HHsearch alignment for GI: 254780456 and conserved domain: cd05790

>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 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=91.55  E-value=0.75  Score=22.44  Aligned_cols=67  Identities=22%  Similarity=0.232  Sum_probs=34.8

Q ss_pred             CCCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCC-CCCCCCCCCEECCCCEEEEEEEEEECCCCEEEEEE
Q ss_conf             896658999981596699985142000000111101-11355742100378457999998621550478752
Q gi|254780456|r  282 EGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISW-TKKNIHPSKILSVGQQVEVVILEVNPARKRISLGL  352 (576)
Q Consensus       282 ~G~~v~g~V~~v~~~G~~V~l~~~v~G~i~~sels~-~~~~~~~~~~~~~G~~v~~~Vl~id~~~~~i~lS~  352 (576)
T Consensus         6 ~gD~VIGiV~~~~~d~y~vdi~~~~~a~L~~laFegATKkn-rP--~L~~GdlVYaRV~~a~~~-~e~EL~C   73 (86)
T cd05790           6 KGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRN-RP--NLNVGDLVYARVVKANRD-MEPELSC   73 (86)
T ss_pred             CCCEEEEEEEEECCCEEEEECCCCCCEEECCCEECCCCCCC-CC--CCCCCCEEEEEEEECCCC-CCEEEEE
T ss_conf             99989999944327668997679866485001017876556-88--788788999999874899-9704898