HHsearch alignment for GI: 254780456 and conserved domain: cd05789

>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit 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=98.32  E-value=6.1e-06  Score=53.28  Aligned_cols=71  Identities=24%  Similarity=0.257  Sum_probs=34.0

Q ss_pred             CCCCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHH----HCCCHHHCCCCCEEEEEEEEECCCCCEEEEEEH
Q ss_conf             78987999999970890899961779849999974718212----104201106898799999997057686998703
Q gi|254780456|r  457 RKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDR----VDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIK  530 (576)
Q Consensus       457 ~~G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~----~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~k  530 (576)
T Consensus         5 ~~GD~ViG~V~~i~~~~w~vdi~--s~~~a~L~ls~v~~~~~~~d~~~mr~~l~iGDli~a~V~~v~-~~~~v~L~~r   79 (86)
T cd05789           5 EVGDVVIGRVTEVGFKRWKVDIN--SPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVD-SDGSVSLHTR   79 (86)
T ss_pred             CCCCEEEEEEEEEECCCEEEECC--CCEEEEEEHHHCCCCCCCHHHHHHHHHCCCCCEEEEEEEEEC-CCCCEEEEEC
T ss_conf             88999999999980881899749--960779874544677763146778865668989999999988-9997999965