HHsearch alignment for GI: 254780809 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=97.97  E-value=0.0001  Score=52.50  Aligned_cols=102  Identities=20%  Similarity=0.276  Sum_probs=63.5

Q ss_pred             CCCEEEECCCCCCHHHHHHHHHCCHHC-CCCCCCCCCEEECCCCCCCCCEEEEEEECCHHCCCCHHHHHHHHHHHHHHHH
Q ss_conf             230243114663188899998552000-2345468721100012456835899950810002410356666788899850
Q gi|254780809|r  219 GYKIVILGHSNAGKSSLFNALAKKDVA-IVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETDDIVEKEGIKRTFLEVE  297 (440)
Q Consensus       219 g~~v~i~G~pN~GKSSL~N~L~~~~~a-IVs~~~GTTRD~i~~~~~i~g~~~~l~DTaGir~t~d~IE~~GI~ra~~~i~  297 (440)
T Consensus        39 P~vVavvGPpgvGKtTLiksLvk~ytk~~l~~i~GPiT-vv----s~K~rRiTfiEc~------nDi~s-----miD~AK  102 (225)
T cd01882          39 PLVVAVVGPPGVGKTTLIKSLVKNYTKQNISDIKGPIT-VV----TGKKRRLTFIECP------NDINA-----MIDIAK  102 (225)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCEE-EE----ECCCEEEEEEECC------CHHHH-----HHHHHH
T ss_conf             96999989899778899999999985443755788879-99----4684268999748------60999-----987887


Q ss_pred             HHCCEEECCCCCCHH---HHHHH-----CCC-CCCCCCCCCCCCCCCC
Q ss_conf             301102013589856---63431-----289-8532222333446542
Q gi|254780809|r  298 NADLILLLKEINSKK---EISFP-----KNI-DFIFIGTKSDLYSTYT  336 (440)
Q Consensus       298 ~aDlil~v~D~~~~~---~~~~~-----~~~-~~i~V~NK~Dl~~~~~  336 (440)
T Consensus       103 vADlVLl~iD~s~GfEmEtfEfLnilq~hG~PkV~GVltHlD~fk~~k  150 (225)
T cd01882         103 VADLVLLLIDASFGFEMETFEFLNILQVHGFPRVMGVLTHLDLFKKNK  150 (225)
T ss_pred             HHHEEEEEECCCCCEEEEHHHHHHHHHHCCCCCEEEEEECCCCCCCHH
T ss_conf             643368886166553520899999999759994378854431015578