Sequence Search and Multiple Sequence Alignment (PKU)

Short Task Description

Perform database searches using different search tools with the PAH protein as query

Create and evaluate multiple sequence alignments

Reference Sequence of PAH

>sp|P00439|PH4H_HUMAN Phenylalanine-4-hydroxylase OS=Homo sapiens GN=PAH PE=1 SV=1
MSTAVLENPGLGRKLSDFGQETSYIEDNCNQNGAISLIFSLKEEVGALAKVLRLFEENDV
NLTHIESRPSRLKKDEYEFFTHLDKRSLPALTNIIKILRHDIGATVHELSRDKKKDTVPW
FPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARRKQFADIAYNYRHGQPIPRVEYM
EEEKKTWGTVFKTLKSLYKTHACYEYNHIFPLLEKYCGFHEDNIPQLEDVSQFLQTCTGF
RLRPVAGLLSSRDFLGGLAFRVFHCTQYIRHGSKPMYTPEPDICHELLGHVPLFSDRSFA
QFSQEIGLASLGAPDEYIEKLATIYWFTVEFGLCKQGDSIKAYGAGLLSSFGELQYCLSE
KPKLLPLELEKTAIQNYTVTEFQPLYYVAESFNDAKEKVRNFAATIPRPFSVRYDPYTQR
IEVLDNTQQLKILADSINSEIGILCSALQKI

Database Searches

Blast

time blast2 -p blastp -d /mnt/project/pracstrucfunc12/data/big/big -i Dropbox/Phenylketonuria/Task1/PAH.fasta -o results_blast2_standard

real 1m47.401s user 1m25.290s sys 0m18.280s

time blast2 -p blastp -d /mnt/project/pracstrucfunc12/data/big/big -i Dropbox/Phenylketonuria/Task1/PAH.fasta -o results_blast2_e-10 -e 0.0000000001 -v 2000

real 1m35.454s user 1m21.700s sys 0m3.100s

HHBlits

time hhblits -i Dropbox/Phenylketonuria/Task1/PAH.fasta -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current -o results_hhblits_standard

real 6m10.059s user 3m15.640s sys 0m40.220s

hhblits -i Dropbox/Phenylketonuria/Task1/PAH.fasta -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current -o results_hhblits_n4_e-7 -n 4 -e 0.0000001 -o results_hhblits_n4_e-7

HHSearch

time hhsearch -i Dropbox/Phenylketonuria/Task1/PAH.fasta -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current_hhm_db

real 13m27.782s user 13m18.120s sys 0m8.480s

PDB

To get structural information not directly contained in big_80, we performed an additional search in PDB at NCBI, with parameters: scoring matrix=PAM70, gap open = 10, gap extend = 1, composition based statistics, max. 1000 target sequences.