how to find conserved region within a protein family for the construction of phylogenetic tree

Question

[star_143_101]

I am working on a protein family from Nicotiana tabacum. I have the full length protein sequences of all the members of family.now I constructed a phylogenetic tree of full length sequences using MEGA5 NJ method but the tree I got is not significant. now I want to construct the tree using conserved region how can I get this region for all members. or what else I can do in this situation

[Sishuo Wang]

You can try gblock or trimal. Also, trees built using Maximum likelihood (available in MEGA5 I think) or Bayes methods instead of NJ might better reflect the evolutionary history of your sequences.

Answer 1

[dago]

If you need just he conserved region you can select the conserved "blocks" inside your proteins. You can do this with different programs (e.g. Gblock, Partitionafinder, Guidance). You take just the conserved "blocks" ant then you can do your phylogenetic analysis again.

However, this is not = to selecting the domains inside the protein. Domains are defined according to specific criteria, such as. catalytic activity, II structure and so on. So the conserved "blocks" and the domain are not necessary the same thing.

[star_143_101]

thanks. which way is better and commonly used?should I construct a tree using specific domain or conserved blocks?

[dago]

Tough question. Which proteins are you working with? There are some proteins, such as megasynthases that have conserved domains but the overall protein seq can be quite variable. Try both and if there is agreement means that your analysis is quite robust

Answer 2

[star_143_101]

i am working on Leucine rich repeat LRR family of tobacoo.now the stategy i am using is"by using TMHMM i will cut my proteins into extracelluar and intacelluar domain.then i will construct phylogenetic tree for both.am I on right way?