HHsearch alignment for GI: 254780270 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=96.95  E-value=0.0013  Score=46.22  Aligned_cols=107  Identities=30%  Similarity=0.473  Sum_probs=60.7

Q ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHHCCCEEEEECCCCCCHHH-H--CCCCCCCCCCCCHHHHHHHHHCCCCCEEEEE
Q ss_conf             446735998605656502799999977088249986188888888-3--5632001456712899999832788739999
Q gi|254780270|r  363 KNKGLILCFVGPPGVGKTSLAQSIAKATGRQYVRMSLGGVYDEAD-I--RGHRRTYIGSMPGRIIQSLKRAKRSNPLLLL  439 (820)
Q Consensus       363 ~~~g~il~l~gppgvGKts~~~sia~al~r~f~~islgg~~d~~~-i--~gh~~ty~ga~pg~ii~~l~~~~~~npv~~l  439 (820)
T Consensus        36 epPP~vVavvGPpgvGKtTLiksLvk----~ytk~~l~~i~GPiTvvs~K~rRiTfiEc-~nDi~smiD~AKvADlVLl~  110 (225)
T cd01882          36 EPPPLVVAVVGPPGVGKTTLIKSLVK----NYTKQNISDIKGPITVVTGKKRRLTFIEC-PNDINAMIDIAKVADLVLLL  110 (225)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHH----HHHHCCCCCCCCCEEEEECCCEEEEEEEC-CCHHHHHHHHHHHHHEEEEE
T ss_conf             99996999989899778899999999----98544375578887999468426899974-86099998788764336888


Q ss_pred             ECHHHHHHHCCCCHHHHHHHHCCCCCCCCEEEEECCCCCCCCCEEEEEECCCC
Q ss_conf             33155423117711556655406001681332010352364427999934865
Q gi|254780270|r  440 DEIDKMGSDLRGDPSAALLEVLDPAQNSSFVDHYLEVEYDLSDVMFIMTANTL  492 (820)
Q Consensus       440 deidk~~~~~~gdp~~allevldp~qn~~f~d~y~~~~~dls~v~fi~tan~~  492 (820)
T Consensus       111 iD-----~s~GfEm--EtfEfLnilq~hG~-----------PkV~GVltHlD~  145 (225)
T cd01882         111 ID-----ASFGFEM--ETFEFLNILQVHGF-----------PRVMGVLTHLDL  145 (225)
T ss_pred             EC-----CCCCEEE--EHHHHHHHHHHCCC-----------CCEEEEEECCCC
T ss_conf             61-----6655352--08999999997599-----------943788544310