HHsearch alignment for GI: 254780787 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=99.15 E-value=1.5e-10 Score=90.17 Aligned_cols=149 Identities=19% Similarity=0.215 Sum_probs=94.5
Q ss_pred EEEEECCCCCHHHHHHHHHHHHHHH-CCC-CCCEECCCEEEEECCCCEEEEEECCCHHHHHHHHHHHHHCCCCEEEEEEC
Q ss_conf 8986236850446777886422210-012-31000121499951784388885166157899986664206805999983
Q gi|254780787|r 386 VTIMGHVDHGKTSLLDAIRKADVAK-GEI-GGITQHIGAYQVAYQGKNITFLDTPGHAAFYEMRARGARVTDIAVLVLAA 463 (884)
Q Consensus 386 v~v~ghvd~GKt~lld~~r~~~~~~-~e~-ggitq~iga~~~~~~~~~~~~iDtPGh~~f~~~r~rg~~~~d~~ilvv~~ 463 (884)
T Consensus 3 ivl~Gd~~vGKTsli~r~~~~~f~~~~~~Tig~~~~~k~~~~~~~~~~l~iwDtaG~e~~~~~~~~~~~~a~~~ilvydi 82 (161)
T cd04113 3 FIIIGSSGTGKSCLLHRFVENKFKEDSQHTIGVEFGSKIIRVGGKRVKLQIWDTAGQERFRSVTRSYYRGAAGALLVYDI 82 (161)
T ss_pred EEEECCCCCCHHHHHHHHHHCCCCCCCCCCCCEEEEEEEEEECCEEEEEEEEECCCCHHHHHHHHHHHHCCCEEEEECCC
T ss_conf 99999499679999999972989998799764578999999999999999998999701226789984057778995368
Q ss_pred CCCCCHHHHHHH-HHHH---HCCCCEEEECCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCC
Q ss_conf 667402357778-9899---709941561233124433200022100001320001234740363110024774112210
Q gi|254780787|r 464 DEEIMPQAIESI-NHAK---AADVSIIVAINKIDKLGADPQKVRMSLLKHDVFVESMGGDILDVEISAKNNLNLDKLLDA 539 (884)
Q Consensus 464 ~~g~~~qt~e~~-~~~~---~~~~p~iva~nk~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 539 (884)
T Consensus 83 t~~~Sf~~~~~w~~~i~~~~~~~~~iilVgNK~Dl~~~r~--V~~~e~--~~~a~~~--~~~~~E~SAk~~~nV~e~F~~ 156 (161)
T cd04113 83 TNRTSFEALPTWLSDARALASPNIVVILVGNKSDLADQRE--VTFLEA--SRFAQEN--GLLFLETSALTGENVEEAFLK 156 (161)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHCCC--CCHHHH--HHHHHHC--CCEEEEECCCCCCCHHHHHHH
T ss_conf 9889999999999999986799964986034344000378--899999--9999985--997999741569058999999
Q ss_pred H
Q ss_conf 0
Q gi|254780787|r 540 I 540 (884)
Q Consensus 540 ~ 540 (884)
T Consensus 157 l 157 (161)
T cd04113 157 C 157 (161)
T ss_pred H
T ss_conf 9