RPS-BLAST 2.2.22 [Sep-27-2009]

Database: pdb70 
           24,244 sequences; 5,693,230 total letters

Searching..................................................done

Query= gi|254780630|ref|YP_003065043.1| ribonuclease PH [Candidatus
Liberibacter asiaticus str. psy62]
         (242 letters)



>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide
           transferase, ATP-GTP diphosphotransferase RNA
           processing, RNA degradation; 2.5A {Streptomyces
           antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4
           d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A
          Length = 757

 Score =  201 bits (514), Expect = 8e-53
 Identities = 43/250 (17%), Positives = 82/250 (32%), Gaps = 30/250 (12%)

Query: 2   RLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATL----EEKVPMWIRNTKHG 57
           R+ GR    +R ++          GS L + G+T +L   TL     E+    +      
Sbjct: 356 RIDGRGVTDIRTLAAEVEAIPRVHGSALFERGETQILGVTTLNMLRMEQQLDTLSPVTRK 415

Query: 58  WITAEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCD 117
                Y   P S G   +     G    R      +  RA+  V+         I    +
Sbjct: 416 RYMHNYNFPPYSVGETGRV----GSPKRREIGHGALAERAIVPVLPTREEFPYAIRQVSE 471

Query: 118 VIQADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLCGY----- 172
            + ++G T   ++  + ++L +    +             K  VA I+ G++        
Sbjct: 472 ALGSNGSTSMGSVCASTMSLLNAGVPL-------------KAPVAGIAMGLISQEINGET 518

Query: 173 ---PIVDLDYGEDSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNLAKDRIAD 229
               + D+   ED+  D+D     T    +  +Q   +          A L  A+D    
Sbjct: 519 HYVALTDILGAEDAFGDMDFKVAGTKEF-VTALQLDTKLDGIPASVLAAALKQARDARLH 577

Query: 230 LIKLQKDVIS 239
           ++ +  + I 
Sbjct: 578 ILDVMMEAID 587



 Score =  117 bits (294), Expect = 3e-27
 Identities = 47/249 (18%), Positives = 83/249 (33%), Gaps = 47/249 (18%)

Query: 12  REISL-TRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHGWITAEYGMLPRST 70
           R I   T R+++ A GS +    D  ++ +AT   K P          +T +      + 
Sbjct: 37  RTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNPK--DQLDFFPLTVDVEERMYAA 94

Query: 71  G----NRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDVIQADGGTR 126
           G    +  +RE   GR    +    R+I R LR           Q++    ++  +    
Sbjct: 95  GKIPGSFFRRE---GRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVV--ATIMALNPDHL 149

Query: 127 T--AAITGAWVALHDCLQHMEDCSNKFQLSQV-LKGHVAAISCGMLCGYPIV-------- 175
               AI  A  +                L+ +   G +  +   ++ G  +         
Sbjct: 150 YDVVAINAASASTQ--------------LAGLPFSGPIGGVRVALIRGQWVAFPTHTELE 195

Query: 176 ----DLDYGEDSTIDVDANFVMTDSG----HIVEVQGSAERATFSQDHFFAMLNLAKDRI 227
               D+        D D   +M ++      I  V+  AE    +++   A L+ AK  I
Sbjct: 196 DAVFDMVVAGRVLEDGDVAIMMVEAEATEKTIQLVKDGAE--APTEEVVAAGLDAAKPFI 253

Query: 228 ADLIKLQKD 236
             L K Q D
Sbjct: 254 KVLCKAQAD 262


>3dd6_A Ribonuclease PH; exoribonuclease, tRNA maturation, RNAse PH.,
           transferase; 1.70A {Bacillus anthracis}
          Length = 255

 Score =  194 bits (494), Expect = 1e-50
 Identities = 112/241 (46%), Positives = 161/241 (66%), Gaps = 3/241 (1%)

Query: 1   MRLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHGWIT 60
           MR+ GR++ ++R I +     K+ EGS L++ GDT ++ +AT+EE+VP ++R    GW+T
Sbjct: 11  MRVDGREKTELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATIEERVPPFMRGEGKGWVT 70

