InterProScan, Conserved domain database, SMART and PFAM

Question

[lukhanyomakhabane]

Hello guys Quick question, I trying to scan for some specific domains and others if present in protein of interest. I used InterProscan, but InterProScan did not predict all the domains. However, when I scan this proteins in PFAM and SMART I find these domains. Based on my knowledge InterProScan also include database such PFAM, SMART and Conserved domain database. How come I am not able to predict them when using InterProScan, whereas if I am using for example PFAM directly I get them.

Thanks in advance

[lieven.sterck]

it is very well likely that Interproscan uses different thresholds (compared to what the individual DBs do) which could indeed result in domains being present/absent .

However, it would be very surprising if those domains score high, aka they are more likely to be borderline/grey zone matches