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