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=99.63 E-value=1.4e-15 Score=111.70 Aligned_cols=68 Identities=25% Similarity=0.429 Sum_probs=43.7
Q ss_pred CCEEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHHCCCHHHCCCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf 98799999997089089996177984999997471821210420110689879999999705768699870
Q gi|254780456|r 459 NDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSI 529 (576)
Q Consensus 459 G~iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~~~~~~~~~vG~~v~~~Vi~id~~~~ri~LS~ 529 (576)
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 GKIYEGKVVKIKDFGAFVEIL--PGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVD-DRGRISLSR 68 (68)
T ss_pred CCEEEEEEEEEECCEEEEEEC--CCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEC-CCCCCCCCC
T ss_conf 999999999997329999957--99624888689345654698890789999999999999-999720529