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
Not familiar with Gene3D but an domain scan at EBI brings back following for original protein:
LONGER Version gets this
Thanks for your reply! As you see, G3DSA:1.10.287.1490 is detected only on the LONGER version.