HHsearch alignment for GI: 254780648 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=98.12 E-value=1.2e-05 Score=54.02 Aligned_cols=128 Identities=19% Similarity=0.339 Sum_probs=78.1
Q ss_pred EEEEECCCCCCCEEEEEECCCCCHHHHHHHCCCEECCE---EEEECCEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf 12442167775303541014540121211000000102---663298689982264212473116775123443333357
Q gi|254780648|r 162 IGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLG---IVKEGYKEFILADIPGIIKNAHQGAGIGDRFLKHTERTH 238 (335)
Q Consensus 162 VglVG~PNaGKSTLln~ls~ak~kIa~ypFTT~~P~lG---vv~~~~~~~~i~D~PGlIegA~~~~glG~~FLrhIer~~ 238 (335)
T Consensus 42 VavvGPpgvGKtTLiksLv------k~ytk~~l~~i~GPiTvvs~K~rRiTfiEc~nDi----------~smiD~AKvAD 105 (225)
T cd01882 42 VAVVGPPGVGKTTLIKSLV------KNYTKQNISDIKGPITVVTGKKRRLTFIECPNDI----------NAMIDIAKVAD 105 (225)
T ss_pred EEEECCCCCCHHHHHHHHH------HHHHHCCCCCCCCCEEEEECCCEEEEEEECCCHH----------HHHHHHHHHHH
T ss_conf 9998989977889999999------9985443755788879994684268999748609----------99987887643
Q ss_pred HHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEE-EEECCCCCCHH-HHHHHHHHHHHHC------CCCEEEEECC
Q ss_conf 88752022221101346667899877766750598899-99746589988-9999999999862------9948999888
Q gi|254780648|r 239 VLLHIVSALEENVQAAYQCILDELSAYNSELRKKIEIV-GLSQIDTVDSD-TLARKKNELATQC------GQVPFEFSSI 310 (335)
Q Consensus 239 vLl~VVD~s~~d~~~~~~~I~~EL~~y~~~L~~Kp~II-VlNKiDl~~~e-~~~~~~~~l~~~~------~~~vi~ISA~ 310 (335)
T Consensus 106 lVLl~iD~s~GfEmEtfEfLn-ilq~-----hG~PkV~GVltHlD~fk~~k~lrk~KK~lk~RFwtE~y~gaKlFylsg~ 179 (225)
T cd01882 106 LVLLLIDASFGFEMETFEFLN-ILQV-----HGFPRVMGVLTHLDLFKKNKTLRKTKKRLKHRFWTEVYQGAKLFYLSGI 179 (225)
T ss_pred EEEEEECCCCCEEEEHHHHHH-HHHH-----CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEECCC
T ss_conf 368886166553520899999-9997-----5999437885443101557889999999999999986599568863353
Q ss_pred C
Q ss_conf 7
Q gi|254780648|r 311 T 311 (335)
Q Consensus 311 t 311 (335)
T Consensus 180 ~ 180 (225)
T cd01882 180 V 180 (225)
T ss_pred C
T ss_conf 2