HHsearch alignment for GI: 254780470 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=94.51 E-value=0.18 Score=29.76 Aligned_cols=76 Identities=26% Similarity=0.388 Sum_probs=47.7
Q ss_pred EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-EEEEEECCCE--EEEEEE
Q ss_conf 9978999815898179998166776533323354433344555544455555445556882-8999912511--201647
Q gi|254780470|r 8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNA-VVIAYTAGRM--RKHRIR 84 (110)
Q Consensus 8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~-~VlA~isGKm--Rk~~IR 84 (110)
T Consensus 4 ~f~g~I~~v~~~GiF-V~l~~~-------------------------~ieGli~~~~l~~d~y~~d~~~~~l~g~~~~~~ 57 (83)
T cd04471 4 EFDGVISGVTSFGLF-VELDNL-------------------------TVEGLVHVSTLGDDYYEFDEENHALVGERTGKV 57 (83)
T ss_pred EEEEEEEEEEEEEEE-EEEECC-------------------------CEEEEEECCCCCCCCEEECCCCEEEECCCCCCE
T ss_conf 999999989830699-998288-------------------------739999822145672244740218981347759
Q ss_pred EECCCEEEEEECCCCCCCCEEEEEE
Q ss_conf 7029969999746757843598842
Q gi|254780470|r 85 ISLGDKVKVAMNPYDMTRARITYRF 109 (110)
Q Consensus 85 Il~GDkV~Ve~SPYDLtkGRItyR~ 109 (110)
T Consensus 58 ~~lGd~v~V~i~~vd~~~~~I~f~l 82 (83)
T cd04471 58 FRLGDKVKVRVVRVDLDRRKIDFEL 82 (83)
T ss_pred EECCCEEEEEEEEEECCCCEEEEEE
T ss_conf 9789999999999943039898997