HHsearch alignment for GI: 254780627 and conserved domain: cd01882

>cd01882 BMS1 Bms1. Bms1 is an essential, evolutionarily conserved, nucleolar protein. Its depletion interferes with processing of the 35S pre-rRNA at sites A0, A1, and A2, and the formation of 40S subunits. Bms1, the putative endonuclease Rc11, and the essential U3 small nucleolar RNA form a stable subcomplex that is believed to control an early step in the formation of the 40S subumit. The C-terminal domain of Bms1 contains a GTPase-activating protein (GAP) that functions intramolecularly. It is believed that Rc11 activates Bms1 by acting as a guanine-nucleotide exchange factor (GEF) to promote GDP/GTP exchange, and that activated (GTP-bound) Bms1 delivers Rc11 to the preribosomes.
Probab=94.62  E-value=0.1  Score=32.15  Aligned_cols=105  Identities=19%  Similarity=0.245  Sum_probs=62.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHC-------------CCCCEEEEEHHHHHHHHHHHHHCCCHHHHHHHHHHCCHHHH
Q ss_conf             89862788885799999999998630-------------68816864698889999999861988999999740310205
Q gi|254780627|r  199 LFIHASVGLGKTHLLQAIANASIKRQ-------------PNLRVVYLTAEYFMWRFASAIRDNCALNLKDSLRNIDLLLI  265 (502)
Q Consensus       199 Lfi~G~~GlGKTHLl~ai~~~~~~~~-------------~~~~v~y~~~e~F~~~~~~a~~~~~~~~fr~~~r~~DvLli  265 (502)
T Consensus        42 VavvGPpgvGKtTLiksLvk~ytk~~l~~i~GPiTvvs~K~rRiTfiEc~nDi~smiD~----------AKvADlVLl~i  111 (225)
T cd01882          42 VAVVGPPGVGKTTLIKSLVKNYTKQNISDIKGPITVVTGKKRRLTFIECPNDINAMIDI----------AKVADLVLLLI  111 (225)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCEEEEECCCEEEEEEECCCHHHHHHHH----------HHHHHEEEEEE
T ss_conf             99989899778899999999985443755788879994684268999748609999878----------87643368886


Q ss_pred             HHHHHHCCCCHHHHHHHHHHHHHHCCCEEEEEC------CCCHHHHCCCCHHHHHHHHC
Q ss_conf             444453175069999999999885698799964------87567613630345765302
Q gi|254780627|r  266 DDMQFLQGKLIQHEFCHLLNSLLDSAKQVVAAA------DRPPSELESLDPRIRSRLQG  318 (502)
Q Consensus       266 DDiqfl~gk~tqee~f~~~n~l~~~gkqiv~ts------d~~P~~l~~l~~rL~SR~~~  318 (502)
T Consensus       112 D~s~-----GfEmEtfEfLnilq~hG~PkV~GVltHlD~fk~~k~lrk~KK~lk~RFwt  165 (225)
T cd01882         112 DASF-----GFEMETFEFLNILQVHGFPRVMGVLTHLDLFKKNKTLRKTKKRLKHRFWT  165 (225)
T ss_pred             CCCC-----CEEEEHHHHHHHHHHCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             1665-----53520899999999759994378854431015578899999999999999