HHsearch alignment for GI: 254781047 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=91.60  E-value=0.22  Score=28.80  Aligned_cols=97  Identities=23%  Similarity=0.188  Sum_probs=55.0

Q ss_pred             CCCCCCCEEEEECCCCCCHHHHHHHHHHHCC--------------CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             6666886499888887728999999998578--------------11146888999999999999997131122466557
Q gi|254781047|r   61 RKYCSMQGIYLHGDVGQGKSMLMNLFFALVP--------------IEKKCRLHFYEFMKDVHSRIIMYRKKIEFGEILES  126 (404)
Q Consensus        61 ~~~~~~kGlYL~G~VG~GKT~LMdlFy~~l~--------------~~~K~R~HFh~FM~~ih~~l~~~~~~~~~~~~~~~  126 (404)
T Consensus        34 ~~epPP~vVavvGPpgvGKtTLiksLvk~ytk~~l~~i~GPiTvvs~K~rRiTfiEc~nDi~smiD--------------   99 (225)
T cd01882          34 PEEPPPLVVAVVGPPGVGKTTLIKSLVKNYTKQNISDIKGPITVVTGKKRRLTFIECPNDINAMID--------------   99 (225)
T ss_pred             CCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCEEEEECCCEEEEEEECCCHHHHHHH--------------
T ss_conf             789999699998989977889999999998544375578887999468426899974860999987--------------


Q ss_pred             CHHHHHHHHHHCCCCEEEEEEEEECCCHHHHHHHHHHHHHHHCCCEEEEECCCCHH
Q ss_conf             80789999996138799984232047135888999999998549689981786867
Q gi|254781047|r  127 DPIPLVASSIALESRVLCFDEFMITNIADAIILSRLFAALFSHGCIIVMTSNFIPE  182 (404)
Q Consensus       127 dpl~~va~~l~~~~~lLCfDEF~V~DiaDAmil~rl~~~lf~~gv~lV~TSN~~P~  182 (404)
T Consensus       100 --~AKv-----ADlVLl~iD~----s~GfEmEtfEfLnilq~hG~PkV~GVltHlD  144 (225)
T cd01882         100 --IAKV-----ADLVLLLIDA----SFGFEMETFEFLNILQVHGFPRVMGVLTHLD  144 (225)
T ss_pred             --HHHH-----HHEEEEEECC----CCCEEEEHHHHHHHHHHCCCCCEEEEEECCC
T ss_conf             --8876-----4336888616----6553520899999999759994378854431