HHsearch alignment for GI: 254780787 and conserved domain: cd04121

>cd04121 Rab40 Rab40 subfamily. This subfamily contains Rab40a, Rab40b, and Rab40c, which are all highly homologous. In rat, Rab40c is localized to the perinuclear recycling compartment (PRC), and is distributed in a tissue-specific manor, with high expression in brain, heart, kidney, and testis, low expression in lung and liver, and no expression in spleen and skeletal muscle. Rab40c is highly expressed in differentiated oligodendrocytes but minimally expressed in oligodendrocyte progenitors, suggesting a role in the vesicular transport of myelin components. Unlike most other Ras-superfamily proteins, Rab40c was shown to have a much lower affinity for GTP, and an affinity for GDP that is lower than for GTP. 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 d
Probab=99.06  E-value=9e-10  Score=84.82  Aligned_cols=147  Identities=17%  Similarity=0.217  Sum_probs=95.2

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHCCC--CCCEECCCEEEEECCCCEEEEEECCCHHHHHHHHHHHHHCCCCEEEEEEC
Q ss_conf             8986236850446777886422210012--31000121499951784388885166157899986664206805999983
Q gi|254780787|r  386 VTIMGHVDHGKTSLLDAIRKADVAKGEI--GGITQHIGAYQVAYQGKNITFLDTPGHAAFYEMRARGARVTDIAVLVLAA  463 (884)
Q Consensus       386 v~v~ghvd~GKt~lld~~r~~~~~~~e~--ggitq~iga~~~~~~~~~~~~iDtPGh~~f~~~r~rg~~~~d~~ilvv~~  463 (884)
T Consensus         9 ivllGd~~VGKTsl~~r~~~~~f~~~y~~Tig~~~~~k~~~~~~~~v~l~iwDtaGqe~f~~l~~~y~r~a~~~ilvyDv   88 (189)
T cd04121           9 FLLVGDSDVGKGEILASLQDGSTESPYGYNMGIDYKTTTILLDGRRVKLQLWDTSGQGRFCTIFRSYSRGAQGIILVYDI   88 (189)
T ss_pred             EEEECCCCCCHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEECCEEEEEEEECCCCCCCHHHHHHHHHHHCCCEEEEECC
T ss_conf             99999899789999999974997898687653798999999999999999981788622116789886633704898227


Q ss_pred             CCCCCHHHHHHHH----HHH--HCCCCEEEECCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCCCCC
Q ss_conf             6674023577789----899--7099415612331244332000221000013200012347403631100247741122
Q gi|254780787|r  464 DEEIMPQAIESIN----HAK--AADVSIIVAINKIDKLGADPQKVRMSLLKHDVFVESMGGDILDVEISAKNNLNLDKLL  537 (884)
Q Consensus       464 ~~g~~~qt~e~~~----~~~--~~~~p~iva~nk~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  537 (884)
T Consensus        89 t~---~~Sf~~l~~w~~~i~~~~~~~p~iLVGNK~DL~~~r--~V~~ee--~~~~A~~~--~~~f~EtSAk~g~nV~e~F  159 (189)
T cd04121          89 TN---RWSFDGIDRWIKEIDEHAPGVPKILVGNRLHLAFKR--QVATEQ--AQAYAERN--GMTFFEVSPLCNFNITESF  159 (189)
T ss_pred             CC---HHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHCC--CCCHHH--HHHHHHHC--CCEEEEECCCCCCCHHHHH
T ss_conf             98---899999999999999976898789961325503308--899999--99999988--9999996006793989999


Q ss_pred             CCHH
Q ss_conf             1000
Q gi|254780787|r  538 DAIL  541 (884)
Q Consensus       538 ~~~~  541 (884)
T Consensus       160 ~~l~  163 (189)
T cd04121         160 TELA  163 (189)
T ss_pred             HHHH
T ss_conf             9999