Query: 61  AEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDVIQ 120
           AEY M+PR+T  R  RE+  G+  GR+ EIQR+IGRALR+VVDL ALG R + IDCDVIQ
Sbjct: 71  AEYAMIPRATEQRTIRESSKGKVTGRTMEIQRLIGRALRAVVDLEALGERTVWIDCDVIQ 130

Query: 121 ADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLCGYPIV-DLDY 179
           ADGGTRTA+ITGA+VA+    + +       ++   +K ++AA S G++    +V DL+Y
Sbjct: 131 ADGGTRTASITGAYVAMVLAFEKLLQAEKVSKI--PVKDYLAATSVGIVEEQGVVLDLNY 188

Query: 180 GEDSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNLAKDRIADLIKLQKDVIS 239
            EDS  DVD N +MT  G  VEVQG+ E ATFS+     +L+ A+  I  LI +QK+ + 
Sbjct: 189 AEDSKADVDMNVIMTGKGQFVEVQGTGEEATFSRAQLNELLDAAEQGIFQLIDIQKEALG 248

Query: 240 N 240
           +
Sbjct: 249 D 249


>3gme_A Polyribonucleotide nucleotidyltransferase; protein-RNA complex,
           cytoplasm, nucleotidyltransferase, RNA- binding,
           transferase, hydrolase; 2.40A {Escherichia coli E24377A}
           PDB: 3gll_A 3gcm_A 3h1c_A 3cdj_A
          Length = 549

 Score =  188 bits (478), Expect = 1e-48
 Identities = 49/247 (19%), Positives = 92/247 (37%), Gaps = 26/247 (10%)

Query: 1   MRLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVP----MWIRNTKH 56
            R+ GR+++ +R + +   V     GS L   G+T  L TATL           +   + 
Sbjct: 314 PRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGERT 373

Query: 57  GWITAEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDC 116
                 Y   P S G         G    R     R+  R + +V+         + +  
Sbjct: 374 DTFLFHYNFPPYSVGETGMV----GSPKRREIGHGRLAKRGVLAVMPDMDKFPYTVRVVS 429

Query: 117 DVIQADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLC----GY 172
           ++ +++G +  A++ GA +AL D    +             K  VA I+ G++       
Sbjct: 430 EITESNGSSSMASVCGASLALMDAGVPI-------------KAAVAGIAMGLVKEGDNYV 476

Query: 173 PIVDLDYGEDSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNLAKDRIADLIK 232
            + D+   ED   D+D     +  G I  +Q   +    +++     LN AK     ++ 
Sbjct: 477 VLSDILGDEDHLGDMDFKVAGSRDG-ISALQMDIKIEGITKEIMQVALNQAKGARLHILG 535

Query: 233 LQKDVIS 239
           + +  I+
Sbjct: 536 VMEQAIN 542



 Score = 46.0 bits (109), Expect = 8e-06
 Identities = 45/245 (18%), Positives = 86/245 (35%), Gaps = 53/245 (21%)

Query: 12  REISL-TRRVSKYAEGSCLVKFGDTHLLTTATLEEKV-------PMWIRNTKHGWITAEY 63
             ++L T  +++ A  + +V   DT +  T   ++K        P+          T  Y
Sbjct: 14  HTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPL----------TVNY 63

Query: 64  -------GMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDC 116
                  G +P   G+  +RE   GR       I R+I R +R +     +   Q+I   
Sbjct: 64  QERTYAAGRIP---GSFFRRE---GRPSEGETLIARLIDRPIRPLFPEGFVNEVQVI--A 115

Query: 117 DVIQADGG--TRTAAITGAWVALHDCLQHMEDCSNKFQLSQV-LKGHVAAISCGMLCGYP 173
            V+  +        A+ GA  AL               LS +   G + A   G +    
Sbjct: 116 TVVSVNPQVNPDIVAMIGASAALS--------------LSGIPFNGPIGAARVGYINDQY 161

