HHsearch alignment for GI: 254780233 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=98.78  E-value=6.6e-08  Score=71.11  Aligned_cols=155  Identities=18%  Similarity=0.243  Sum_probs=95.8

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCCEECCCCHHHHHCCCEEEEEEEEEE-ECCEEEEEECCCCCCCCHHHH
Q ss_conf             4999854689877889999998396142322000003885779870960646799999-899799997289875407999
Q gi|254780233|r   21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIV-WNDVRINIVDTPGHADFGGEV   99 (624)
Q Consensus        21 NiaIiaHvDhGKTTL~d~LL~~sG~~~~~~~v~~~vmD~~~~EreRGITI~a~~~~~~-~~~~~iNiiDTPGH~DF~gEV   99 (624)
T Consensus         4 KivllGd~~VGKTsL~~rf~~--~~F~~~~~~--T----------ig~df~~k~i~i~dg~~v~l~IwDTaGqe~~~si~   69 (211)
T cd04111           4 RLIVIGDSTVGKSSLLKRFTE--GRFAEVSDP--T----------VGVDFFSRLIEIEPGVRIKLQLWDTAGQERFRSIT   69 (211)
T ss_pred             EEEEECCCCCCHHHHHHHHHH--CCCCCCCCC--C----------CCEEEEEEEEEECCCCEEEEEEEECCCCCCCCCCH
T ss_conf             999999999619999999981--999998687--2----------01688998999779959999999798863456442


Q ss_pred             HHHHHHHCEEEEEEECCCCCCHHHHHHHHH-HHH----CCCCEEEEEECCCCCCCCHHHHH-HHHHHHHHHCCCCHHHCC
Q ss_conf             999874217899997687886478999999-997----29978999975436674025689-999988862267301104
Q gi|254780233|r  100 ERILCMVESVVVLVDAAEGPMPQTKFVVGK-ALK----IGLRPIVVVNKVDRSDARADEVI-NEVFDLFSALDATDAQLD  173 (624)
Q Consensus       100 er~l~~~DgaiLvVdA~eGv~~QT~~vl~~-A~~----~~l~~IvvINKiDr~~a~~~~v~-~ei~dlf~~l~a~de~ld  173 (624)
T Consensus        70 ~~yyr~a~g~ilVyDvt~~~SF~~l~~W~~ei~~~~~~~~~~iiLVGNK~DL~~~R--~Vs~ee~~~~A-------~~~~  140 (211)
T cd04111          70 RSYYRNSVGVLLVFDITNRESFEHVHDWLEEARSHIQPHRPVFILVGHKCDLESQR--QVTREEAEKLA-------KDLG  140 (211)
T ss_pred             HHHHHHCCEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCHHHHC--CCCHHHHHHHH-------HHHC
T ss_conf             87742124468971477779999999999999997498885389887423128567--88999999999-------9839


Q ss_pred             HHHHHHHHHCCEECCCCCCCCCCCCHHHHHHHHCCC
Q ss_conf             266887886591646742233486413555321024
Q gi|254780233|r  174 FPILYGSGRFGWMSDSSDGSRDQGMVPLLNLIVDHV  209 (624)
Q Consensus       174 ~Pv~~~Sa~~G~~~~~~~~~~~~gl~~Lld~Ii~~i  209 (624)
T Consensus       141 ~~f~EtSAK~g-----------~nV~e~F~~la~~i  165 (211)
T cd04111         141 MKYIETSARTG-----------DNVEEAFELLTQEI  165 (211)
T ss_pred             CEEEEECCCCC-----------CCHHHHHHHHHHHH
T ss_conf             97999759998-----------19899999999999