Sequence-based mutation analysis of ARSA

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 -Q psiblast.mat -o psiblast_eval10E_6.it.5.new.txt

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 ClustalW and Muscle. The Jalview images of the alignments are shown below.

Multiple sequence alignments of all 75 homologuous sequences using muscle

Multiple sequence alignments of all 75 homologuous sequences using clustalw

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