Query: 174 IVDLDYGEDSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNLAKDRIADLIKL 233
           +++    E     +D   V      ++ V+  AE    S+D     +    ++   +I+ 
Sbjct: 162 VLNPTQDELKESKLDL-VVAGTEAAVLMVESEAE--LLSEDQMLGAVVFGHEQQQVVIQN 218

Query: 234 QKDVI 238
             +++
Sbjct: 219 INELV 223


>1oys_A Ribonuclease PH; transferase, tRNA processing; 2.40A {Bacillus
           subtilis} SCOP: d.14.1.4 d.101.1.1 PDB: 1oyp_A 1oyr_A
          Length = 245

 Score =  188 bits (477), Expect = 1e-48
 Identities = 103/239 (43%), Positives = 152/239 (63%), Gaps = 1/239 (0%)

Query: 1   MRLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHGWIT 60
           MR  GRQ +++R I+       + EGS L+  G+T ++  A++E++VP ++R    GWIT
Sbjct: 1   MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWIT 60

Query: 61  AEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDVIQ 120
           AEY MLP++T  +  +E+  G+  GR+ EIQR+IGRALR+VVDL  LG R I IDCDVIQ
Sbjct: 61  AEYSMLPQATNQQTIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQ 120

Query: 121 ADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLCGYPIVDLDYG 180
           ADGGTRTA+ITGA++A+   +  +   +   + + +     A           ++DL+Y 
Sbjct: 121 ADGGTRTASITGAFLAMAIAIGKLIK-AGTIKTNPITDFLAAISVGIDKEQGILLDLNYE 179

Query: 181 EDSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNLAKDRIADLIKLQKDVIS 239
           EDS+ +VD N +MT SG  VE+QG+ E ATFS++    +L LA+  I +LI  QK+V+ 
Sbjct: 180 EDSSAEVDMNVIMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQELIDKQKEVLG 238


>1r6l_A Ribonuclease PH; beta-alpha-beta-alpha fold, hexamer, phosphate
           bound, transferase; HET: NHE; 1.90A {Pseudomonas
           aeruginosa} SCOP: d.14.1.4 d.101.1.1 PDB: 1r6m_A
          Length = 239

 Score =  188 bits (477), Expect = 1e-48
 Identities = 124/238 (52%), Positives = 163/238 (68%), Gaps = 2/238 (0%)

Query: 2   RLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHGWITA 61
           R SGR  +Q+R I +TR  +K+AEGS LV+FGDT ++ T + E  VP +++    GW+TA
Sbjct: 3   RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWLTA 62

Query: 62  EYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDVIQA 121
           EYGMLPRSTG R +REA  G+QGGR+ EIQR+IGR+LR+ +DLS LG   + IDCDVIQA
Sbjct: 63  EYGMLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQA 122

Query: 122 DGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLCGYPIVDLDYGE 181
           DGGTRTA+ITGA VAL D L  ++           LK  VAA+S G+  G P++DLDY E
Sbjct: 123 DGGTRTASITGATVALIDALAVLKKRGALKGN--PLKQMVAAVSVGIYQGVPVLDLDYLE 180

Query: 182 DSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNLAKDRIADLIKLQKDVIS 239
           DS  + D N VMTD+G  +EVQG+AE A F      AML LA+  + +L +LQ+  ++
Sbjct: 181 DSAAETDLNVVMTDAGGFIEVQGTAEGAPFRPAELNAMLELAQQGMQELFELQRAALA 238


>2nn6_A Polymyositis/scleroderma autoantigen 1; RNA, exosome, PM/SCL,
           phosphorolytic, hydrolase/transferase complex; 3.35A
           {Homo sapiens} SCOP: d.14.1.4 d.101.1.1
          Length = 358

 Score =  185 bits (471), Expect = 7e-48
 Identities = 51/261 (19%), Positives = 91/261 (34%), Gaps = 30/261 (11%)

Query: 1   MRLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHGWIT 60
            RL GRQ    R I ++        G C+V+ G T +L   + E   P   R T+ G + 
Sbjct: 39  KRLDGRQTYDYRNIRISFGT---DYGCCIVELGKTRVLGQVSCELVSPKLNRATE-GILF 94

