HHsearch alignment for GI: 254780788 and conserved domain: cd04472
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=97.69 E-value=0.00017 Score=52.32 Aligned_cols=61 Identities=28% Similarity=0.444 Sum_probs=52.9
Q ss_pred CCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHC------CCCCCCCCCCEEEEEEEEECCCCCEEEEEEEC
Q ss_conf 838999998405763899957-93587447874------88751152766999997611358702898715
Q gi|254780788|r 139 GEIISGTVKRVEYGNVIVDLG-NSDGVIRRDET------ISRENLRPGDRVKSYIYDVRREQRGPQVLLSR 202 (526)
Q Consensus 139 Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSR 202 (526)
T Consensus 1 G~iv~G~V~~i~~fG~FV~l~~g~~GLiHiSeis~~~v~~~~~~~~~Gd~v~vkVi~iD~~~---ri~LSr 68 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDRG---RISLSR 68 (68)
T ss_pred CCEEEEEEEEEECCEEEEEECCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEECCCC---CCCCCC
T ss_conf 99999999999732999995799624888689345654698890789999999999999999---720529