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