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