HHsearch alignment for GI: 254780788 and conserved domain: cd04471
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=96.88 E-value=0.0071 Score=40.37 Aligned_cols=58 Identities=26% Similarity=0.402 Sum_probs=50.2
Q ss_pred CCCEEEEEEEECCCCEEEEEEC--CCEEEEEHHHCC-----------------CCCCCCCCCEEEEEEEEECCCCCE
Q ss_conf 0838999998405763899957--935874478748-----------------875115276699999761135870
Q gi|254780788|r 138 VGEIISGTVKRVEYGNVIVDLG--NSDGVIRRDETI-----------------SRENLRPGDRVKSYIYDVRREQRG 195 (526)
Q Consensus 138 ~Geiv~G~V~r~e~~~iiVdlg--~~ea~Lp~~e~i-----------------p~E~~~~Gdrika~i~~V~~~~rg 195 (526)
T Consensus 1 IG~~f~g~I~~v~~~GiFV~l~~~~ieGli~~~~l~~d~y~~d~~~~~l~g~~~~~~~~lGd~v~V~i~~vd~~~~~ 77 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRK 77 (83)
T ss_pred CCCEEEEEEEEEEEEEEEEEEECCCEEEEEECCCCCCCCEEECCCCEEEECCCCCCEEECCCEEEEEEEEEECCCCE
T ss_conf 99999999998983069999828873999982214567224474021898134775997899999999999430398