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