HHsearch alignment for GI: 254780711 and conserved domain: cd04155

>cd04155 Arl3 Arl3 subfamily. Arl3 (Arf-like 3) is an Arf family protein that differs from most Arf family members in the N-terminal extension. In is inactive, GDP-bound form, the N-terminal extension forms an elongated loop that is hydrophobically anchored into the membrane surface; however, it has been proposed that this region might form a helix in the GTP-bound form. The delta subunit of the rod-specific cyclic GMP phosphodiesterase type 6 (PDEdelta) is an Arl3 effector. Arl3 binds microtubules in a regulated manner to alter specific aspects of cytokinesis via interactions with retinitis pigmentosa 2 (RP2). It has been proposed that RP2 functions in concert with Arl3 to link the cell membrane and the cytoskeleton in photoreceptors as part of the cell signaling or vesicular transport machinery. In mice, the absence of Arl3 is associated with abnormal epithelial cell proliferation and cyst formation.
Probab=96.29  E-value=0.012  Score=40.43  Aligned_cols=94  Identities=17%  Similarity=0.299  Sum_probs=49.3

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             88418996234433346889999999986148950782054221004779999851034742223321036899999999
Q gi|254780711|r   98 PSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRYLGEQIQVDTLEVIPEQSPEKIAIRATQ  177 (461)
Q Consensus        98 ~~p~vIllvGl~GsGKTTT~aKLA~~~~~~~~~kV~lv~~Dt~R~aA~eQL~~~a~~~~v~~~~~~~~~dp~~i~~~a~~  177 (461)
T Consensus        12 ~~~~Ki~ilG~~~sGKTsll~~l~----~-~~~~~------~------------~pT~g~~~~~----------------   52 (173)
T cd04155          12 SEEPRILILGLDNAGKTTILKQLA----S-EDISH------I------------TPTQGFNIKT----------------   52 (173)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHH----C-CCCCC------C------------CCCCCEEEEE----------------
T ss_conf             877589999799998899999985----6-99866------0------------6811323799----------------


Q ss_pred             HHHHCCCCEEEEECCCCCCCHHHHHHHH-HHHHHHCCCCCCCCCCCHHCCHHHHHHH-HHHHHH
Q ss_conf             9974158869983344222112468999-9998513851100031011122568888-988763
Q gi|254780711|r  178 SARDGGYDAVILDTAGRNHINDSLMQEI-SEIKSLTNPHEILLVADALTGQDAVHLA-RNFDKI  239 (461)
Q Consensus       178 ~a~~~~~D~iiiDTaGR~~~d~~lm~El-~~i~~~~~p~e~~lV~da~~Gq~a~~~a-~~F~~~  239 (461)
T Consensus        53 -v~~~~~~~~lwD~~G~~~~-----~~~~~~y~~--~a~~iI~VvD~td-~~~~~~~~~~l~~~  107 (173)
T cd04155          53 -VQSDGFKLNVWDIGGQRAI-----RPYWRNYFE--NTDCLIYVIDSAD-KKRLEEAGAELVEL  107 (173)
T ss_pred             -EEECCEEEEEEECCCCHHH-----HHHHHHHCC--CCCEEEEEEECCC-HHHHHHHHHHHHHH
T ss_conf             -9989999999855875101-----268997655--5637999996675-68899999999999