Most of the domains listed in tables of InterPro matches for proteins occur many (hundreds) times. What sense do these numbers have?
Each domain can indeed occur many times in a protein. Strictly speaking, what is shown is not the domain boundary but the signature boundary, i.e. that portion of the domain used to identify its existence by one of InterPro’s methods. For some methods (e.g. Pfam and PROSITE profiles), the signature is equivalent to the entire domain, for other methods (e.g. PROSITE patterns) the signature is not. As there are many InterPro methods (some of which identify the same domain), it is possible that a single domain in a single protein will be multiply identified, e.g. where methods from ProDom, SMART, PROSITE and Pfam each identify the same domain. Of course, the same domain may also occur many times in one protein.
