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