HHsearch alignment for GI: 254780648 and conserved domain: cd04111

>cd04111 Rab39 Rab39 subfamily. Found in eukaryotes, Rab39 is mainly found in epithelial cell lines, but is distributed widely in various human tissues and cell lines. It is believed to be a novel Rab protein involved in regulating Golgi-associated vesicular transport during cellular endocytosis. 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 nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.
Probab=99.61  E-value=2.8e-15  Score=112.40  Aligned_cols=159  Identities=18%  Similarity=0.204  Sum_probs=112.1

Q ss_pred             EEEEECCCCCCCEEEEEECCCCCHHHHHHHCCCEECCE------EEEEC-C--EEEEEECCCCCCCCCCCCCCCHHHHHH
Q ss_conf             12442167775303541014540121211000000102------66329-8--689982264212473116775123443
Q gi|254780648|r  162 IGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLG------IVKEG-Y--KEFILADIPGIIKNAHQGAGIGDRFLK  232 (335)
Q Consensus       162 VglVG~PNaGKSTLln~ls~ak~kIa~ypFTT~~P~lG------vv~~~-~--~~~~i~D~PGlIegA~~~~glG~~FLr  232 (335)
T Consensus         5 ivllGd~~VGKTsL~~rf~~~~F~-~-----~~~~Tig~df~~k~i~i~dg~~v~l~IwDTaGq----e~~~si~~~y--   72 (211)
T cd04111           5 LIVIGDSTVGKSSLLKRFTEGRFA-E-----VSDPTVGVDFFSRLIEIEPGVRIKLQLWDTAGQ----ERFRSITRSY--   72 (211)
T ss_pred             EEEECCCCCCHHHHHHHHHHCCCC-C-----CCCCCCCEEEEEEEEEECCCCEEEEEEEECCCC----CCCCCCHHHH--
T ss_conf             999999996199999999819999-9-----868720168899899977995999999979886----3456442877--


Q ss_pred             HHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHH-HHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             33335788752022221101346667899877766750598899997465899889-99999999986299489998887
Q gi|254780648|r  233 HTERTHVLLHIVSALEENVQAAYQCILDELSAYNSELRKKIEIVGLSQIDTVDSDT-LARKKNELATQCGQVPFEFSSIT  311 (335)
Q Consensus       233 hIer~~vLl~VVD~s~~d~~~~~~~I~~EL~~y~~~L~~Kp~IIVlNKiDl~~~e~-~~~~~~~l~~~~~~~vi~ISA~t  311 (335)
T Consensus        73 -yr~a~g~ilVyDvt~~~SF~~l~~W~~ei~~~~~~-~~~~iiLVGNK~DL~~~R~Vs~ee~~~~A~~~~~~f~EtSAK~  150 (211)
T cd04111          73 -YRNSVGVLLVFDITNRESFEHVHDWLEEARSHIQP-HRPVFILVGHKCDLESQRQVTREEAEKLAKDLGMKYIETSART  150 (211)
T ss_pred             -HHHCCEEEEEECCCCHHHHHHHHHHHHHHHHHCCC-CCCEEEEEEECCCHHHHCCCCHHHHHHHHHHHCCEEEEECCCC
T ss_conf             -42124468971477779999999999999997498-8853898874231285678899999999998399799975999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             88999999999999985452303
Q gi|254780648|r  312 GHGIPQILECLHDKIFSIRGENE  334 (335)
Q Consensus       312 g~GI~eL~~~I~e~L~~~r~e~E  334 (335)
T Consensus       151 g~nV~e~F~~la~~i~~~~~~~~  173 (211)
T cd04111         151 GDNVEEAFELLTQEIYERIKRGE  173 (211)
T ss_pred             CCCHHHHHHHHHHHHHHHHHCCC
T ss_conf             81989999999999999987389