HHsearch alignment for GI: 254780229 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=95.83  E-value=0.015  Score=41.67  Aligned_cols=60  Identities=20%  Similarity=0.366  Sum_probs=36.8

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHCC-----CEEEEEECCHHHH------HHHHHHHHHCCCCCEEEECCC
Q ss_conf             59942878770389999999999679-----8289960105899------999986443584413654026
Q gi|254780229|r  422 LIIEGPPGTGKSQTITNIIAAAMLHG-----KKILFCAQKMAAI------EVVRHRLEKAGLGEFCLELHS  481 (1775)
Q Consensus       422 ~vi~GPPGTGKSQTIaNlIa~~la~G-----k~VLfVaeK~aAL------dVV~~RL~~~gLg~~cleLHs  481 (1775)
T Consensus        42 VavvGPpgvGKtTLiksLvk~ytk~~l~~i~GPiTvvs~K~rRiTfiEc~nDi~smiD~AKvADlVLl~iD  112 (225)
T cd01882          42 VAVVGPPGVGKTTLIKSLVKNYTKQNISDIKGPITVVTGKKRRLTFIECPNDINAMIDIAKVADLVLLLID  112 (225)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCEEEEECCCEEEEEEECCCHHHHHHHHHHHHHEEEEEEC
T ss_conf             99989899778899999999985443755788879994684268999748609999878876433688861