HHsearch alignment for GI: 254780843 and conserved domain: pfam02487

>pfam02487 CLN3 CLN3 protein. This is a family of proteins from the CLN3 gene. A missense mutation of glutamic acid (E) to lysine (K) at position 295 in the human protein has been implicated in Juvenile neuronal ceroid lipofuscinosis (Batten disease).
Probab=98.85  E-value=2.2e-06  Score=48.33  Aligned_cols=139  Identities=12%  Similarity=0.099  Sum_probs=95.3

Q ss_pred             HHHHHHHHHHHHHH-----HHHHHHHHHH-------------------HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999998738-----9989999998-------------------09998999999999999999999999999985
Q gi|254780843|r   17 FILFFLFGGITSLN-----SILVPKLQNS-------------------FSLTYLQAMLVEAIFFSCYFFFSIPAGMFIQR   72 (420)
Q Consensus        17 ~~~ff~~g~~~~~~-----~~~~p~l~~~-------------------~~~s~~~~g~i~s~~~~~~~i~~~~~G~l~Dr   72 (420)
T Consensus         2 ~vaFwl~Gl~NN~~YVvilSAA~-Di~~~~~~~~~~~~~~~~~~~~~~~~c~~~~t~~vLlAdi~P~l~~kl~aP~fi~~   80 (409)
T pfam02487         2 YVAFWLLGLCNNFGYVVMLSAAE-DILSHQRGHVDSDPPPTCLPHSTRRECKSLSTAAVLLADILPSLIIKLTAPFFIHR   80 (409)
T ss_pred             EEHHHHHHHHHHHHHHHHHHHHH-HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             65489888741015431496599-88601025667777765555433334466635588887678899999986773331


Q ss_pred             HCHHHHHHHHHHHHHHHHHCCHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHCCCCHHHHHHHHHHHHHHCCCHHH
Q ss_conf             26289999999976432100000013202467899988777567888765310000123035788776644311000034
Q gi|254780843|r   73 YGYIKGICTGLLIMSLGCILFTATIEITTFKVFLIALCILAIGVVIIQVALNPFISLLGDPNTAVSRLTFAQFFNSLGTA  152 (420)
Q Consensus        73 ~Grr~~l~~~~~~~~i~~ll~~~a~~~~~~~~~~~~~~i~g~g~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~g~~  152 (420)
T Consensus        81 vpy~~Ri~~~~~ls~~g~l~Va~s---~~~~~~L~GVvlas~ssg~GE~tfL~lt~~y-~~----~~lsawsSGTG~AGl  152 (409)
T pfam02487        81 FPFGFRVWIVILLQASSFFLVAFS---KSIAMSLAGVVFASIGSGLGEITFLALTAHY-PR----IVIAGWSSGTGGAGL  152 (409)
T ss_pred             CCCHHHHHHHHHHHHHCEEEEEEE---CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHC-CH----HHHHHCCCCCCCHHH
T ss_conf             783099999999986126899983---6189999999988633130299999998545-71----454300356671567


Q ss_pred             HHHHHHHHHHHC
Q ss_conf             547888886412
Q gi|254780843|r  153 IFPYIGSVLMLG  164 (420)
Q Consensus       153 ~g~~~~~~l~~~  164 (420)
T Consensus       153 ~Gs~~Y~~lT~~  164 (409)
T pfam02487       153 IGAFSYAFLTQI  164 (409)
T ss_pred             HHHHHHHHHHHH
T ss_conf             778899988733