Chromosome 1 open reading frame 41 Evolution: Difference between revisions

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== Blast ==
[[Image:BLAST.png|centre|framed|'''Figure 1:''' BLAST result]]


[[Image:BLAST.png]]


The above shows the result from BLASTP search. The sequences of these proteins are aligned to observe the conserved regions.
H-(2x)-W-(29x)-R-(2x)-S-(2x)-E residues critical for galactose binding site


== ClustalX ==


Multiple sequence alignment with all of the 27 sequences obtained from BLAST is shown below:
[[Image:Msa16.png|centre|framed|'''Figure 2:''' Conserved region of alpha B domain.]]




[[Image:Platypus.png]]
[[Image:Msa17.png|centre|framed|'''Figure 3:''' Residues involved in binding of Ca2+ and possible binding site.]]




The sequence of platypus, urchin_156 and urchin_159 was removed due to poor alignment. Besides that, the sequence for g.alga_fap was removed as it was a subsequence of g.alga_itp25.  
[[Image:Treecolour.png|centre|framed|'''Figure 4:''' Phylogenetic tree of c1orf41 with its homologues. Red is marine eukaryote, blue is amphibian and green is terrestrial eukaryotes.]]




[[Image:Tree.png|centre|framed|'''Figure 5:''' Phylogenetic tree with bootstrap values]]


[[Image:Msafinal.png]]


The residues involved in binding site were highlighted. However, these residues were only conserved in terrestrial eukaryotes and some marine eukaryotes. Changes in the conserved amino acids may lead to higher binding affinity to ligand or different folding of the protein leading to different function.
[[Chromosome 1 open reading frame 41 Function|Next]]
 
 
== Phylogenetic Tree ==
 
After obtaining multiple sequence alignment, phylogenetic tree was construct based on the result from multiple sequence alignment. Bootstrap values are shown on each branch.
 
[[Image:Treecolour.png]]
 
The unrooted tree above gave information on the evolutionary relationship between different organisms. This protein seems to have evolved from marine eukaryotes (red) to amphibians (blue) and then to terrestrial eukaryotes (green).
 
[[Image:Tree.png]]
 
 
The bootstrap value shows the reliability of the branch. Higher bootstrap value show higher reliability.

Latest revision as of 06:26, 16 June 2009

Figure 1: BLAST result


H-(2x)-W-(29x)-R-(2x)-S-(2x)-E residues critical for galactose binding site


Figure 2: Conserved region of alpha B domain.


Figure 3: Residues involved in binding of Ca2+ and possible binding site.


Figure 4: Phylogenetic tree of c1orf41 with its homologues. Red is marine eukaryote, blue is amphibian and green is terrestrial eukaryotes.


Figure 5: Phylogenetic tree with bootstrap values


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