HHsearch alignment for GI: 254780630 and conserved domain: TIGR01966

>TIGR01966 RNasePH ribonuclease PH; InterPro: IPR002381 Prokaryotic ribonuclease PH (2.7.7.56 from EC) (RNase PH) is a phosphorolytic exoribonuclease that removes nucleotide residues following the -CCA terminus of tRNA and adds nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates . There is a similar protein in Caenorhabditis elegans that belongs to this group. More information about these proteins can be found at Protein of the Month: RNA Exosomes .; GO: 0000049 tRNA binding, 0004549 tRNA-specific ribonuclease activity, 0008033 tRNA processing.
Probab=100.00  E-value=0  Score=333.22  Aligned_cols=237  Identities=55%  Similarity=0.873  Sum_probs=230.1

Q ss_pred             CCCCCCCCCEEEEEEEECCCCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCC
Q ss_conf             67899801178799997663268828999968948999999333245310155434211001005556532223334444
Q gi|254780630|r    2 RLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHGWITAEYGMLPRSTGNRVKREAVSG   81 (242)
Q Consensus         2 R~DGR~~~e~R~i~i~~g~~~~a~GSa~v~~G~T~Vl~~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~   81 (242)
T Consensus         1 R~dGR~~dqLRpv~i~r~f~~haEGSvLi~~G~TkVlCTASv~e~VP~flrG~G~GWiTAEY~MLPraT~~R~~REa~~G   80 (237)
T TIGR01966         1 RPDGRKPDQLRPVKITRDFLKHAEGSVLIEFGDTKVLCTASVEEKVPPFLRGSGEGWITAEYGMLPRATQTRNRREAAKG   80 (237)
T ss_pred             CCCCCCCCCCCCEEECCCCCCCCCCEEEEEECCEEEEEEEEECCCCCCCCCCCCCEEEEHHHHHHHHHHCCCCHHHHHHC
T ss_conf             98988553453625546887888872689787924666787558728523588942550411000330303124668617


Q ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEECCCCCCCCHHHHCCCCCCCHHHCCCCCCCCCCCCEECCCCCCC
Q ss_conf             77731023444432242100022004880222344203555763101000122210110010000014631011243783
Q gi|254780630|r   82 RQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDVIQADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHV  161 (242)
Q Consensus        82 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~i~i~v~v~~~dg~~~~a~~~a~~~Al~~a~i~~~~~~~~~~~~~~~~~~~  161 (242)
T Consensus        81 K~~GRTqEIQRLIGRaLRavvDl~aLGErTI~iDCDVlQADGGTRTAsITGAfVAL~dAi~~L~~~~~~~~~-~P~~~~V  159 (237)
T TIGR01966        81 KQSGRTQEIQRLIGRALRAVVDLEALGERTIWIDCDVLQADGGTRTASITGAFVALADAIKKLQKRGILKES-EPIRDFV  159 (237)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCEEECCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCC-CCCCCCC
T ss_conf             878750567778888988773462348502798533433887612467888999999999999857862346-8711052


Q ss_pred             CEEECCCCCCCCEECCCCCCCCCCCEEEEEEECCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             102004545541003343101234303688875998689999218636868999999999999999999999999977
Q gi|254780630|r  162 AAISCGMLCGYPIVDLDYGEDSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNLAKDRIADLIKLQKDVIS  239 (242)
Q Consensus       162 ~~~~~~~~~~~~~~d~~~~ee~~~~~~l~v~~~~~~~i~~i~~~g~~~~~~~~~l~~~l~~a~~~~~~i~~~i~~~L~  239 (242)
T Consensus       160 AAVSVGiv~g~~~LDL~Y~EDs~A~vD~NvVmT~~G~fvEvQGTaE~~pFsr~EL~~LL~LA~~Gi~eL~~~Qk~aL~  237 (237)
T TIGR01966       160 AAVSVGIVDGEPVLDLDYEEDSAADVDMNVVMTGSGGFVEVQGTAEEEPFSRDELNELLDLAEKGIRELIELQKQALG  237 (237)
T ss_pred             CEEEEEEECCEEEECCCCCCCCCCCCCCEEEECCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             438988766806763588555646335205885787658887057889701899999999988889999999999719