Sequence and multiple alignments

Sequence Alignments

Database search

We used different tools for the search in a non-reduntant(NR) database like BLAST, FASTA and PSI-BLAST. Because of the absence of the database in a hmm format, we decided not to integrate the hhpred web-results. These results are not compareable.

Blastaufruf: blast -p blastp -i 1a6z.fasta -d /data/nr/nr -o blastp_1a6z_on_NR.txt runtime 5:34
Fastaaufruf: ../../Desktop/fasta-36.3.4/bin/fasta36 -q 1a6z.fasta /data/nr/nr >fasta_1a5z_on_nr.txt runtime 10:44

psiblast: blastpgp -i 1a6z.fasta -d /data/nr/nr runtime 21:40
blastpgp -i 1a6z.fasta -d /data/nr/nr -j 6 -e 10E-6 > psiblast_on_NR_itera3_e-val_10E-6.txt runtime 23:49
blastpgp -i 1a6z.fasta -d /data/nr/nr -j 3 -e 10E-6 > psiblast_on_NR_itera6_e-val_10E-6.txt runtime 15:08
blastpgp -i 1a6z.fasta -d /data/nr/nr -j 3 > psiblast_on_NR_itera3.txt runtime 9:41
blastpgp -i 1a6z.fasta -d /data/nr/nr -j 6 > psiblast_on_NR_itera6.txt runtime 23:30

Multiple Alignments

Multiple Alignments

Used Sequences

SeqIdentifier	Seq Identity	source	Protein function
99-90% Sequence Identity
xxx	%	xxx	xxx
xxx	%	xxx	xxx
xxx	%	xxx	xxx
xxx	%	xxx	xxx
xxx	%	xxx	xxx
89-60% Sequence Identity
xxx	%	xxx	xxx
xxx	%	xxx	xxx
xxx	%	xxx	xxx
xxx	%	xxx	xxx
xxx	%	xxx	xxx
59-40% Sequence Identity
xxx	%	xxx	xxx
xxx	%	xxx	xxx
xxx	%	xxx	xxx
xxx	%	xxx	xxx
xxx	%	xxx	xxx
39-20% Sequence Identity
xxx	%	xxx	xxx
xxx	%	xxx	xxx
xxx	%	xxx	xxx
xxx	%	xxx	xxx
xxx	%	xxx	xxx

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. Unfortunately no sequences in the range between 99-90% with known 3D-structure were found, so only sequences without known structure were used here.