Query: 61  AEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRS--------VVDLSALGSRQI 112
               +   +           GRQ     ++ R++ R LR+        +  ++     QI
Sbjct: 95  FNLELSQMAA-----PAFEPGRQSDLLVKLNRLMERCLRNSKCIDTESLCVVAGEKVWQI 149

Query: 113 IIDCDVIQADGGTRTAAITGAWVALHDCLQHM----------EDCSNKFQLSQVLKGHVA 162
            +D  ++  DG    AA   A VAL    +                 +  +   +     
Sbjct: 150 RVDLHLLNHDGNIIDAASIAAIVALCHFRRPDVSVQGDEVTLYTPEERDPVPLSIHHMPI 209

Query: 163 AISCGMLC--GYPIVDLDYGEDSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAML 220
            +S        Y +VD +  E+  +D      M     I  +Q S       +D      
Sbjct: 210 CVSFAFFQQGTYLLVDPNEREERVMDGLLVIAMNKHREICTIQSS-GGIMLLKDQVLRCS 268

Query: 221 NLAKDRIADLIKLQKDVISNE 241
            +A  ++A++ +L    + N+
Sbjct: 269 KIAGVKVAEITELILKALEND 289


>3m7n_D Probable exosome complex exonuclease 1; exosome, RNA, exonuclease,
           hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus
           fulgidus} PDB: 3m85_D 2ba0_F 2ba1_E
          Length = 258

 Score =  173 bits (439), Expect = 4e-44
 Identities = 58/242 (23%), Positives = 102/242 (42%), Gaps = 20/242 (8%)

Query: 1   MRLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKV-PMWIRNTKHGWI 59
           +RL GR+ +++R I +   V K A+GSC ++ G   ++       +V P  +++     I
Sbjct: 16  LRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPEHLQDPSKAII 75

Query: 60  TAEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDVI 119
              Y M P S   R +          RS EI ++   A  +V+         I I  +V+
Sbjct: 76  RYRYNMAPFSVEERKRPG-----PDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVL 130

Query: 120 QADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLCGYPIVDLDY 179
           QAD G+RTA +  A VAL D    M+               + +++ G   G  ++D   
Sbjct: 131 QADAGSRTACLNAASVALVDAGVPMKGM-------------ITSVAVGKADGQLVLDPMK 177

Query: 180 GEDSTIDVDANFV-MTDSGHIVEVQGSAERATFSQDHFFAMLNLAKDRIADLIKLQKDVI 238
            ED+  + D  F  +  +G I  +         ++D     + LAK     + ++Q++ I
Sbjct: 178 EEDNFGEADMPFAFLIRNGKIESIALLQMDGRMTRDEVKQAIELAKKGALQIYEMQREAI 237

Query: 239 SN 240
             
Sbjct: 238 LR 239


>2wnr_B Probable exosome complex exonuclease 1; phosphate binding, 3'-5'
           exoribonuclease, hydrolase; 2.65A
           {Methanothermobacterthermautotrophicus}
          Length = 240

 Score =  172 bits (436), Expect = 7e-44
 Identities = 57/240 (23%), Positives = 97/240 (40%), Gaps = 23/240 (9%)

Query: 2   RLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPM-WIRNTKHGWIT 60
           R  GR  +++R + +   + + A+GS  ++FG   +L       +  +  ++      I 
Sbjct: 17  REDGRAFDELRPLKIEAGILERADGSSYLEFGGNKILVAVYGPREAQIRKLQRPDRAVIR 76

Query: 61  AEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDVIQ 120
             Y M P S   R +          RS EI ++   ALR  + L       I +  +V++
Sbjct: 77  CRYNMAPFSVEERKRP-----GPDRRSVEISKITAEALRPALILEKFPRSVIDVFIEVLE 131

Query: 121 ADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLCGYPIVDLDYG 180
           A+GGTR A IT A VAL D    M D              V A + G +    ++DL   
Sbjct: 132 AEGGTRCAGITAASVALADAGIPMRDM-------------VVACAAGKVGDQVVLDLSEE 178

