HHsearch alignment for GI: 254780456 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=99.61 E-value=6.6e-16 Score=113.67 Aligned_cols=66 Identities=41% Similarity=0.814 Sum_probs=36.4
Q ss_pred CCEEEEEEEEEECCCCEEEE-CCCEEEEEEEECCCCCCCCCCEEECCCCEEEEEEEEECCCCCEEEEE
Q ss_conf 33024678875314717774-48315788642024444433113326972589999874765279985
Q gi|254780456|r 198 GQVIEGTVKNITDYGVFVDL-SGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLG 264 (576)
Q Consensus 198 G~~v~g~V~~i~~~g~~V~~-~g~~g~i~~~~ls~~~~~~~~~~~~~G~~v~~~Vl~~d~~~~~i~ls 264 (576)
T Consensus 1 G~iv~G~V~~i~~fG~FV~l~~g~~GLiHiSeis~~~v~~~~~~~~~Gd~v~vkVi~iD-~~~ri~LS 67 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVD-DRGRISLS 67 (68)
T ss_pred CCEEEEEEEEEECCEEEEEECCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEC-CCCCCCCC
T ss_conf 99999999999732999995799624888689345654698890789999999999999-99972052