Sequence-based mutation analysis of ARSA

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Revision as of 10:38, 22 June 2011 by Zacher (talk | contribs) (Intro)

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
synonymous Asp [D]-Asp [D] 381
synonymous Pro [P]-Pro [P] 195
synonymous His [H]-His [H] 151
missense Trp [W]-Cys [C] 193
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

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