Query: 181 EDSTIDVDANFVMT-DSGHIVEVQGSAERATFSQDHFFAMLNLAKDRIADLIKLQKDVIS 239
           ED     D    +   +  I  +Q        + + F   L+LA +    + ++QK+ + 
Sbjct: 179 EDKEGQADVPVAILPRTREITLLQSDGN---LTPEEFERALDLAVEGCLRIHEVQKEALR 235


>2wnr_A Probable exosome complex exonuclease 2; phosphate binding, 3'-5'
           exoribonuclease, hydrolase; 2.65A
           {Methanothermobacterthermautotrophicus}
          Length = 271

 Score =  158 bits (400), Expect = 1e-39
 Identities = 50/254 (19%), Positives = 98/254 (38%), Gaps = 22/254 (8%)

Query: 1   MRLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHGWIT 60
            R+ GR  ++ R+IS+   V   AEGS  VK G+T ++     +   P      + G I 
Sbjct: 24  ERIDGRSLHEFRDISIETGVISKAEGSSRVKLGNTQIIVGVKPQIGEPFP-DTPEMGVIL 82

Query: 61  AEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRS--VVDLSALGS------RQI 112
               +LP ++          G    RS E+ R++ R +R   ++DL  L          +
Sbjct: 83  TNSELLPMASPTFEP-----GPPDERSVELSRVVDRCIRESRMIDLEKLCIIEGSKVWML 137

Query: 113 IIDCDVIQADGGTRTAAITGAWVALHDCLQHMED-------CSNKFQLSQVLKGHVAAIS 165
            +D  +I  DG    AA+     AL D      +        + +      +       +
Sbjct: 138 FLDLHIIDYDGNLFDAAVLATVAALLDTRIPAAEVEDGEVVINREKMQPLPVNRKALMCT 197

Query: 166 CGMLCGYPIVDLDYGEDSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNLAKD 225
              +    ++D    E+  +    +  +T+ G I  +Q   E    ++D     +++A +
Sbjct: 198 FAKIGNEIVLDPSLEEEDILTARISIGVTEEGSICAMQKGGE-GPLTRDDVLKAVSIAVE 256

Query: 226 RIADLIKLQKDVIS 239
           ++  LI+     ++
Sbjct: 257 KVPQLIEYLDKSMT 270


>1udn_A Ribonuclease PH, RNAse PH; transferase, riken structural
           genomics/proteomics initiative, RSGI, structural
           genomics; 2.30A {Aquifex aeolicus} SCOP: d.14.1.4
           d.101.1.1 PDB: 1udq_A 1uds_A 1udo_A
          Length = 255

 Score =  156 bits (395), Expect = 4e-39
 Identities = 115/239 (48%), Positives = 158/239 (66%), Gaps = 2/239 (0%)

Query: 1   MRLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHGWIT 60
           MR  GR+E+Q+R +S+ R   +Y EGSCL+ FG T ++ TA++ E VP W++    GWIT
Sbjct: 1   MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWIT 60

Query: 61  AEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDVIQ 120
           AEY MLPR+T  R  RE+V GR GGR+ EIQRMIGRA+R+ V+L+ +G R I +DCDVIQ
Sbjct: 61  AEYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQ 120

Query: 121 ADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLCGYPIVDLDYG 180
           ADGGTRTAAITGA+VA+ D +  +            +K  VAA+S G++    ++DL++ 
Sbjct: 121 ADGGTRTAAITGAFVAVADAIIKLHK--EGIIEETPIKDFVAAVSVGIVNDRILLDLNFE 178

Query: 181 EDSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNLAKDRIADLIKLQKDVIS 239
           EDS   VD N V T SG + EV    E  +F++D    ML+LA+  I +LI+LQK +  
Sbjct: 179 EDSAAQVDMNVVGTGSGRLSEVHTMGEEYSFTKDELIKMLDLAQKGINELIELQKKLYV 237


>3m7n_G Probable exosome complex exonuclease 2; exosome, RNA, exonuclease,
           hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus
           fulgidus} PDB: 2ba1_H 2ba0_I 3m85_G
          Length = 259

