Metachromatic leukodystrophy reference aminoacids

Sequence

>sp|P15289|ARSA_HUMAN Arylsulfatase A OS=Homo sapiens GN=ARSA PE=1 SV=3
MGAPRSLLLALAAGLAVARPPNIVLIFADDLGYGDLGCYGHPSSTTPNLDQLAAGGLRFT
DFYVPVSLCTPSRAALLTGRLPVRMGMYPGVLVPSSRGGLPLEEVTVAEVLAARGYLTGM
AGKWHLGVGPEGAFLPPHQGFHRFLGIPYSHDQGPCQNLTCFPPATPCDGGCDQGLVPIP
LLANLSVEAQPPWLPGLEARYMAFAHDLMADAQRQDRPFFLYYASHHTHYPQFSGQSFAE
RSGRGPFGDSLMELDAAVGTLMTAIGDLGLLEETLVIFTADNGPETMRMSRGGCSGLLRC
GKGTTYEGGVREPALAFWPGHIAPGVTHELASSLDLLPTLAALAGAPLPNVTLDGFDLSP
LLLGTGKSPRQSLFFYPSYPDEVRGVFAVRTGKYKAHFFTQGSAHSDTTADPACHASSSL
TAHEPPLLYDLSKDPGENYNLLGGVAGATPEVLQALKQLQLLKAQLDAAVTFGPSQVARG
EDPALQICCHPGCTPRPACCHCPDPHA

Source

• Uniprot

Database Searches

BLAST against NR

How To

With BLAST being installed, the following steps were performed:

• typed blastall -p blastp -i refSeq.fasta -d /data/blast/nr/nr > blastp with refSeq.fasta being the file containing the reference sequence and blastp the outfile

PSI-BLAST against NR

How To

With PSI-BLAST being installed, the following command was executed:

• blastpgp -i refSeq.fasta -d /data/blast/nr/nr -e"e-value" -j "#iterations" > psiblast_"e-value"_"#iterations"

FASTA against NR

How To

fasta was not yet installed on the computer, so it was installed, executing the following command from the ./src directory from the software's sourc code:

• make -f ../make/Makefile.linux_sse2 all

We aligned the sequences, using the parameters written below:

• ./bin/fasta36 -q ~/Documents/refSeq.fasta /data/blast/nr/nr > fasta_results.txt

hhsearch

How To

We used the online version of hhPred <ref>http://toolkit.lmb.uni-muenchen.de/hhpred</ref> with the following parameters

• local alignment
• 3 iterations

Due to the fact that only PDB-IDs could be extracted from the HHpred-output, we had to do a mapping from PDB ID to RefSeq AC. This was done by mapping PDB ID to UniProt AC and then to RefSeq AC by PIR ID Mapping <ref>http://pir.georgetown.edu/pirwww/search/idmapping.shtml</ref>

Multiple Alignments

For building the multiple Alignments the results of the Psiblast run with e-value cutoff of 10E-6 and 5 iterations were divided into 6 groups by sequence identity:

• <20%
• 20% - 39%
• 40% - 59%
• 60% - 89%
• 90% - 99%
• >99%

The sequences with <20% and >99% sequence identitiy were ignored and 5 samples were randomly picked from the other ranges. So 20 sequences were available for the multiple alignments.

References

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