Difference between revisions of "Task 2: Multiple Sequence Alignment"

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(Results)
(Results)
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==== result for clustalw: ====
 
==== result for clustalw: ====
 
[[File:Clustal high.jpg|800px|thumb|ClustalW MSA >60%]]
 
[[File:Clustal high.jpg|800px|thumb|ClustalW MSA >60%]]
result for t-coffee: [[File:T-coffee high.jpg|800px|thumb|T-Coffee MSA >60%]]
+
==== result for t-coffee: ====
  +
[[File:T-coffee high.jpg|800px|thumb|T-Coffee MSA >60%]]
 
result for muscle: [[File:Muscle high.jpg|800px|thumb|Muscle MSA >60%]]
 
result for muscle: [[File:Muscle high.jpg|800px|thumb|Muscle MSA >60%]]
 
=== >40% fraction ===
 
=== >40% fraction ===

Revision as of 10:45, 11 May 2012

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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%.

Distribution of evalues in BLAST.

Psi-Blast

HHBlits

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 using jalview and compare the tools 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:

Marinobacter sp. ELB17F2GCR2_ALTMD Alpha keto acid dehydrogenase complex, E1 component, alpha subunit OS=Alteromonas macleodii (strain DSM 17117 / Deep ecotype)
IdentifierIdentityOrganismDescription
ref seq
P12694100%humanODBA_HUMAN 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial
high identity ( >60% )
B4DP4790%humanB4DP47_HUMAN Uncharacterized protein
H2L9X980%Oryzias latipesH2L9X9_ORYLA Uncharacterized protein
H2NYX790%Pongo abeliiH2NYX7_PONAB Uncharacterized protein
G3RDZ399%Gorilla gorilla gorillaG3RDZ3_GORGO Uncharacterized protein
G7PXN692%Macaca fascicularisG7PXN6_MACFA Putative uncharacterized protein
C1BZX061%Caligus clemensiC1BZX0_9MAXI 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial
E9C2J862%Capsaspora owczarzakiE9C2J8_CAPO3 Branched chain keto acid dehydrogenase E1
A8XMR663%Caenorhabditis briggsaeA8XMR6_CAEBR Putative uncharacterized protein
F1L13161%Ascaris suumF1L131_ASCSU 2-oxoisovalerate dehydrogenase subunit alpha
B3S5B466%Trichoplax adhaerensB3S5B4_TRIAD Putative uncharacterized protein
moderate identity ( >40% )
F7NS2050%Rheinheimera sp. A13LF7NS20_9GAMM Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase component alpha subunit
A3JES250%A3JES2_9ALTE 2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit
F2GCR249%Alteromonas macleodii (strain DSM 17117 / Deep ecotype)
E1VBY448%Halomonas elongataE1VBY4_HALED 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)
A9TD4447%Physcomitrella patens subsp. patensA9TD44_PHYPA Predicted protein
E1ZBL651%Chlorella variabilisE1ZBL6_CHLVA Putative uncharacterized protein
F2Q10751%Trichophyton equinumF2Q107_TRIEC 2-oxoisovalerate dehydrogenase subunit alpha
B6GYK752%Penicillium chrysogenumB6GYK7_PENCW Pc12g08790 protein
G2QH9153%Thielavia heterothallicaG2QH91_THIHA Dehydrogenase-like protein
G0S8V251%Chaetomium thermophilumG0S8V2_CHATD Alpha subunit-like protein
whole range identity ( 0-100% )
F6EVQ939%Sphingobium chlorophenolicumF6EVQ9_SPHCR 3-methyl-2-oxobutanoate dehydrogenase
B1YII639%Exiguobacterium sibiricumB1YII6_EXIS2 Pyruvate dehydrogenase
Q9HN7734%Halobacterium salinariumQ9HN77_HALSA Pyruvate dehydrogenase
G2QH9153%Thielavia heterothallicaG2QH91_THIHA Dehydrogenase-like protein
A9TD4447%Physcomitrella patens subsp. patensA9TD44_PHYPA Predicted protein
G0S8V251%Chaetomium thermophilumG0S8V2_CHATD Alpha subunit-like protein
B4DP4790%humanB4DP47_HUMAN Uncharacterized protein
H2L9X980%Oryzias latipesH2L9X9_ORYLA Uncharacterized protein
H2NYX790%Pongo abeliiH2NYX7_PONAB Uncharacterized protein
C1BZX061%Caligus clemensiC1BZX0_9MAXI 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial

clustalW

T-Coffee

Muscle

Results

>60% fraction

result for clustalw:

ClustalW MSA >60%

result for t-coffee:

T-Coffee MSA >60%

result for muscle:

Muscle MSA >60%

>40% fraction

whole range fraction