HHsearch alignment for GI: 254780941 and conserved domain: cd04115

>cd04115 Rab33B_Rab33A Rab33B/Rab33A subfamily. Rab33B is ubiquitously expressed in mouse tissues and cells, where it is localized to the medial Golgi cisternae. It colocalizes with alpha-mannose II. Together with the other cisternal Rabs, Rab6A and Rab6A', it is believed to regulate the Golgi response to stress and is likely a molecular target in stress-activated signaling pathways. Rab33A (previously known as S10) is expressed primarily in the brain and immune system cells. In humans, it is located on the X chromosome at Xq26 and its expression is down-regulated in tuberculosis patients. Experimental evidence suggests that Rab33A is a novel CD8+ T cell factor that likely plays a role in tuberculosis disease processes. 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 promote the formation of the GTP-bound state. Rabs are further regulated by guanine
Probab=99.56  E-value=1e-13  Score=108.54  Aligned_cols=154  Identities=18%  Similarity=0.228  Sum_probs=99.8

Q ss_pred             EEEEEECCCCCCHHHHHHHHHCCCEEEECCCCCCEE--EEEEEEEEECC--EEEEEEECCCCHHHCCCCCCCCCCHHHHH
Q ss_conf             189983389986889999986892021058888602--12789997399--48999987984010123575321002345
Q gi|254780941|r   23 GCVALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTR--SIVRGIVSEKE--SQIVFLDTPGIFNAKDSYHKLMIRLSWST   98 (311)
Q Consensus        23 g~VaivG~pN~GKSTL~N~l~g~~vsivS~k~~TTr--~~i~gi~~~~~--~qiifvDTPG~~~~~~~l~~~~~~~~~~~   98 (311)
T Consensus         3 ~Kiv~lGd~~VGKTsli~r~~~~~F~---~~~~~Tig~d~~~k~i~v~~~~v~l~iwDtaG~e~----~~~s---~~~~~   72 (170)
T cd04115           3 FKIIVIGDSNVGKTCLTYRFCAGRFP---ERTEATIGVDFRERTVEIDGERIKVQLWDTAGQER----FRKS---MVQHY   72 (170)
T ss_pred             EEEEEECCCCCCHHHHHHHHHCCCCC---CCCCCCEEEEEEEEEEEECCEEEEEEEEECCCCHH----HHHH---HHHHH
T ss_conf             99999997997799999999539889---98788630787899999999999999997788530----5677---78998


Q ss_pred             HHHHHHHCCCCHHHHHHHCC-HHHHHHHHHH----CCCCCEEEEEECCCHHHHHH-HHHHHHHHHCCCCCCCCCCCCC--
Q ss_conf             55532100110000100000-0012234544----28720257872110104345-7888864100123343110001--
Q gi|254780941|r   99 IKHADIVCLVVDSHRELKVN-IHDLLKEIAK----RSSRLILILNKIDCVKPERL-LEQAEIANKLVFIEKTFMVSAT--  170 (311)
Q Consensus        99 l~~aDiil~VvDa~~~~~~~-~~~il~~l~~----~~~p~IiVlNKiDlv~~~~l-~~~~~~~~~~~~~~~i~~ISAk--  170 (311)
T Consensus        73 ~~~a~~~ilvydvt~~~Sf~~~~~w~~~i~~~~~~~~~p~vlVGNK~DL~~~r~Vs~~e~~~~a~~~~-~~~~E~SAK~~  151 (170)
T cd04115          73 YRNVHAVVFVYDVTNMASFHSLPSWIEECEQHSLPNEVPRILVGNKCDLREQIQVPTDLAQRFADAHS-MPLFETSAKDP  151 (170)
T ss_pred             HCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCHHHCCCCHHHHHHHHHHCC-CEEEEECCCCC
T ss_conf             45773579995047476799999999999986588899799999982134117879999999999779-99999888998


Q ss_pred             -CCCCHHHHHHHHHHHCC
Q ss_conf             -38742678999998366
Q gi|254780941|r  171 -KGHGCDDVLNYLCSTLP  187 (311)
Q Consensus       171 -~g~Gid~L~~~L~~~lp  187 (311)
T Consensus       152 ~~~~nV~~~F~~la~~i~  169 (170)
T cd04115         152 SENDHVEAIFMTLAHKLK  169 (170)
T ss_pred             CCCCCHHHHHHHHHHHHC
T ss_conf             517088999999999960