Dear all,

I realized if I try to find the InterPro domains on the following sequence, Gene3D does not find any domains.

MSTENEGESKENPSYLTVELEHVGHVSIDAIEHHYMELQKELAMEPHLRPLREEYEKIHRLLRKSHDGEKRLMAKIKELDHDLITHAANVESALKLARQDEDVIEALRREIEKAWSLADSAHAREKETREQIQELRQQVVRLNGLVDKNTSSTLGQENFLRDLIKAKKEFENERLMAQAKAERLVDERLFAQRKMHKLREDSECVRHSLENTLKNYEGCLRNLSDTKRDRESLEQQVREYRVEADEHLKEIASVRQSVAELAKEEEKLKALALSERDSVGQLAKQLEEQQDRFKKEADKLAAVEAHNAEMKQEIPKMRMTLKGRHAEVERLALSLRKARKGAGVQQTEIDKQMQTRASLMEQTEKMHTAIEELLRTLDDHVKALHDEEVRLKGAMPIKTKLLTENSRVDSEKAMMEGQRMLEEGKRRNLTQQLEKLLRDNETMRKKIFELEQNQAKILDNGQREALQYHRVLEQTRKQQGQAKLLQQQLEDNEKRLKAQQDLLDRVSADRARTEKRLKESELECSGLKQRYNHNGEEIQLLKMQIIGKEGALCRIHMVRKQLQRDIANAEERASHLKEDGTSATNRYETLKGEVKQLSHLIAECDAEKSKYQSKFAALVNERNVLATQLVRRNEELRLLHSKIRLQECSIEKGAEDYNKRVRAVMGKRSELEELRLRCRVALARMLHAEKLRRRKQKIERDLFTEKRRSRALADELQRPVNVHRWRRLEGNAPEILDGIYKVHTLERQILKKQDLLVEKTKQLAARNAEYETVRKKLAELQGPEVAGELSLYDENLQCRREQIRGLDTELQEVEQHVDVVAEEVKQLTVELCEVKRRYYNAKHKNDLLRREQGAFRAMWGGSSAVARTALAAIENASERRQLQQQGSISSRRQPLWRTRAQKRREQIKQEEQIVQVLSTGAPAPSFPLQVPPGQRIFLGGGFALTR

Strangely, when I add "SHHA" to the beginning of the sequence, a Gene3D domain is identified. I know that the e-value is dependent on the protein length, and longer proteins will have less significant hits. However, I am finding a domain on the longer sequence rather than the shorter one, so this could not be the reason behind what I see.

Does anyone have a clue what is going on here?

Thanks

The modified sequence is : SHHAMSTENEGESKENPSYLTVELEHVGHVSIDAIEHHYMELQKELAMEPHLRPLREEYEKIHRLLRKSHDGEKRLMAKIKELDHDLITHAANVESALKLARQDEDVIEALRREIEKAWSLADSAHAREKETREQIQELRQQVVRLNGLVDKNTSSTLGQENFLRDLIKAKKEFENERLMAQAKAERLVDERLFAQRKMHKLREDSECVRHSLENTLKNYEGCLRNLSDTKRDRESLEQQVREYRVEADEHLKEIASVRQSVAELAKEEEKLKALALSERDSVGQLAKQLEEQQDRFKKEADKLAAVEAHNAEMKQEIPKMRMTLKGRHAEVERLALSLRKARKGAGVQQTEIDKQMQTRASLMEQTEKMHTAIEELLRTLDDHVKALHDEEVRLKGAMPIKTKLLTENSRVDSEKAMMEGQRMLEEGKRRNLTQQLEKLLRDNETMRKKIFELEQNQAKILDNGQREALQYHRVLEQTRKQQGQAKLLQQQLEDNEKRLKAQQDLLDRVSADRARTEKRLKESELECSGLKQRYNHNGEEIQLLKMQIIGKEGALCRIHMVRKQLQRDIANAEERASHLKEDGTSATNRYETLKGEVKQLSHLIAECDAEKSKYQSKFAALVNERNVLATQLVRRNEELRLLHSKIRLQECSIEKGAEDYNKRVRAVMGKRSELEELRLRCRVALARMLHAEKLRRRKQKIERDLFTEKRRSRALADELQRPVNVHRWRRLEGNAPEILDGIYKVHTLERQILKKQDLLVEKTKQLAARNAEYETVRKKLAELQGPEVAGELSLYDENLQCRREQIRGLDTELQEVEQHVDVVAEEVKQLTVELCEVKRRYYNAKHKNDLLRREQGAFRAMWGGSSAVARTALAAIENASERRQLQQQGSISSRRQPLWRTRAQKRREQIKQEEQIVQVLSTGAPAPSFPLQVPPGQRIFLGGGFALTR