HHsearch alignment for GI: 254780784 and conserved domain: TIGR00358
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases; InterPro: IPR004476 This family is defined to identify a pair of paralogous 3'->5' exoribonucleases in Escherichia coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterised originally as required for the expression of virulence genes, but is now recognised as the exoribonuclease RNase R (Rnr). Its paralog in Escherichia coli and Haemophilus influenzae is designated exoribonuclease II (Rnb) . Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cut-off to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3' exoribonucleases.; GO: 0003723 RNA binding, 0004540 ribonuclease activity, 0016070 RNA metabolic process.
Probab=91.01 E-value=0.19 Score=30.45 Aligned_cols=65 Identities=31% Similarity=0.456 Sum_probs=54.2
Q ss_pred CCCC--CEEEEEEEEEEECCEEEECC-CCCCEEEEEEECCC--C-----------CCCCHHHHCCCCCEEEEEEEEECCC
Q ss_conf 5468--67899999994153699828-79710488663144--4-----------5478556032598899999978689
Q gi|254780784|r 617 PEVN--KIYKGQVVKVMDFGAFVHFC-GARDGLVHISQLST--E-----------RVAKTSDVVKEGDTVWVKLLDFDDR 680 (699)
Q Consensus 617 ~e~g--~~y~~~v~~i~~fGafve~~-~g~~gl~HiS~l~~--~-----------~v~~~~d~~~~Gd~i~vk~~~~d~~ 680 (699)
T Consensus 596 ~~~g~~~~f~g~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gd~~~~~~~~~~~~ 675 (684)
T TIGR00358 596 DKVGTDEEFSGEISSVTGFGLFVRLDDNGIDGLVPVSTLPNNKDYYRFDKEKLALIGKGTGKVYRLGDRLEVKLTEVNLD 675 (684)
T ss_pred HHCCCCCCHHHHHHHHHCCCEEEEEECCCCCEEEEECCCCCCCHHEEECCCCCEEEECCCCCEEEECCEEEEEEEHHHHH
T ss_conf 54167530012221220264068750356310354122224311203421322687615673575154147752012122
Q ss_pred C
Q ss_conf 9
Q gi|254780784|r 681 G 681 (699)
Q Consensus 681 g 681 (699)
T Consensus 676 ~ 676 (684)
T TIGR00358 676 E 676 (684)
T ss_pred H
T ss_conf 3