Sequence-based mutation analysis of ARSA
From Bioinformatikpedia
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
PSI-BLAST
blastpgp -i ARSA.fasta -d /data/blast/nr/nr -e 10E-6 -j 5 > psiblast_eval10E_6.it.5.txt#
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 ClustalW and Muscle. The Jalview images of the alignments are shown below.
29 153 274 409 489 193 356 440
> cons[muts]
[1] 0.8648649 0.1486486 0.8783784 0.3513514 0.7972973 0.1351351 0.1486486
[8] 0.1486486