 Score =  155 bits (391), Expect = 1e-38
 Identities = 50/245 (20%), Positives = 95/245 (38%), Gaps = 15/245 (6%)

Query: 1   MRLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHGWIT 60
            R+ GR  ++ R++ +   V + AEGS LVK GDT ++    ++   P      + G I 
Sbjct: 22  ERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPGEPYPDTPDR-GVII 80

Query: 61  AEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRS--VVDLSAL------GSRQI 112
               ++P ++          G     S E+ R++ R +R    VDLS L          +
Sbjct: 81  VNAELVPLASPTFE-----PGPPDENSIELARVVDRGIRESEAVDLSKLVIEEGEKVWIV 135

Query: 113 IIDCDVIQADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLCGY 172
            +D   +  DG    A+   A  AL +     E           ++    +++  ++   
Sbjct: 136 FVDIHALDDDGNLLDASALAAIAALMNTKVPAERFDLGEDYLLPVRDLPVSVTSLIVGNK 195

Query: 173 PIVDLDYGEDSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNLAKDRIADLIK 232
            +VD    E S  D           ++V +Q S       +  F  +L+++ +    L +
Sbjct: 196 YLVDPSREEMSVGDTTLTITTDKDDNVVAMQKSGG-YLLDEKLFDELLDVSINCARKLRE 254

Query: 233 LQKDV 237
             K++
Sbjct: 255 KFKEI 259


>3hkm_A OS03G0854200 protein; RNAse PH domain, phosphorylase; 1.98A {Oryza
           sativa japonica group}
          Length = 246

 Score =  154 bits (390), Expect = 2e-38
 Identities = 49/256 (19%), Positives = 84/256 (32%), Gaps = 41/256 (16%)

Query: 2   RLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHGWITA 61
           R  GR  NQ+R  S TR     A GS     GDT +L         P   +       + 
Sbjct: 5   RADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVY--GPKPGTRKGENPEKASI 62

Query: 62  EYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDVIQA 121
           E    P            +G+ G + +E +  + R L+S+  L+   +    +   V+  
Sbjct: 63  EVVWKPM-----------TGQIGKQEKEYEMTLKRTLQSICLLTVHPNTTTSVILQVVGN 111

Query: 122 DGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLC-GYPIVDLDYG 180
           DG     AI     AL                   LK    AI CG+L  G  I+D +  
Sbjct: 112 DGSLLPCAINACCAALVFA-------------GIPLKHLAVAIGCGVLEDGEVILDTNKA 158

Query: 181 EDSTIDVDANFVMTDSGHIVEVQGSAE--------------RATFSQDHFFAMLNLAKDR 226
           E+  +   A+ V  +S      +   +                  S++ +F+ +      
Sbjct: 159 EEQQLKSFAHLVFPNSRKSASSKEPNQKEEDSERGLITSITHGVMSEEDYFSCIERGLAA 218

Query: 227 IADLIKLQKDVISNEV 242
            + +    +  +  + 
Sbjct: 219 SSRISDFMRTTLQKQA 234


>3krn_A Protein C14A4.5, confirmed by transcript evidence; RNAse PH domain,
           homodimer, exosome, cell-death-related DNAse; 3.92A
           {Caenorhabditis elegans}
          Length = 222

 Score =  152 bits (384), Expect = 9e-38
 Identities = 38/235 (16%), Positives = 69/235 (29%), Gaps = 29/235 (12%)

Query: 9   NQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHGWITAEYGMLPR 68
            ++RE+       K A+GS     G T +  + +    V     + +   +   Y     
Sbjct: 3   GRLREMRCELSFLKNADGSACFSQGATCIWASCSGPGDVHASKASDEAMTLDISYRA--- 59

Query: 69  STGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDVIQADGGTRTA 128
                            +   +  +I   L + ++L       I +    IQ DG     
Sbjct: 60  ------------NCGDNKFNVLNNIIHSTLSNAINLELFPHTTISVTVHGIQDDGSMGAV 107

