BLAST SCOP and ASTRAL database
Structural Classification of Proteins (SCOP) (here and here) is a database (mostly) manually curated ordering of domains from the majority of proteins of known structure in a hierarchy according to structural and evolutionary relationships. The ASTRAL compendium provides non redundant subsets of SCOP domains on the basis of sequence similarity such that no two domains in a given subset share more than a defined degree of sequence similarity. Although one can query SCOP through different identifiers (SCOPe) and browser the database using SCOP2-browser or SCOP2-graph in official websites, you cannot search your proteins by sequence, so far as May, 2014, which I find is pretty useful in my research projects of phosphatases.
Note: The field right after sequence ID (e.g. c.60.1.4) is the SCOP identifier (sccs), which can be used to query SCOP database.