HHsearch alignment for GI: 254780751 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=97.97 E-value=1.6e-05 Score=57.38 Aligned_cols=37 Identities=27% Similarity=0.493 Sum_probs=33.6
Q ss_pred CCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCC
Q ss_conf 878798997836388231353278977130222137121
Q gi|254780751|r 40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDY 78 (723)
Q Consensus 40 GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y 78 (723)
T Consensus 1 G~iv~G~V~~i~~--fG~FV~l~~g~~GLiHiSeis~~~ 37 (68)
T cd04472 1 GKIYEGKVVKIKD--FGAFVEILPGKDGLVHISELSDER 37 (68)
T ss_pred CCEEEEEEEEEEC--CEEEEEECCCCEEEEEHHHHCCCC
T ss_conf 9999999999973--299999579962488868934565