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

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P136A Non-neutral 4 82%
  
P136A Non-neutral 4 82%
 
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{| border="1" style="text-align:center; border-spacing:0;"
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! ref\mutation || A || R || N || D || C || Q || E || G || H || I || L || K || M || F || P || S || T || W || Y || V
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|-
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| D29 || Non-neutral || Non-neutral || Non-neutral || || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral
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|-
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| Q153 || Non-neutral || Non-neutral || Neutral || Non-neutral || Non-neutral || || Non-neutral || Non-neutral || Neutral || Non-neutral || Non-neutral || Non-neutral || Neutral || Non-neutral || Neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral
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|-
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| T274 || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || || Non-neutral || Non-neutral || Non-neutral
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|-
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| T409 || Neutral || Non-neutral || Neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || || Non-neutral || Non-neutral || Non-neutral
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|-
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| C489 || Non-neutral || Non-neutral || Non-neutral || Non-neutral || || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral
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|-
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| W193 || Non-neutral || Non-neutral || Neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || Non-neutral || || Non-neutral || Non-neutral
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|-
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|}
   
 
=== Multiple sequence alignments ===
  
=== Multiple sequence alignments ===

Revision as of 16:43, 23 June 2011

Intro

SNP type mutation position
missense Asp-Asn 29
missense Gln-His 153
missense Thr-Met 274
missense Thr-Ile 409
missense Cys-Gly 489
missense Trp [W]-Cys [C] 193
missense Phe [F]-Val [V] 356
missense Asn [N]-Ser [S] 440
missense R - H 496
missense P - A 136

SNAP

We ran snap using the following command: 


snapfun -i ARSA.fasta -m mutants.txt -o snap.out


output: 


nsSNP	Prediction	Reliability Index	Expected Accuracy
-----	------------	-------------------	-------------------
D29N	Non-neutral		7			96%
Q153H	 Neutral 		0			53%
T274M	Non-neutral		6			93%
T409I	Non-neutral		1			63%
C489G	Non-neutral		5			87%
W193C	Non-neutral		3			78%
F356V	 Neutral 		1			60%
N440S	Non-neutral		2			70%
R496H	 Neutral 		1			60%
P136A	Non-neutral		4			82%
ref\mutation A R N D C Q E G H I L K M F P S T W Y V
D29 Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral
Q153 Non-neutral Non-neutral Neutral Non-neutral Non-neutral Non-neutral Non-neutral Neutral Non-neutral Non-neutral Non-neutral Neutral Non-neutral Neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral
T274 Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral
T409 Neutral Non-neutral Neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral
C489 Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral
W193 Non-neutral Non-neutral Neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral Non-neutral

Multiple sequence alignments

First, we downloaded the HSSP file for ARSA to get all proteins, which are homolog to it. Then we extracted from it all 75 mammalian proteins and downloaded their sequences. Uniprot identifiers of these are listed below:

  • sp|Q08DD1|ARSA_BOVIN
  • sp|P15289|ARSA_HUMAN
  • sp|P50428|ARSA_MOUSE
  • sp|P15848|ARSB_HUMAN
  • sp|P50429|ARSB_MOUSE
  • sp|P50430|ARSB_RAT
  • sp|P51689|ARSD_HUMAN
  • sp|P51690|ARSE_HUMAN
  • sp|Q60HH5|ARSE_MACFA
  • sp|P54793|ARSF_HUMAN
  • sp|Q32KH9|ARSG_CANFA
  • sp|Q96EG1|ARSG_HUMAN
  • sp|Q3TYD4|ARSG_MOUSE
  • sp|Q32KJ9|ARSG_RAT
  • sp|Q32KH8|ARSH_CANFA
  • sp|Q5FYA8|ARSH_HUMAN
  • sp|Q32KH7|ARSI_CANFA
  • sp|Q5FYB1|ARSI_HUMAN
  • sp|Q32KI9|ARSI_MOUSE
  • sp|Q32KJ8|ARSI_RAT
  • sp|Q32KH5|GALNS_CANFA
  • sp|P34059|GALNS_HUMAN
  • sp|Q571E4|GALNS_MOUSE
  • sp|Q8WNQ7|GALNS_PIG
  • sp|Q32KJ6|GALNS_RAT
  • sp|P08842|STS_HUMAN
  • sp|P50427|STS_MOUSE
  • sp|P15589|STS_RAT
  • tr|Q8N322|Q8N322_HUMAN
  • tr|Q96I49|Q96I49_HUMAN
  • tr|Q6YL38|Q6YL38_HUMAN
  • tr|Q63HL5|Q63HL5_HUMAN
  • tr|Q6ZNJ9|Q6ZNJ9_HUMAN
  • tr|B4DVI5|B4DVI5_HUMAN
  • tr|A8K4A0|A8K4A0_HUMAN
  • tr|C9J5G7|C9J5G7_HUMAN
  • tr|B7XD04|B7XD04_HUMAN
  • tr|B7Z267|B7Z267_HUMAN
  • tr|B2R6P1|B2R6P1_HUMAN
  • tr|B7Z6V4|B7Z6V4_HUMAN
  • tr|B4DQ74|B4DQ74_HUMAN
  • tr|B7WNL6|B7WNL6_HUMAN
  • tr|A1L484|A1L484_HUMAN
  • tr|B2R7S0|B2R7S0_HUMAN
  • tr|B7Z1M0|B7Z1M0_HUMAN
  • tr|A5D7J7|A5D7J7_BOVIN
  • tr|Q32KI0|Q32KI0_CANFA
  • tr|Q32KI2|Q32KI2_CANFA
  • tr|D2HFI0|D2HFI0_AILME
  • tr|Q2XQY2|Q2XQY2_MACFA
  • tr|Q32KI1|Q32KI1_CANFA
  • tr|D2HFI1|D2HFI1_AILME
  • tr|A6MKC3|A6MKC3_CALJA
  • tr|D2H6D4|D2H6D4_AILME
  • tr|D2HFI2|D2HFI2_AILME
  • tr|Q8WNR3|Q8WNR3_PIG
  • tr|D2HXW7|D2HXW7_AILME
  • tr|Q32KI3|Q32KI3_CANFA
  • tr|A6QLR7|A6QLR7_BOVIN
  • tr|D2I3S5|D2I3S5_AILME
  • tr|A1XI21|A1XI21_HORSE
  • tr|Q32KI5|Q32KI5_CANFA
  • tr|Q19AM0|Q19AM0_BOVIN
  • tr|D2HFH9|D2HFH9_AILME
  • tr|A6QLZ3|A6QLZ3_BOVIN
  • tr|Q15B85|Q15B85_MACFA
  • tr|Q9DC66|Q9DC66_MOUSE
  • tr|Q32KK2|Q32KK2_RAT
  • tr|B5DEF1|B5DEF1_RAT
  • tr|B2RWQ7|B2RWQ7_MOUSE
  • tr|B4F7E2|B4F7E2_RAT
  • tr|Q8CC47|Q8CC47_MOUSE
  • tr|Q32KK0|Q32KK0_RAT
  • tr|Q3KR80|Q3KR80_RAT
  • tr|D3ZC09|D3ZC09_RAT

