HHsearch alignment for GI: 254780787 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=98.96  E-value=3.8e-09  Score=80.53  Aligned_cols=143  Identities=20%  Similarity=0.265  Sum_probs=92.9

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHCCCCCCEECCCE------EEEECCCCEEEEEECCCHHHH-HHHHHHHHHCCCCEE
Q ss_conf             8986236850446777886422210012310001214------999517843888851661578-999866642068059
Q gi|254780787|r  386 VTIMGHVDHGKTSLLDAIRKADVAKGEIGGITQHIGA------YQVAYQGKNITFLDTPGHAAF-YEMRARGARVTDIAV  458 (884)
Q Consensus       386 v~v~ghvd~GKt~lld~~r~~~~~~~e~ggitq~iga------~~~~~~~~~~~~iDtPGh~~f-~~~r~rg~~~~d~~i  458 (884)
T Consensus         5 iv~lGd~~VGKTsli~r~~~~~F~~~~----~~Tig~d~~~k~i~v~~~~v~l~iwDtaG~e~~~~s~~~~~~~~a~~~i   80 (170)
T cd04115           5 IIVIGDSNVGKTCLTYRFCAGRFPERT----EATIGVDFRERTVEIDGERIKVQLWDTAGQERFRKSMVQHYYRNVHAVV   80 (170)
T ss_pred             EEEECCCCCCHHHHHHHHHCCCCCCCC----CCCEEEEEEEEEEEECCEEEEEEEEECCCCHHHHHHHHHHHHCCCCEEE
T ss_conf             999997997799999999539889987----8863078789999999999999999778853056777899845773579


Q ss_pred             EEEECCCCCCHHHHHHHH----HHH----HCCCCEEEECCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCEEEEEEEC--
Q ss_conf             999836674023577789----899----7099415612331244332000221000013200012347403631100--
Q gi|254780787|r  459 LVLAADEEIMPQAIESIN----HAK----AADVSIIVAINKIDKLGADPQKVRMSLLKHDVFVESMGGDILDVEISAK--  528 (884)
Q Consensus       459 lvv~~~~g~~~qt~e~~~----~~~----~~~~p~iva~nk~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--  528 (884)
T Consensus        81 lvydvt~---~~Sf~~~~~w~~~i~~~~~~~~~p~vlVGNK~DL~~~r--~Vs~~e~~--~~a~~~--~~~~~E~SAK~~  151 (170)
T cd04115          81 FVYDVTN---MASFHSLPSWIEECEQHSLPNEVPRILVGNKCDLREQI--QVPTDLAQ--RFADAH--SMPLFETSAKDP  151 (170)
T ss_pred             EEEECCC---HHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCHHHC--CCCHHHHH--HHHHHC--CCEEEEECCCCC
T ss_conf             9950474---76799999999999986588899799999982134117--87999999--999977--999999888998


Q ss_pred             -CCCCCCCCCCCHH
Q ss_conf             -2477411221000
Q gi|254780787|r  529 -NNLNLDKLLDAIL  541 (884)
Q Consensus       529 -~~~~~~~~~~~~~  541 (884)
T Consensus       152 ~~~~nV~~~F~~la  165 (170)
T cd04115         152 SENDHVEAIFMTLA  165 (170)
T ss_pred             CCCCCHHHHHHHHH
T ss_conf             51708899999999