HHsearch alignment for GI: 254780784 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=99.97  E-value=4.5e-30  Score=263.32  Aligned_cols=220  Identities=28%  Similarity=0.373  Sum_probs=205.7

Q ss_pred             CCCCCCCCCEEEEEEEECCCCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCC-
Q ss_conf             6588677533787998447546670089998797689999816865212233445442035877405887544533455-
Q gi|254780784|r  313 RMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPCATGEVSRM-  391 (699)
Q Consensus       313 R~DGR~~dEIRpIs~EvgvLPrvHGSALFtRGETQaL~tvTLG~~~d~Q~iD~l~~~~~k~fmlHYNFPpfsvGE~~~~-  391 (699)
T Consensus         1 R~dGR~~dqLRpv~i~r~f~~haEGSvLi~~G~TkVlCTASv~e~VP~flrG~G~GWiTAE----Y~MLPraT~~R~~RE   76 (237)
T TIGR01966         1 RPDGRKPDQLRPVKITRDFLKHAEGSVLIEFGDTKVLCTASVEEKVPPFLRGSGEGWITAE----YGMLPRATQTRNRRE   76 (237)
T ss_pred             CCCCCCCCCCCCEEECCCCCCCCCCEEEEEECCEEEEEEEEECCCCCCCCCCCCCEEEEHH----HHHHHHHHCCCCHHH
T ss_conf             9898855345362554688788887268978792466678755872852358894255041----100033030312466


Q ss_pred             ---CCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHC-----------C-CCCC
Q ss_conf             ---676502467999999987410786446873899985311027852235667777987625-----------9-5022
Q gi|254780784|r  392 ---GAPSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDA-----------G-VPIS  456 (699)
Q Consensus       392 ---~~~~RREiGHg~la~ral~~~~P~~~~~p~tirv~~evl~sngsssma~vc~~slal~da-----------g-vp~~  456 (699)
T Consensus        77 a~~GK~~GRTqEIQRLIGRaLRavvDl~aLGErTI~iDCDVlQADGGTRTAsITGAfVAL~dAi~~L~~~~~~~~~~P~~  156 (237)
T TIGR01966        77 AAKGKQSGRTQEIQRLIGRALRAVVDLEALGERTIWIDCDVLQADGGTRTASITGAFVALADAIKKLQKRGILKESEPIR  156 (237)
T ss_pred             HHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCEEECCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf             86178787505677788889887734623485027985334338876124678889999999999998578623468711


Q ss_pred             CCCCEEEEEEEEECCEEEEEEECCCCCCCCCCCCEEEEECCCC-CEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5412133200440882899863144220136551001005565-124432453655688999999999999999999999
Q gi|254780784|r  457 KPVAGIAMGLVKDGDDFIILSDISGDEDHLGHMDFKVAGTDSG-ITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEM  535 (699)
Q Consensus       457 ~~VaGiamGLi~~~~~~~iLtDI~G~ED~~GdMDFKvaGT~~G-iTa~QmDiK~~gi~~~il~~al~~A~~gr~~il~~m  535 (699)
T Consensus       157 ~~VAAVSVGiv---~g~~~L-DL~Y~EDs~A~vD~NvVmT~~G~fvEvQGTaE~~pFsr~EL~~LL~LA~~Gi~eL~~~Q  232 (237)
T TIGR01966       157 DFVAAVSVGIV---DGEPVL-DLDYEEDSAADVDMNVVMTGSGGFVEVQGTAEEEPFSRDELNELLDLAEKGIRELIELQ  232 (237)
T ss_pred             CCCCEEEEEEE---CCEEEE-CCCCCCCCCCCCCCEEEECCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             05243898876---680676-35885556463352058857876588870578897018999999999888899999999


Q ss_pred             HHCCC
Q ss_conf             84356
Q gi|254780784|r  536 SKVLS  540 (699)
Q Consensus       536 ~~~~~  540 (699)
T Consensus       233 k~aL~  237 (237)
T TIGR01966       233 KQALG  237 (237)
T ss_pred             HHHCC
T ss_conf             99719