HHsearch alignment for GI: 254780784 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=98.81  E-value=2.3e-08  Score=86.67  Aligned_cols=69  Identities=33%  Similarity=0.570  Sum_probs=59.8

Q ss_pred             CCCEEEEEEEEEEECCEEEECCC-CCCEEEEEEECCCCCC-----------CCHHHHCCCCCEEEEEEEEECC-CCCEEE
Q ss_conf             68678999999941536998287-9710488663144454-----------7855603259889999997868-998666
Q gi|254780784|r  619 VNKIYKGQVVKVMDFGAFVHFCG-ARDGLVHISQLSTERV-----------AKTSDVVKEGDTVWVKLLDFDD-RGKIKL  685 (699)
Q Consensus       619 ~g~~y~~~v~~i~~fGafve~~~-g~~gl~HiS~l~~~~v-----------~~~~d~~~~Gd~i~vk~~~~d~-~g~i~l  685 (699)
T Consensus         1 IG~~f~g~I~~v~~~GiFV~l~~~~ieGli~~~~l~~d~y~~d~~~~~l~g~~~~~~~~lGd~v~V~i~~vd~~~~~I~f   80 (83)
T cd04471           1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF   80 (83)
T ss_pred             CCCEEEEEEEEEEEEEEEEEEECCCEEEEEECCCCCCCCEEECCCCEEEECCCCCCEEECCCEEEEEEEEEECCCCEEEE
T ss_conf             99999999998983069999828873999982214567224474021898134775997899999999999430398989


Q ss_pred             EE
Q ss_conf             87
Q gi|254780784|r  686 SM  687 (699)
Q Consensus       686 Sr  687 (699)
T Consensus        81 ~l   82 (83)
T cd04471          81 EL   82 (83)
T ss_pred             EE
T ss_conf             97