Hi Nikita,
The amino acid sequence alignment between remotely but related proteins has been challenging problems for computational biologist. However, certain improvements have been achieved by incorporating information that enhances the diversity of the substitution matrices. The NdPASA algorithms look into the complexity and improve the alignment at some extents. http://bioinformatics.oxfordjournals.org/content/21/19/3803.full
There are several other protocol http://www.nature.com/protocolexchange/protocols/604 to assist you to detect the sequence alignment of distantly related proteins whose structural information is available.
RDF2 can be useful http://genome.cbs.dtu.dk/cgi-bin/nph-runsafe?man=rdf2 ... detail paper at http://www.pnas.org/content/85/8/2444.abstract?ijkey=6b8fb6d2067f633fbf7e8df961db4d41bd7b7163&keytype2=tf_ipsecsha
For more information http://www.ncbi.nlm.nih.gov/pubmed/17993679
http://csb.stanford.edu/levitt/Lesk_PE86_Distant_sequence_alignment_SM.pdf
Thanks
Hi Nikita,
...tried stand alone BLAST, but it is not working .... ??? Is there any error, or you did not find any matches?
There are other option like BLAT (BLAST-like Alignment Tool) which is comparatively quick and easy but it needs an exact or nearly-exact match to find a hit. Therefore, not very suitable for your current problem, but you can try and see the differences.
Thanks