HHsearch alignment for GI: 254780784 and conserved domain: TIGR02065

>TIGR02065 ECX1 exosome complex exonuclease 1; InterPro: IPR011807 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function. An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) , as well as in archaeal and eukaryotic RNA exosomes , , the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber . Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel , . This entry represents a family of archaeal proteins that are orthologous to the eukaryotic exosome protein Rrp41. It is somewhat more distantly related to the bacterial protein ribonuclease PH. An exosome-like complex has been demonstrated experimentally for the Archaea in Sulfolobus solfataricus, so members of this family are designated exosome complex exonuclease 1, after usage in SwissProt .; GO: 0016896 exoribonuclease activity producing 5'-phosphomonoesters, 0000178 exosome (RNase complex).
Probab=99.78  E-value=7.3e-18  Score=163.98  Aligned_cols=200  Identities=27%  Similarity=0.429  Sum_probs=176.1

Q ss_pred             EEEEEEECEECCCCCCEEEEEECCCEEEEEEEECCCCCCCCCCCC----CEEEEECCCCCC-CCCCCCCCCCCCCCCHHH
Q ss_conf             899999140045467289999789489999972788887777354----068665232013-367888735789887145
Q gi|254780784|r   14 RPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFP----LTVNYQERTYAV-GKIPGGYLRRESRPTENE   88 (699)
Q Consensus        14 r~i~~ETGklArqA~GsV~v~~G~T~VLaTv~~~~~~~~~~dFfP----LtVdY~Ek~yAa-GkIPGgF~kREgrpsd~E   88 (699)
T Consensus        19 Rp~KI~~GvL~r-ADGSA~~E~G~tki~aAVYGPrE~hpRh~~~PDRAV~R~RY~MAPFSvkDE-----RK~Pg-PdRR~   91 (231)
T TIGR02065        19 RPVKIEAGVLKR-ADGSAYLEFGATKIVAAVYGPREAHPRHLQLPDRAVLRVRYNMAPFSVKDE-----RKRPG-PDRRE   91 (231)
T ss_pred             CCEEEEEECCCC-CCCHHHHCCCCCEEEEEEECCCCCCCCCCCCCCCEEEEEEECCCCCCCCCC-----CCCCC-CCCCE
T ss_conf             201001311112-760010113797999986377667775457888357760013898874346-----78722-29441


Q ss_pred             HHHHHHHHCCCCC-CCCCCCC-CCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCEEECCC
Q ss_conf             3111123212677-6746886-8837899998218888778999999999987326882354112355204773243685
Q gi|254780784|r   89 ILISRMIDRSIRP-LFSKCYK-NETQVIINVMQHDLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYVLNPR  166 (699)
Q Consensus        89 iL~sRlIDR~lRP-LFPkgf~-~evQIv~~VLS~D~~~dpdvlAi~aASaAL~ISdIPf~GPVaaVRVG~idge~ViNPt  166 (699)
T Consensus        92 iEiSKv~~EALepai~~E~fPRt~IDVF~EvLQADaGTR--~AgltAASlALADAGIpMRDLV~gvavGKv~G~vVLDl~  169 (231)
T TIGR02065        92 IEISKVIREALEPAILLEQFPRTAIDVFVEVLQADAGTR--CAGLTAASLALADAGIPMRDLVVGVAVGKVDGVVVLDLS  169 (231)
T ss_pred             EHHHHHHHHHCCCEEEEECCCCCCCEEEEEEEECCCCHH--HHHHHHHHHHHHHCCCHHHHHHHEEEEEEECCEEEECCC
T ss_conf             215668888513101322388950105789985276504--788999999998479402422000034556788898366


Q ss_pred             CCC-CC--CCCEEEEEECCCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             000-22--2101355305443233312444324899998875316889999999999999
Q gi|254780784|r  167 LDE-DQ--GSLDLFVSGTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAK  223 (699)
Q Consensus       167 ~ee-~e--sdLDLvVAGT~d~IlMIE~~A~EVsEe~mleAI~~Ahe~Ik~iI~~Q~eL~~  223 (699)
T Consensus       170 ~~ED~yGEAD~P~A~mP~~~~iTLLQldG~-~T~dEF~~A~~lA~~g~~~v~~~~r~ALk  228 (231)
T TIGR02065       170 ELEDMYGEADVPLAIMPKLGEITLLQLDGD-LTPDEFRQALDLAVKGIKRVYEIQREALK  228 (231)
T ss_pred             CCCCCCCCCCCHHHHCCCCCCEEEEEECCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             124675765656651589982689974798-68678999999999998899999999864