Query: 129 AITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLCGYPIVDLDYGEDSTIDVD 188
           AI GA  AL D     E                  +    +    I+D    +++     
Sbjct: 108 AINGACFALLDNGMPFETVFC-------------GVLIVRVKDELIIDPTAKQEAASTGR 154

Query: 189 ANF-VMTDSGHIVEVQGSAERATFSQDHFFAMLNLAKDRIADLIKLQKDVISNEV 242
             F V   S    EV        +      A  +LA+   + +    K V+  ++
Sbjct: 155 VLFSVCKGSDGHPEVCAMDAIGHWDFIQLEAAWSLAQPSASAIFDFYKTVMKRKL 209


>3b4t_A Ribonuclease PH; RNAse, tRNA nucleotidyltransferase, RPHA,
           structural genomics, TBSGC; 2.10A {Mycobacterium
           tuberculosis H37RV}
          Length = 262

 Score =  150 bits (379), Expect = 3e-37
 Identities = 110/238 (46%), Positives = 158/238 (66%), Gaps = 1/238 (0%)

Query: 2   RLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHGWITA 61
           R  GR ++++R + +TR  ++   GS L++FG T +L TA++ E VP W + T  GW+TA
Sbjct: 7   REDGRLDHELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGVPRWRKATGLGWLTA 66

Query: 62  EYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDVIQA 121
           EY MLP +T +R  RE+V GR  GR+QEI R+IGR+LR+ +DL+ALG   I IDCDV+QA
Sbjct: 67  EYAMLPSATHSRSDRESVRGRLSGRTQEISRLIGRSLRACIDLAALGENTIAIDCDVLQA 126

Query: 122 DGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLCGYPIVDLDYGE 181
           DGGTRTAAITGA+VAL D + ++   + K    + L   +AA+S G++ G   VDL Y E
Sbjct: 127 DGGTRTAAITGAYVALADAVTYLS-AAGKLSDPRPLSCAIAAVSVGVVDGRIRVDLPYEE 185

Query: 182 DSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNLAKDRIADLIKLQKDVIS 239
           DS  +VD N V TD+G +VE+QG+ E ATF++     +L++A      L   Q+D ++
Sbjct: 186 DSRAEVDMNVVATDTGTLVEIQGTGEGATFARSTLDKLLDMALGACDTLFAAQRDALA 243


>2wp8_A Exosome complex component RRP45; nucleus, hydrolase, cytoplasm,
           RNA-binding, RNA binding, mitochondrion, rRNA
           processing; 3.00A {Saccharomyces cerevisiae}
          Length = 305

 Score =  146 bits (369), Expect = 4e-36
 Identities = 36/269 (13%), Positives = 73/269 (27%), Gaps = 33/269 (12%)

Query: 1   MRLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHGWIT 60
            RL GR  +Q R++ +T        G   VK G+T +    + +   P   R  +     
Sbjct: 23  YRLDGRSFDQFRDVEITF---GKEFGDVSVKMGNTKVHCRISCQIAQPYEDRPFEG-LFV 78

Query: 61  AEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALR----SVVDLSALGSRQIIIDC 116
               + P +             +   S+ I++ + R+       +  ++      +  D 
Sbjct: 79  ISTEISPMAGSQFENGNITGEDEVLCSRIIEKSVRRSGALDVEGLCIVAGSKCWAVRADV 138

Query: 117 DVIQADGGTRTAAITGAWVALHDC------------LQHMEDCSNKFQLS---------- 154
             +  DGG   A+       L               + H  +      L           
Sbjct: 139 HFLDCDGGFIDASCIAVMAGLMHFKKPDITVHGEQIIVHPVNEREPVPLGILHIPICVTF 198

Query: 155 --QVLKGHVAAISCGMLCGYPIVDLDYGEDSTIDVDANFVMTDSGHIVEVQGSAERATFS 212
                +     I         I+D    E+   D      +  +  +V+V   A      
Sbjct: 199 SFFNPQDTEENIKGETNSEISIIDATLKEELLRDGVLTVTLNKNREVVQVSK-AGGLPMD 257

