HHsearch alignment for GI: 254780818 and conserved domain: cd06147

>cd06147 Rrp6p_like_exo Yeast Rrp6p and its human homolog, the Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.
Probab=98.32  E-value=1.9e-06  Score=60.23  Aligned_cols=131  Identities=18%  Similarity=0.210  Sum_probs=82.4

Q ss_pred             CCCEEEEECCCCCCCCCCCE--EEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHH
Q ss_conf             77589998467888888888--9999999999998803137989858882288657242021012322485210023447
Q gi|254780818|r    6 KMRKIVFDIETTGLDSKNDR--IIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEF   83 (245)
Q Consensus         6 ~mr~iv~D~ETTGl~~~~d~--Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f   83 (245)
T Consensus        23 ~~~~ialDtE~~~~~~~~~~l~LiQiat---~~-----~~y--liD~l--~l~---------------------~~~~~L   69 (192)
T cd06147          23 NCKEIAVDLEHHSYRSYLGFTCLMQIST---RE-----EDY--IVDTL--KLR---------------------DDMHIL   69 (192)
T ss_pred             CCCEEEEECCCCCCCCCCCEEEEEEEEC---CC-----CCE--EEEEC--CCC---------------------CCHHHH
T ss_conf             6996999797378856998279999950---99-----887--98743--430---------------------037999


Q ss_pred             HHHHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCCCCHHCCCHHCCCCCCCCCCCCHHHHHHH-HCCCCCC--------
Q ss_conf             7753002320231023224311210000011222210000110000000177642223789997-1875455--------
Q gi|254780818|r   84 WDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKR-YGITISH--------  154 (245)
Q Consensus        84 ~~fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~l~~~-~~i~~~~--------  154 (245)
T Consensus        70 ~~ll~~~~I~KV~H~~~~Dl~~L~~~---~gi~---~~n~fDT~iaa~~l~-~~~~sL~~Lv~~~lg~~l~K~~q~SdW~  142 (192)
T cd06147          70 NEVFTDPNILKVFHGADSDIIWLQRD---FGLY---VVNLFDTGQAARVLN-LPRHSLAYLLQKYCNVDADKKYQLADWR  142 (192)
T ss_pred             HHHHCCCCEEEEEECHHHHHHHHHHH---HCCC---CCCCHHHHHHHHHHC-CCCHHHHHHHHHHHCCCCCCCCEECCCC
T ss_conf             99975988379985578779999998---5898---766042899999848-8811199999999395887323114379


Q ss_pred             ------CCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             ------5666402699999999999973
Q gi|254780818|r  155 ------RSKHGALLDSHLLSDVYIKMMV  176 (245)
Q Consensus       155 ------r~~H~Al~Da~~~a~v~~~ll~  176 (245)
T Consensus       143 ~RPLs~~Ql~YAA~Dv~~Ll~ly~~L~~  170 (192)
T cd06147         143 IRPLPEEMIKYAREDTHYLLYIYDRLRN  170 (192)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9989999999999999999999999999