HHsearch alignment for GI: 254780941 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=99.26  E-value=3.8e-11  Score=91.95  Aligned_cols=150  Identities=21%  Similarity=0.311  Sum_probs=101.4

Q ss_pred             HHHHHHHCCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHCCCEEEECCCCCCEEEEEEE---EEEECCEEEEEEECCCC
Q ss_conf             776541014332436851218998338998688999998689202105888860212789---99739948999987984
Q gi|254780941|r    4 GEITFFNEHKDFVQDNSRSGCVALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRG---IVSEKESQIVFLDTPGI   80 (311)
Q Consensus         4 ~e~~~~~~~~~~~~~~~ksg~VaivG~pN~GKSTL~N~l~g~~vsivS~k~~TTr~~i~g---i~~~~~~qiifvDTPG~   80 (311)
T Consensus        21 ~ekk~hvp~vdr~~~epPP~vVavvGPpgvGKtTLiksLvk~yt-------k~~l~~i~GPiTvvs~K~rRiTfiEc~nD   93 (225)
T cd01882          21 EEKKLHVPVVDRTPEEPPPLVVAVVGPPGVGKTTLIKSLVKNYT-------KQNISDIKGPITVVTGKKRRLTFIECPND   93 (225)
T ss_pred             HHHHHHCCCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHH-------HCCCCCCCCCEEEEECCCEEEEEEECCCH
T ss_conf             88876266413587899996999989899778899999999985-------44375578887999468426899974860


Q ss_pred             HHHCCCCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHCCHHHHHHHHHHCCCC-CEEEEEECCCHHHHHHHHHH------H
Q ss_conf             0101235753210023455553210011000010000000122345442872-02578721101043457888------8
Q gi|254780941|r   81 FNAKDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAKRSSR-LILILNKIDCVKPERLLEQA------E  153 (311)
Q Consensus        81 ~~~~~~l~~~~~~~~~~~l~~aDiil~VvDa~~~~~~~~~~il~~l~~~~~p-~IiVlNKiDlv~~~~l~~~~------~  153 (311)
T Consensus        94 ------i~-----smiD~AKvADlVLl~iD~s~GfEmEtfEfLnilq~hG~PkV~GVltHlD~fk~~k~lrk~KK~lk~R  162 (225)
T cd01882          94 ------IN-----AMIDIAKVADLVLLLIDASFGFEMETFEFLNILQVHGFPRVMGVLTHLDLFKKNKTLRKTKKRLKHR  162 (225)
T ss_pred             ------HH-----HHHHHHHHHHEEEEEECCCCCEEEEHHHHHHHHHHCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHH
T ss_conf             ------99-----9987887643368886166553520899999999759994378854431015578899999999999


Q ss_pred             HHHHCCCCCCCCCCCCCC
Q ss_conf             641001233431100013
Q gi|254780941|r  154 IANKLVFIEKTFMVSATK  171 (311)
Q Consensus       154 ~~~~~~~~~~i~~ISAk~  171 (311)
T Consensus       163 FwtE~y~gaKlFylsg~~  180 (225)
T cd01882         163 FWTEVYQGAKLFYLSGIV  180 (225)
T ss_pred             HHHHHCCCCEEEEECCCC
T ss_conf             999865995688633532