HHsearch alignment for GI: 254780233 and conserved domain: cd01861
>cd01861 Rab6 Rab6 subfamily. Rab6 is involved in microtubule-dependent transport pathways through the Golgi and from endosomes to the Golgi. Rab6A of mammals is implicated in retrograde transport through the Golgi stack, and is also required for a slow, COPI-independent, retrograde transport pathway from the Golgi to the endoplasmic reticulum (ER). This pathway may allow Golgi residents to be recycled through the ER for scrutiny by ER quality-control systems. Yeast Ypt6p, the homolog of the mammalian Rab6 GTPase, is not essential for cell viability. Ypt6p acts in endosome-to-Golgi, in intra-Golgi retrograde transport, and possibly also in Golgi-to-ER trafficking. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate
Probab=98.99 E-value=1.2e-08 Score=75.95 Aligned_cols=154 Identities=19% Similarity=0.222 Sum_probs=96.4
Q ss_pred EEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCCEECCCCHHHHHCCCEEEEEEEEEEECCEEEEEECCCCCCCCHHHHHH
Q ss_conf 99985468987788999999839614232200000388577987096064679999989979999728987540799999
Q gi|254780233|r 22 IAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWNDVRINIVDTPGHADFGGEVER 101 (624)
Q Consensus 22 iaIiaHvDhGKTTL~d~LL~~sG~~~~~~~v~~~vmD~~~~EreRGITI~a~~~~~~~~~~~iNiiDTPGH~DF~gEVer 101 (624)
T Consensus 3 i~vvG~~~vGKTsli~r~~~--~~f~~~~------------~~tig~d~~~k~v~~~~~~~~l~i~D~~g~e~~~~~~~~ 68 (161)
T cd01861 3 LVFLGDQSVGKTSIITRFMY--DTFDNQY------------QATIGIDFLSKTMYLEDKTVRLQLWDTAGQERFRSLIPS 68 (161)
T ss_pred EEEECCCCCCHHHHHHHHHH--CCCCCCC------------CCCCCEEEEEEEEEECCEEEEEEEEECCCCHHHHHHHHH
T ss_conf 99999799789999999931--9999984------------897567889999999999999999979985315788898
Q ss_pred HHHHHCEEEEEEECCCCCCHHHHHHHHH-HHHC---CCCEEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCHHHCCHHHH
Q ss_conf 9874217899997687886478999999-9972---99789999754366740256899999888622673011042668
Q gi|254780233|r 102 ILCMVESVVVLVDAAEGPMPQTKFVVGK-ALKI---GLRPIVVVNKVDRSDARADEVINEVFDLFSALDATDAQLDFPIL 177 (624)
Q Consensus 102 ~l~~~DgaiLvVdA~eGv~~QT~~vl~~-A~~~---~l~~IvvINKiDr~~a~~~~v~~ei~dlf~~l~a~de~ld~Pv~ 177 (624)
T Consensus 69 ~~~~~~~~ilvfd~t~~~Sf~~~~~w~~~i~~~~~~~~~ivlvGnK~Dl~~~r~v~-~~e~~~~a~-------~~~~~y~ 140 (161)
T cd01861 69 YIRDSSVAVVVYDITNRQSFDNTDKWIDDVRDERGNDVIIVLVGNKTDLSDKRQVS-TEEGEKKAK-------ELNAMFI 140 (161)
T ss_pred HHHHHCEEEEEEECCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCHHCCCCC-HHHHHHHHH-------HCCCEEE
T ss_conf 86652589999847998999999999999998657898499961021102217789-999999999-------8499899
Q ss_pred HHHHHCCEECCCCCCCCCCCCHHHHHHHHCC
Q ss_conf 8788659164674223348641355532102
Q gi|254780233|r 178 YGSGRFGWMSDSSDGSRDQGMVPLLNLIVDH 208 (624)
Q Consensus 178 ~~Sa~~G~~~~~~~~~~~~gl~~Lld~Ii~~ 208 (624)
T Consensus 141 E~Sak~~-----------~nV~e~F~~la~~ 160 (161)
T cd01861 141 ETSAKAG-----------HNVKELFRKIASA 160 (161)
T ss_pred EECCCCC-----------CCHHHHHHHHHHH
T ss_conf 9834778-----------0889999999970