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