Difference between revisions of "Sequence-based mutation analysis of ARSA"
From Bioinformatikpedia
(→Intro) |
(→SNAP) |
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| + | output: |
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| − | The relevant lines of the psiblast matrix are shown below: |
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| + | <code> |
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| + | nsSNP Prediction Reliability Index Expected Accuracy |
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| + | ----- ------------ ------------------- ------------------- |
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| + | D29N Non-neutral 7 96% |
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| + | Q153H Neutral 0 53% |
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| + | T274M Non-neutral 6 93% |
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| + | T409I Non-neutral 1 63% |
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| + | C489G Non-neutral 5 87% |
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| + | D381D Neutral 5 89% |
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| + | P195P Neutral 6 92% |
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| + | H151H Neutral 4 85% |
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| + | W193C Non-neutral 3 78% |
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| + | </code> |
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=== Multiple sequence alignments === |
=== Multiple sequence alignments === |
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Revision as of 15:33, 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%
D381D Neutral 5 89%
P195P Neutral 6 92%
H151H Neutral 4 85%
W193C Non-neutral 3 78%
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.
| 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
