HHsearch alignment for GI: 254780456 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=99.11 E-value=5.5e-10 Score=77.81 Aligned_cols=70 Identities=20% Similarity=0.261 Sum_probs=29.7
Q ss_pred CCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHH-H----------CCCHHHCCCCCEEEEEEEEECCCCCEEEE
Q ss_conf 987999999970890899961779849999974718212-1----------04201106898799999997057686998
Q gi|254780456|r 459 NDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDR-V----------DQDPGRFSKGQIVDACVVNVSKKDGKVSL 527 (576)
Q Consensus 459 G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~-~----------~~~~~~~~vG~~v~~~Vi~id~~~~ri~L 527 (576)
T Consensus 2 G~~f~g~I~~v~~~GiFV~l~~-~~ieGli~~~~l~~d~y~~d~~~~~l~g~~~~~~~~lGd~v~V~i~~vd~~~~~I~f 80 (83)
T cd04471 2 GEEFDGVISGVTSFGLFVELDN-LTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF 80 (83)
T ss_pred CCEEEEEEEEEEEEEEEEEEEC-CCEEEEEECCCCCCCCEEECCCCEEEECCCCCCEEECCCEEEEEEEEEECCCCEEEE
T ss_conf 9999999998983069999828-873999982214567224474021898134775997899999999999430398989
Q ss_pred EE
Q ss_conf 70
Q gi|254780456|r 528 SI 529 (576)
Q Consensus 528 S~ 529 (576)
T Consensus 81 ~l 82 (83)
T cd04471 81 EL 82 (83)
T ss_pred EE
T ss_conf 97