Hi everyone:
If I do protein alignment to two proteins, what percentage of identity between them would be required to consider them as homologous proteins? Is there any other parameters I need to consider? such as similar domains, hydrophobicity, etc. Do you have any recommendations for online tools or programs to do it?
Thank you for the help!
Homologous, simply means "shared a common ancestor". Homologous proteins can be orthologs or paralogs.
Article Orthologs and paralogs - We need to get it right (multiple l...
Very different proteins can have homolgous parts, for example the DNA-binding domain of many different proteins may have all originated from one common ancestor that then become incorporated into different proteins by "domain swapping" or exon shuffling in evolution.
There is no set limit of similarity or identity between two protein sequences that can be taken as evidence of shared ancestry. Some protein sequences are more likely to occur by random chance than others. If you want to know if a gene from a fungus and a similar gene from a human are homologs, it is quite a different question than if you are comparing a gene from a human to a gene from a mouse or a gene from a mammal to a similar gene from an amphibian.
I am attaching a multiple sequence alignment of the Wnt2 protein. I started with human and got BLAST hits for vertebrates, then added some invertebrates, then searched specifically in insects and Drosophila. For insects/Drosophila the proteins were not all named "Wnt2" some were named as "Wnt7" or "Wnt5" etc...
If two proteins shares more than 25% identity, it will be considered as a homologous protein. But it may be orthologs or paralogs. the presence of domains or motifs is also important parameter to decide whether two proteins are homologous or not. BLAST is the efficient tool for that. BLAST provides FALSE-POSITIVE, FALSE-NEGATIVE, TRUE-POSITIVE AND TRUE-NEGATIVE result. To take precautions while interpreting BLAST result.
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