I want to identify if certain phosphorylation sites are conserved for protein X across humans and yeast. I know from MS data that there are 4 phospho sites in Human protein X. In order to identify if these residues and therefore potentially the phospho sites are conserved, is it correct to align both sequences using pairwise softwares like Needle? should I maybe do a bigger alignment with more species and use clustal omega rather? is there a better aproach?
I think needle would be a good approach. You can use clustalw with more species, but since you are looking at species that are evolutionary very far from each other. Clustalw in such cases may misalign some residues in order to fit better species that are not that distant.
You can try needle first and then go to clustalw or you can do clustalw with human and yeast and use this alignment to guide new analysis with more species. Look at clistalw documentation, this is explained there.
In addition to alignment I would have a look at data bases or algorithms that have included mass spectrometry data from large scale approaches or that predict PTM sites such as PhosphositePlus or GPS 3.0, respectively. If you find the same sites already there, this further argues for conservation.
I would recommend you to use HomoloGene from NCBI.
http://www.ncbi.nlm.nih.gov/homologene
Just search for your gene and than you can display the results as protein multiple alignments.
Here is an example for PCNA:
http://www.ncbi.nlm.nih.gov/homologene/1945
Specifically for PTM I would always check PhosphositePlus, as Otmar already said.
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