Difference between revisions of "Sequence-based mutation analysis BCKDHA"
From Bioinformatikpedia
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!colspan="3"|Reference amino acid |
!colspan="3"|Reference amino acid |
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!colspan="3"|Mutated amino acid |
!colspan="3"|Mutated amino acid |
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− | !rowspan="2"|BLOSUM62 |
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− | !rowspan="2"|PAM1 |
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− | !rowspan="2"|PAM250 |
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!rowspan="2"|Secondary Structure |
!rowspan="2"|Secondary Structure |
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!Structure |
!Structure |
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− | |29||G||tiny, small||||E||charged, polar|| |
+ | |29||G||tiny, small||||E||charged, polar|| ||C |
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− | |125||Q||acidic, polar||||E||charged, polar|| |
+ | |125||Q||acidic, polar||||E||charged, polar|| ||C |
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− | |166||Y||hydrophobic, aromatic, polar||||N||acidic, polar, small|| |
+ | |166||Y||hydrophobic, aromatic, polar||||N||acidic, polar, small|| ||H |
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− | |249||G||tiny, small||||S||polar, small, tiny, hydroxylic|| || |
+ | |249||G||tiny, small||||S||polar, small, tiny, hydroxylic|| || H |
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− | |264||C||sulphur containing, hydrophobic, tiny, small, polar||||W||hydrophobic, aromatic, polar|| |
+ | |264||C||sulphur containing, hydrophobic, tiny, small, polar||||W||hydrophobic, aromatic, polar|| ||E |
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− | |265||R||charged, positive (basic), polar||||W|||| |
+ | |265||R||charged, positive (basic), polar||||W|||| ||E |
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− | |326||I||||||T|||| |
+ | |326||I||||||T|||| ||E |
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− | |361||I||||||V|||| |
+ | |361||I||||||V|||| ||H |
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− | |409||F||||||C|| |
+ | |409||F||||||C||||||C |
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− | |438||Y||||||N|||| |
+ | |438||Y||||||N|||| ||C |
+ | |} |
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+ | |||
+ | |||
+ | {|border="1" |
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+ | !rowspan="2"|Position |
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+ | !rowspan="2"|AA1/AA2 |
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+ | !colspan="2"|BLOSUM62 |
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+ | !colspan="2"|PAM1 |
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+ | !colspan="2"|PAM250 |
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+ | |- |
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+ | !score |
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+ | !worst |
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+ | !score |
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+ | !worst |
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+ | !score |
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+ | !worst |
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+ | |- |
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+ | |29||G/E|| -2 || -4 (I + L) |
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+ | |- |
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+ | |125||Q/E || 2 || -3 (C + F +I) |
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+ | |- |
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+ | |166||Y/N || -2 || -3 (D + G + P) |
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+ | |- |
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+ | |249||G/S || 0 || -4 (I + L) |
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+ | |- |
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+ | |264||C/W|| -2 || -4 (E) |
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+ | |- |
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+ | |265||R/W|| -3 || -3 (W + V + F + I + C) |
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+ | |- |
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+ | |326||I/T|| -1 || -4 (G) |
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+ | |- |
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+ | |361||I/V|| 3|| -4 (G) |
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+ | |- |
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+ | |409||F/C|| -2|| -4 (P) |
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+ | |- |
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+ | |438||Y/N|| -2 || -3 (D + G + P) |
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Revision as of 21:36, 21 June 2011
Contents
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
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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