inconsistency using fragment or whole protein

[twaksman001]

I used HHBlits via the MPI website

If I submit whole protein sequence - 10000 matches, mostly kinase proteins, and the alignment is to a subsection of the query.

If I resubmit this subsection, <50 matches and no kinases.

Please can you explain how this happens?

Protein sequence: NPLCPYMNRGNPNLLPQQKSSTTQGDQVYAPSMPQFSMEGNRQMYPMPPPMMPPPPMMQGFQPPFPFNPMNQQQLSMLLMSSYARAMALAQLMNMQNRFQFYQPNQYSDPAINNYSSMPATLPQQPQVDLQNNLKTEMSPEQEKQGEPGEPRESELETSQQQGELQQQEEPLNSGEGQETEVSGEREEPETRDQDILEKRKMQRALDIEIERRERLQKRKAEENELERQQKEMERMLREEEEMKRQEEETKRQILEEERKEREEKEKDIKLRQEEELRFKKIEAEKKKRNQVNNKPQGTSVRRQRKQKHTKKTVTEDIIERL