HHsearch alignment for GI: 254780277 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=99.78  E-value=1.5e-18  Score=153.89  Aligned_cols=172  Identities=17%  Similarity=0.251  Sum_probs=138.7

Q ss_pred             CCCEEECCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCC
Q ss_conf             65035479999999999998668523233222433110012442010257766544345502313744333456500178
Q gi|254780277|r  366 DSYTKIVNTKDIQQWVQKLETIGSASFKIITDTMDAFHSKPIAIAISTLDQKDDTSFKVETIFIDLSVHTSQDSTGKNTL  445 (976)
Q Consensus       366 ~~y~~I~~~~~L~~li~~L~~~~~ia~DtETt~ld~~~~~ivGisls~~~~~~~~~~~~~~~yip~~~~~~~d~~~~~~~  445 (976)
T Consensus         3 ~p~~~Idt~~~L~~~~~~L~~~~~ialDtE~~~~~~~~~~l~LiQiat~~~---------~yliD~l~------------   61 (192)
T cd06147           3 TPLTFVDTEEKLEELVEKLKNCKEIAVDLEHHSYRSYLGFTCLMQISTREE---------DYIVDTLK------------   61 (192)
T ss_pred             CCEEEECCHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCEEEEEEEECCCC---------CEEEEECC------------
T ss_conf             873998899999999999826996999797378856998279999950998---------87987434------------


Q ss_pred             HHHHHHHHHHHHCCCCCHHHHCCCCHHHHHHHH-CCCCCCCCCCHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCCCCCCC
Q ss_conf             899997444420222100110032123788986-1886664210023455431687667724667762244422335654
Q gi|254780277|r  446 TKEILSYLKKFFENEHFLKIGHNIKYDKLVLHR-YGISMRGFEDIMLMSYVLDSGRSSHDIASIAQKWLSYTRKEILKSR  524 (976)
Q Consensus       446 ~~evl~~L~~lle~~~i~kIgHN~KfD~~~L~~-~GI~l~~i~DTmlaayLLdp~~~~~~L~~la~~yL~~~~~e~~~~~  524 (976)
T Consensus        62 l~~~~~~L~~ll~~~~I~KV~H~~~~Dl~~L~~~~gi~~~n~fDT~iaa~~l~~~--~~sL~~Lv~~~lg~~l~K---~~  136 (192)
T cd06147          62 LRDDMHILNEVFTDPNILKVFHGADSDIIWLQRDFGLYVVNLFDTGQAARVLNLP--RHSLAYLLQKYCNVDADK---KY  136 (192)
T ss_pred             CCCCHHHHHHHHCCCCEEEEEECHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCC--CHHHHHHHHHHHCCCCCC---CC
T ss_conf             3003799999975988379985578779999998589876604289999984888--111999999993958873---23


Q ss_pred             CCCCCCHHHC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             3222100000-012333322211111245677632221000
Q gi|254780277|r  525 KSSIPIDKIS-DSQVQEHAIENSNVILQLWLLLRPKLIVEK  564 (976)
Q Consensus       525 k~~~~~~~i~-~e~~~~Yaa~Da~~t~~L~~~l~~~L~~~~  564 (976)
T Consensus       137 -q~SdW~~RPLs~~Ql~YAA~Dv~~Ll~ly~~L~~~L~e~~  176 (192)
T cd06147         137 -QLADWRIRPLPEEMIKYAREDTHYLLYIYDRLRNELLERA  176 (192)
T ss_pred             -EECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             -1143799989999999999999999999999999999842