Task 2: Multiple Sequence Alignment

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We researched the protein sequence of the branched-chain alpha-keto acid dehydrogenase complex subunit alpha (BCKDHA) with the following original sequence:

• BCKDHA

>sp|P12694|ODBA_HUMAN 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial OS=Homo sapiens GN=BCKDHA PE=1 SV=2
MAVAIAAARVWRLNRGLSQAALLLLRQPGARGLARSHPPRQQQQFSSLDDKPQFPGASAE
FIDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKEKVLKLYKSMTLLNTMDRILY
ESQRQGRISFYMTNYGEEGTHVGSAAALDNTDLVFGQYREAGVLMYRDYPLELFMAQCYG
NISDLGKGRQMPVHYGCKERHFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGA
ASEGDAHAGFNFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDG
NDVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDEVNYWDKQDHP
ISRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERKPKPNPNLLFSDVYQEMPAQL
RKQQESLARHLQTYGEHYPLDHFDK

Blast

To calculate the sequence alignments we used the blast and psiblast binaries from NCBI (version 2.2.26+) As the standard blast alignment hits the limit of 250 matches per alignment, and all of them still seemed very significant (Evalue of < 1e-60) we increased the number of max target hits to 2000 and set an Evalue threshold of 0.002. With this method we found about 1550 matching alignments.

As can be seen in the figure to the right

Distibution of sequence similarity with the BCKDHA blast-query against the big80 database.

, the sequence alignments mainly have a similarity between 15% and 40%.

Multiple Sequence Alignment (MSA)

In this task we are to produce MSA´s out of our database search results. The first step here is to create representative datasets, followed by creating MSA´s using different tools, and finally review the alignments and compare the tool against each other.

Dataset creation

We have chosen the following sequences from the Psi-Blast run with evalue E-10 and 10 iterations, trying to fit into the scheme given on the task-page:

Identifier	Identity	Organism	Description
ref seq
P12694	100%	human	ODBA_HUMAN 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial
high identity
B4DP47	90%	human	B4DP47_HUMAN Uncharacterized protein
H2L9X9	80%	Oryzias latipes	H2L9X9_ORYLA Uncharacterized protein
H2NYX7	90%	Pongo abelii	H2NYX7_PONAB Uncharacterized protein