
|-
 
|-
|438||Y||||||N|||| || || ||||C
+
|438||Y||||||N|||| ||C
  +
|}
  +
  +
  +
{|border="1"
  +
!rowspan="2"|Position
  +
!rowspan="2"|AA1/AA2
  +
!colspan="2"|BLOSUM62
  +
!colspan="2"|PAM1
  +
!colspan="2"|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)
 
|}
 
|}
   

Revision as of 21:36, 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

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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