HHsearch alignment for GI: 254780150 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=99.22  E-value=6.9e-11  Score=86.58  Aligned_cols=144  Identities=22%  Similarity=0.308  Sum_probs=104.6

Q ss_pred             CCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHCCCEEEEEEEEEECCCEEEEEEECCCCHHHHHHHH
Q ss_conf             88279999904689887899999987644420013126868698629206378999821990899984787302467798
Q gi|254780150|r   10 KESLGLSTIGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGITIATAHVSYETDKRFYSHIDCPGHADYVKNMI   89 (392)
Q Consensus        10 k~~~ni~~iGhvd~GKSTL~~~L~~~~~~~~~~~~~~D~~~~E~~rGiTi~~~~~~~~~~~~~i~iiD~PGH~~f~~~mi   89 (392)
T Consensus        37 pPP~vVavvGPpgvGKtTLiksLvk~ytk~~l~---------~i~GPiTvv------s~K~rRiTfiEc~n--D-i~smi   98 (225)
T cd01882          37 PPPLVVAVVGPPGVGKTTLIKSLVKNYTKQNIS---------DIKGPITVV------TGKKRRLTFIECPN--D-INAMI   98 (225)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCC---------CCCCCEEEE------ECCCEEEEEEECCC--H-HHHHH
T ss_conf             999699998989977889999999998544375---------578887999------46842689997486--0-99998


Q ss_pred             HHHHCCCCEEEEECCCCCCCCCHHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCCCCEEEEEEEEEEEEECCCCE
Q ss_conf             77400233145201234433210677888863187602331002333561222110123210011101453221023311
Q gi|254780150|r   90 TGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNKVDAVDDDELLDISEYEIRDLLKEHKYSDDTPIIRGS  169 (392)
Q Consensus        90 ~g~~~~D~ailvVda~~G~~~QT~eh~~l~~~lgi~~iIv~iNKmD~v~~~~~~~~i~~~i~~~l~~~~~~~~~pii~~s  169 (392)
T Consensus        99 D~AKvADlVLl~iD~s~GfEmEtfEfLnilq~hG~PkV~GVltHlD~fk~~k~lrk~KK~lk~RFwtE~-y~gaKlFyls  177 (225)
T cd01882          99 DIAKVADLVLLLIDASFGFEMETFEFLNILQVHGFPRVMGVLTHLDLFKKNKTLRKTKKRLKHRFWTEV-YQGAKLFYLS  177 (225)
T ss_pred             HHHHHHHEEEEEECCCCCEEEEHHHHHHHHHHCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHH-CCCCEEEEEC
T ss_conf             788764336888616655352089999999975999437885443101557889999999999999986-5995688633


Q ss_pred             EEE
Q ss_conf             467
Q gi|254780150|r  170 ALC  172 (392)
Q Consensus       170 a~~  172 (392)
T Consensus       178 g~~  180 (225)
T cd01882         178 GIV  180 (225)
T ss_pred             CCC
T ss_conf             532