Personally, I used a tool from the T-coffe server called "Expresso". This tool aligns protein sequences using structural information. The only thing the tool ask for is your sequences. The server will do an automatic retrieval of the related structures.

http://tcoffee.crg.cat/apps/tcoffee/do:expresso

In addition, this link from Weizmann institute provide a list of related tools:

https://bip.weizmann.ac.il/toolbox/structure/seq_align.htm

Hope this will help.

Good luck

Try NCBI COBALT

I would recommend the FATCAT server (http://fatcat.sanfordburnham.org/) for Protein structure based alignment, and CD-Search (https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi) for domain prediction.

Anuj Kumar I was wondering about the application of FATCAT. Since questioner has the protein sequences and FATCAT takes input as PDB format, how can it be directly used. It would be interesting to know. I know that sequences can be used to predict the structure in I-TASSEL and later can be used in FATCAT, but what would you suggest?

1. InterProScan (www.ebi.ac.uk/interpro/scan.html)

InterProScan is a database developed by EBI that integrates protein domains and functional sites. InterProScan provides a comprehensive analysis tool by unifying various local patterns, such as domains and motifs, in the protein sequences provided by SWISS-PROT, TrEMBL.PROTSITE.PRINTS.PFAM.ProDom and other databases.

2. SMART (http://smart.embl-heidelberg.de/)

Simple modular architecture research tool (SMART) is a good database, which can be used for the analysis of protein functional domains, while providing links to related resources.