HHsearch alignment for GI: 254780809 and conserved domain: cd04113
>cd04113 Rab4 Rab4 subfamily. Rab4 has been implicated in numerous functions within the cell. It helps regulate endocytosis through the sorting, recycling, and degradation of early endosomes. Mammalian Rab4 is involved in the regulation of many surface proteins including G-protein-coupled receptors, transferrin receptor, integrins, and surfactant protein A. Experimental data implicate Rab4 in regulation of the recycling of internalized receptors back to the plasma membrane. It is also believed to influence receptor-mediated antigen processing in B-lymphocytes, in calcium-dependent exocytosis in platelets, in alpha-amylase secretion in pancreatic cells, and in insulin-induced translocation of Glut4 from internal vesicles to the cell surface. Rab4 is known to share effector proteins with Rab5 and Rab11. 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 p
Probab=99.45 E-value=4.8e-13 Score=110.30 Aligned_cols=132 Identities=27% Similarity=0.295 Sum_probs=91.1
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 ~Kivl~Gd~~vGKTsli~r~~~~~f--~~~~~~Tig~~~~~k~~~~~~~~~~l~iwDtaG~e~~~--------~~~~~~~ 70 (161)
T cd04113 1 FKFIIIGSSGTGKSCLLHRFVENKF--KEDSQHTIGVEFGSKIIRVGGKRVKLQIWDTAGQERFR--------SVTRSYY 70 (161)
T ss_pred CEEEEECCCCCCHHHHHHHHHHCCC--CCCCCCCCCEEEEEEEEEECCEEEEEEEEECCCCHHHH--------HHHHHHH
T ss_conf 9899999499679999999972989--99879976457899999999999999999899970122--------6789984
Q ss_pred HHHCCEEECCCCCCHHHHH-------HH-----CCCCCCCCCCCCCCCCCCCHH-------------HHHHHHHHHHHHH
Q ss_conf 0301102013589856634-------31-----289853222233344654200-------------0001333323235
Q gi|254780809|r 297 ENADLILLLKEINSKKEIS-------FP-----KNIDFIFIGTKSDLYSTYTEE-------------YDHLISSFTGEGL 351 (440)
Q Consensus 297 ~~aDlil~v~D~~~~~~~~-------~~-----~~~~~i~V~NK~Dl~~~~~~~-------------~~~~ISaktg~Gi 351 (440)
T Consensus 71 ~~a~~~ilvydit~~~Sf~~~~~w~~~i~~~~~~~~~iilVgNK~Dl~~~r~V~~~e~~~~a~~~~~~~~E~SAk~~~nV 150 (161)
T cd04113 71 RGAAGALLVYDITNRTSFEALPTWLSDARALASPNIVVILVGNKSDLADQREVTFLEASRFAQENGLLFLETSALTGENV 150 (161)
T ss_pred HCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHCCCCCHHHHHHHHHHCCCEEEEECCCCCCCH
T ss_conf 05777899536898899999999999999867999649860343440003788999999999985997999741569058
Q ss_pred HHHHHHHHHH
Q ss_conf 8999999999
Q gi|254780809|r 352 EELINKIKSI 361 (440)
Q Consensus 352 ~~L~~~I~~~ 361 (440)
T Consensus 151 ~e~F~~la~~ 160 (161)
T cd04113 151 EEAFLKCARS 160 (161)
T ss_pred HHHHHHHHHH
T ss_conf 9999999970