HHsearch alignment for GI: 254780709 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=95.84  E-value=0.015  Score=38.31  Aligned_cols=33  Identities=42%  Similarity=0.552  Sum_probs=29.0

Q ss_pred             CCCCCCEEECCCCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             366741231135444442478999999985226
Q gi|254780709|r  107 FSHRPHVILVVGVNGVGKTTVIGKLSKKMSDAG  139 (321)
Q Consensus       107 ~~~~p~vil~vG~nG~GKTTT~aKLA~~~~~~g  139 (321)
T Consensus        35 ~epPP~vVavvGPpgvGKtTLiksLvk~ytk~~   67 (225)
T cd01882          35 EEPPPLVVAVVGPPGVGKTTLIKSLVKNYTKQN   67 (225)
T ss_pred             CCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCC
T ss_conf             899996999989899778899999999985443