Difference between revisions of "Sequence-based mutation analysis of ARSA"
From Bioinformatikpedia
(→Multiple sequence alignments) |
|||
| Line 116: | Line 116: | ||
* tr|D3ZC09|D3ZC09_RAT |
* tr|D3ZC09|D3ZC09_RAT |
||
| − | Next, we calculated multiple sequence alignments of these proteins (including ARSA) with |
+ | Next, we calculated multiple sequence alignments of these proteins (including ARSA) with Muscle. The Jalview images of the alignments are shown below. |
[[File:homomusclearsa.png | 200px | center | thumb | Multiple sequence alignments of all 75 homologuous sequences using muscle]] |
[[File:homomusclearsa.png | 200px | center | thumb | Multiple sequence alignments of all 75 homologuous sequences using muscle]] |
||
| − | [[File:homoclustalarsa.png | 200px | center | thumb | Multiple sequence alignments of all 75 homologuous sequences using clustalw]] |
||
{| border="1" style="text-align:center; border-spacing:0;" |
{| border="1" style="text-align:center; border-spacing:0;" |
||
Revision as of 15:26, 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 |
SNAP
We ran snap using the following command:
snapfun -i ARSA.fasta -m mutants.txt -o snap.out
The relevant lines of the psiblast matrix are shown below:
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
