Question: how to find conserved region within a protein family for the construction of phylogenetic tree
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gravatar for star_143_101
5.9 years ago by
star_143_10110
China
star_143_10110 wrote:

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

phylogenetic analysis • 2.6k views
ADD COMMENTlink modified 2.7 years ago by saraholiver3070 • written 5.9 years ago by star_143_10110

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.

ADD REPLYlink written 2.7 years ago by Sishuo Wang200
1
gravatar for dago
5.9 years ago by
dago2.6k
Germany
dago2.6k wrote:

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.

ADD COMMENTlink written 5.9 years ago by dago2.6k

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

ADD REPLYlink written 5.9 years ago by star_143_10110

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

ADD REPLYlink written 5.9 years ago by dago2.6k
0
gravatar for star_143_101
5.9 years ago by
star_143_10110
China
star_143_10110 wrote:

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?

ADD COMMENTlink written 5.9 years ago by star_143_10110
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