HHsearch alignment for GI: 254780809 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=99.41  E-value=1.1e-12  Score=107.71  Aligned_cols=133  Identities=22%  Similarity=0.305  Sum_probs=94.0

Q ss_pred             CCEEEECCCCCCHHHHHHHHHCCHHCCCCCCCCCC-EEECCCCCCCCCE--EEEEEECCHHCCCCHHHHHHHHHHHHHHH
Q ss_conf             30243114663188899998552000234546872-1100012456835--89995081000241035666678889985
Q gi|254780809|r  220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTT-RDVLTIDLDLEGY--LVKISDTAGIRETDDIVEKEGIKRTFLEV  296 (440)
Q Consensus       220 ~~v~i~G~pN~GKSSL~N~L~~~~~aIVs~~~GTT-RD~i~~~~~i~g~--~~~l~DTaGir~t~d~IE~~GI~ra~~~i  296 (440)
T Consensus         1 ~Ki~vvG~~~vGKTsli~r~~~~~f--~~~~~~tig~d~~~k~v~~~~~~~~l~i~D~~g~e~~~~--------~~~~~~   70 (161)
T cd01861           1 HKLVFLGDQSVGKTSIITRFMYDTF--DNQYQATIGIDFLSKTMYLEDKTVRLQLWDTAGQERFRS--------LIPSYI   70 (161)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHCCC--CCCCCCCCCEEEEEEEEEECCEEEEEEEEECCCCHHHHH--------HHHHHH
T ss_conf             9799999799789999999931999--998489756788999999999999999997998531578--------889886


Q ss_pred             HHHCCEEECCCCCCHHHHHH------------HCCCCCCCCCCCCCCCCCCCHH-------------HHHHHHHHHHHHH
Q ss_conf             03011020135898566343------------1289853222233344654200-------------0001333323235
Q gi|254780809|r  297 ENADLILLLKEINSKKEISF------------PKNIDFIFIGTKSDLYSTYTEE-------------YDHLISSFTGEGL  351 (440)
Q Consensus       297 ~~aDlil~v~D~~~~~~~~~------------~~~~~~i~V~NK~Dl~~~~~~~-------------~~~~ISaktg~Gi  351 (440)
T Consensus        71 ~~~~~~ilvfd~t~~~Sf~~~~~w~~~i~~~~~~~~~ivlvGnK~Dl~~~r~v~~~e~~~~a~~~~~~y~E~Sak~~~nV  150 (161)
T cd01861          71 RDSSVAVVVYDITNRQSFDNTDKWIDDVRDERGNDVIIVLVGNKTDLSDKRQVSTEEGEKKAKELNAMFIETSAKAGHNV  150 (161)
T ss_pred             HHHCEEEEEEECCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCHHCCCCCHHHHHHHHHHCCCEEEEECCCCCCCH
T ss_conf             65258999984799899999999999999865789849996102110221778999999999984998999834778088


Q ss_pred             HHHHHHHHHHH
Q ss_conf             89999999996
Q gi|254780809|r  352 EELINKIKSIL  362 (440)
Q Consensus       352 ~~L~~~I~~~l  362 (440)
T Consensus       151 ~e~F~~la~~l  161 (161)
T cd01861         151 KELFRKIASAL  161 (161)
T ss_pred             HHHHHHHHHHC
T ss_conf             99999999709