Next, we calculated multiple sequence alignments of these proteins (including ARSA) with Muscle. The Jalview images of the alignments are shown below.

Multiple sequence alignments of all 75 homologuous sequences using muscle
pos conservation - reference conservation - mutant
29 0.86 0
153 0.14 0
274 0.87 0
409 0.35 0.16
489 0.80 0.05
193 0.13 0
356 0.15 0
440 0.15 0
496 0.14 0.01
136 0.93 0

PSI-BLAST


blastpgp -i ARSA.fasta -d /data/blast/nr/nr -e 10E-6 -j 5 -Q psiblast.mat -o psiblast_eval10E_6.it.5.new.txt



Last position-specific scoring matrix computed, weighted observed percentages rounded down, information per position, and relative weight of gapless real matches to pseudocounts
          A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V   A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V
  29 D   -5 -5 -2  8 -7 -3 -1 -4 -4 -6 -7 -4 -6 -7 -5 -3 -4 -7 -6 -6    0   0   0 100   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  2.49 1.56
 153 Q    3  2 -1  4 -4 -1 -1 -2  0 -2 -3 -3  4 -2 -3 -1 -2 -3 -2 -2   26  10   3  23   0   3   3   3   2   2   1   1  13   2   1   3   2   0   1   2  0.53 1.48
 274 T   -3 -4 -3 -4 -2 -4 -4 -5 -5 -4 -4 -4 -3 -5 -4  1  8 -6 -5 -3    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   7  92   0   0   0  1.94 1.62
 409 T   -1  0  0 -1 -2 -1 -1  0 -1 -1 -1  0 -1 -1  3  0  1  6  0 -1    5   5   5   4   1   3   4   8   1   3   6   5   1   2  13   6   8  11   3   4  0.26 0.95
 489 C    2 -1  1 -4  8 -4 -4 -2 -1 -1 -2 -3 -1 -4 -4  0  0  5 -1 -3   15   4   8   0  36   0   0   2   1   3   3   1   1   0   0   6   5   9   2   0  0.99 1.22
 440 N   -5 -3  6  5 -6 -2 -1 -4 -3 -6 -6 -3 -6 -6  2 -2 -3 -6 -6 -5    0   1  46  36   0   1   2   0   0   0   0   1   0   0  10   1   1   0   0   0  1.48 1.67
 356 F   -3 -1 -5 -5 -3  0 -1 -6  1  3  0 -1  0  2 -6 -3 -2 -3  5  3    1   4   0   0   1   5   4   0   3  18   8   5   2   8   0   1   2   0  20  20  0.59 1.62
 193 W   -2  4  2  3 -5  0  0 -2  0 -3 -4  1 -3 -1 -2 -1 -2  1  1 -3    3  25  11  16   0   4   5   3   2   2   1   7   0   2   2   4   2   2   5   2  0.46 1.45
 136 P   -3 -5 -5 -5 -6 -4 -4 -5 -5 -6 -6 -4 -6 -7  9 -4 -4 -7 -6 -5    1   0   0   0   0   0   0   0   0   0   0   0   0   0  98   0   0   0   0   0  3.03 1.61
 496 R   -3  1  0 -3 -4  1  1 -1  1 -3  1  1 -2  2  4  0 -3 -1 -1 -3    1   7   4   1   0   5  10   4   3   1  16   9   0   9  20   8   1   1   1   1  0.34 0.96
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