>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".

Probab=96.13 E-value=0.016 Score=37.78 Aligned_cols=70 Identities=23% Similarity=0.378 Sum_probs=54.7 Q ss_pred HHHHCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHH------HCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEECCCHH Q ss_conf 98520838999998405763899957-935874478------74887511527669999976113587028987159889 Q gi|254780788|r 134 FKDKVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRD------ETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQ 206 (526) Q Consensus 134 f~~r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~------e~ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p~ 206 (526) T Consensus 2 Y~P~vGDvVigrV~~v~~~~w~vdI~~~~~a~l~~~~~~~~D~~~m~~~f~~GDlI~A~V~~~~~~~~---~~L~T~~~~ 78 (82) T cd04454 2 YLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDDMN---VLLTTADNE 78 (82) T ss_pred CCCCCCCEEEEEEEEECCCEEEEEECCCEEEEEEEHHCCCCCHHHHHHHCCCCCEEEEEEEEECCCCC---EEEEECCCC T ss_conf 87989999999999970781899968632889730216773066798745877689999999769997---899956655

HHsearch alignment for GI: 254780788 and conserved domain: cd04454