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