HHsearch alignment for GI: 254780648 and conserved domain: cd00878
>cd00878 Arf_Arl Arf (ADP-ribosylation factor)/Arl (Arf-like) small GTPases. Arf proteins are activators of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. Arfs are N-terminally myristoylated. Members of the Arf family are regulators of vesicle formation in intracellular traffic that interact reversibly with membranes of the secretory and endocytic compartments in a GTP-dependent manner. They depart from other small GTP-binding proteins by a unique structural device, interswitch toggle, that implements front-back communication from N-terminus to the nucleotide binding site. Arf-like (Arl) proteins are close relatives of the Arf, but only Arl1 has been shown to function in membrane traffic like the Arf proteins. Arl2 has an unrelated function in the folding of native tubulin, and Arl4 may function in the nucleus. Most other Arf family proteins are so far relatively poorly characterized. Thu
Probab=99.84 E-value=4.7e-21 Score=147.48 Aligned_cols=153 Identities=20% Similarity=0.176 Sum_probs=104.7
Q ss_pred EEEEECCCCCCCEEEEEECCCCCHHHHHHHCCCEECCEEEEECCEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 12442167775303541014540121211000000102663298689982264212473116775123443333357887
Q gi|254780648|r 162 IGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGIIKNAHQGAGIGDRFLKHTERTHVLL 241 (335)
Q Consensus 162 VglVG~PNaGKSTLln~ls~ak~kIa~ypFTT~~P~lGvv~~~~~~~~i~D~PGlIegA~~~~glG~~FLrhIer~~vLl 241 (335)
T Consensus 2 i~ilG~~~vGKTsll~~l~~~~~--~~-~~pTig~~~~~i~~~~~~l~iwDt~G~~----~~~~~~~---~y~~~a~~~i 71 (158)
T cd00878 2 ILILGLDGAGKTTILYKLKLGEV--VT-TIPTIGFNVETVEYKNVSFTVWDVGGQD----KIRPLWK---HYYENTNGII 71 (158)
T ss_pred EEEECCCCCCHHHHHHHHHCCCC--CC-CCCEECCCEEEEEECCEEEEEEECCCCC----CCCHHHH---HHHCCCCEEE
T ss_conf 99999999988999999953998--87-4456074089998488999999889972----2144899---8727687768
Q ss_pred HHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHH----HHCCCCEEEEECCCCCCHHH
Q ss_conf 52022221101346667899877766750598899997465899889999999999----86299489998887889999
Q gi|254780648|r 242 HIVSALEENVQAAYQCILDELSAYNSELRKKIEIVGLSQIDTVDSDTLARKKNELA----TQCGQVPFEFSSITGHGIPQ 317 (335)
Q Consensus 242 ~VVD~s~~d~~~~~~~I~~EL~~y~~~L~~Kp~IIVlNKiDl~~~e~~~~~~~~l~----~~~~~~vi~ISA~tg~GI~e 317 (335)
T Consensus 72 ~V~D~t~~~s~~~~~~~~~~~~~-~~~~~~~piliv~NK~Dl~~~~~~~ei~~~l~~~~~~~~~~~~~~~SAktg~gI~e 150 (158)
T cd00878 72 FVVDSSDRERIEEAKEELHKLLN-EEELKGVPLLIFANKQDLPGALSVSELIEKLGLEKILGRRWHIQPCSAVTGDGLDE 150 (158)
T ss_pred EEEECCCHHHHHHHHHHHHHHHH-HCCCCCCEEEEEEECCCCCCCCCHHHHHHHHHHHHHCCCCCEEEEEECCCCCCHHH
T ss_conf 99837988899999999999986-60557653898760547665789999999985875107998999998887929899
Q ss_pred HHHHHHHH
Q ss_conf 99999999
Q gi|254780648|r 318 ILECLHDK 325 (335)
Q Consensus 318 L~~~I~e~ 325 (335)
T Consensus 151 ~f~~L~eq 158 (158)
T cd00878 151 GLDWLLQQ 158 (158)
T ss_pred HHHHHHCC
T ss_conf 99999569