HHsearch alignment for GI: 254780357 and conserved domain: TIGR00360
>TIGR00360 ComEC_N-term ComEC/Rec2-related protein; InterPro: IPR004477 This family is defined to identify a pair of paralogous 3' 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 recognized 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..
Probab=97.55 E-value=0.00075 Score=40.27 Aligned_cols=110 Identities=18% Similarity=0.257 Sum_probs=70.5
Q ss_pred ECCCCCCHHHHHHHHHHHHCCCCHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 02668855589998888820485567152135879999999999999861264113577764211456788888889999
Q gi|254780357|r 4 ITKKYDPFPAETTIEGIARLSPPSGPAFPGLFDFNFSSYYKGISAIGYFYSIPKMIYSSESHNTWTWKKISSIKQSFLNE 83 (394)
Q Consensus 4 ~~~~~~p~~~g~~i~~~v~L~~P~~p~~PGlFD~SF~asF~aVaaigff~~~p~~~~~~~~~~~~~~~~l~~Lr~~i~~~ 83 (394)
T Consensus 77 ~~~~~~~~~~~~~~~~~~~~~~p~~~~~~g-----~~~~~~~~~~~~~w~~~~~~~-----~~~~~---~~~~~~~~~~~ 143 (187)
T TIGR00360 77 SLPKLNLIGALLLSALLLLLVDPVALLSLG-----FWLSFLATFGLLLWYRVLLFP-----NFQWL---LRPLSGWIASL 143 (187)
T ss_pred HHHCCCHHHHHHHHHHHHHHHCCHHHHHHH-----HHHHHHHHHHHHHHHHHHHHH-----HHHHH---HHHHHHHHHHH
T ss_conf 620122047899999999984202466654-----578999999999999999743-----25553---12210378999
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999965555888999999860102327883888999999999999
Q gi|254780357|r 84 IRANIGTYGSASASIFLIKHFHCIPVYGLIANILAIPILSFVVIP 128 (394)
Q Consensus 84 I~a~ls~~~~~a~~p~~~~~F~~~~~~~~~aNl~avP~~~~~v~p 128 (394)
T Consensus 144 ~--~~~~~~~~~~~p~~~~~~~~~~~~~~~~n~~~~p~~~~~~~~ 186 (187)
T TIGR00360 144 L--TLSLGLLLLSTPLLLYLFHGLSPLSVLANLLAVPLLSFLLLP 186 (187)
T ss_pred H--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 9--999999999877888874002588999999999999997606