MOTIF Search seems to be quite the all-rounder for motif scanning in proteins! It also provides information on functions + related genes. MOTIF Search facilitates the following searches:
1. Protein sequence vs motif databases
Using Motiffind for PROSITE patterns, Profilefind for PROSITE profiles, RPS-BLAST for NCBI-CDD + HMMscan for Pfam.
2. Protein sequence vs user-defined profile (database)
The profile (database) must be in PROSITE or Pfam format.
3. Profile vs sequence database
The profile should be in PROSITE or Pfam format, resulting in the use of Pfsearch or HMMsearch, respectively. Sequence databases include: SwissProt, RefSeq, PDBSTR, GENES, MGENES + VGENES.
4. Pattern vs sequence database
The pattern should be in PROSiTE's regex-like pattern format. Sequence databases include: SwissProt, RefSeq, PDBSTR, GENES, MGENES + VGENES.
5. Create your own profile
Using Pfmake for PROSITE format profiles or HMMbuild for Pfam format profiles.
You can read further details here + please email me if you know what paper to cite for this tool, I was unable to find it!