Query: 213 QDHFFAMLNLAKDRIADLIKLQKDVISNE 241
                   + A   I  +      ++  +
Sbjct: 258 ALTLMKCCHEAYSIIEKITDQILQLLKED 286


>2nn6_E Exosome complex exonuclease RRP42; RNA, exosome, PM/SCL,
           phosphorolytic, hydrolase/transferase complex; 3.35A
           {Homo sapiens} SCOP: d.14.1.4 d.101.1.1
          Length = 305

 Score =  138 bits (347), Expect = 1e-33
 Identities = 39/263 (14%), Positives = 75/263 (28%), Gaps = 29/263 (11%)

Query: 1   MRLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHGWIT 60
           +R+ GR     R + +   V     GS  VK G T +L      E     +     G++ 
Sbjct: 36  LRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKA-EMGTPKLEKPNEGYLE 94

Query: 61  AEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRS--VVDLSAL------GSRQI 112
                   +T     R            EI   + R   +   VDL  L          +
Sbjct: 95  FFVDCSASATPEFEGR-----GGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVL 149

Query: 113 IIDCDVIQADGGTRTAAITGAWVALHDC--------------LQHMEDCSNKFQLSQVLK 158
            +D  +++  G    A       AL +                           +   ++
Sbjct: 150 YVDVLLLECGGNLFDAISIAVKAALFNTRIPRVRVLEDEEGSKDIELSDDPYDCIRLSVE 209

Query: 159 GHVAAISCGMLCGYPIVDLDYGEDSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFA 218
                ++   +    +VD    E++         +T  G +  ++    + +   +  F 
Sbjct: 210 NVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTCMR-KVGKGSLDPESIFE 268

Query: 219 MLNLAKDRIADLIKLQKDVISNE 241
           M+   K     L    + V+  E
Sbjct: 269 MMETGKRVGKVLHASLQSVVHKE 291


>2po1_B Probable exosome complex exonuclease 2; RNAse PH,
           hydrolase/hydrolase/RNA complex; 1.94A {Pyrococcus
           abyssi} PDB: 2po0_B* 2pnz_B 2po2_B*
          Length = 277

 Score =  136 bits (343), Expect = 4e-33
 Identities = 46/248 (18%), Positives = 80/248 (32%), Gaps = 11/248 (4%)

Query: 2   RLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHGWITA 61
           R+  R     R I +   V + AEGS LVK G T +L         P           T 
Sbjct: 27  RIDDRGFEDYRPIEIEVGVIEKAEGSALVKLGSTQVLVGIKTSLGEPFPDTPNMGVMTTN 86

Query: 62  EYGMLPRSTGNRVKREAVSGRQGGR--SQEIQRMIGRALRSVVDLSALGSRQIIIDCDVI 119
              +   S             +  R   + I+      L  +V +     R + ID  V+
Sbjct: 87  VELVPLASPTFEPGPPDERAIELARVIDRGIRESKALNLEKMVIVPGKIVRVVFIDVHVL 146

Query: 120 QADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQV--------LKGHVAAISCGMLCG 171
             DG    A    A  AL +        + +    +         ++     ++   +  
Sbjct: 147 DHDGNLMDAIGIAAIAALLNARVPKVRYNEETGEVETLDETEPLPVEKIPVPVTFAKIGN 206

Query: 172 YPIVDLDYGEDSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNLAKDRIADLI 231
             +VD    E+  +D        ++GHI  VQ  +E   F  +     +  A  +  ++ 
Sbjct: 207 ILVVDPSLDEELVMDGKITITTDETGHISAVQ-KSEGGAFKLEEVMYAVETAFKKAEEIR 265

Query: 232 KLQKDVIS 239
           KL  + + 
Sbjct: 266 KLILEAVE 273


>2nn6_C Exosome complex exonuclease RRP43; RNA, exosome, PM/SCL,
           phosphorolytic, hydrolase/transferase complex; 3.35A
           {Homo sapiens} SCOP: d.14.1.4 d.101.1.1
          Length = 278

 Score =  136 bits (342), Expect = 5e-33
 Identities = 44/258 (17%), Positives = 83/258 (32%), Gaps = 25/258 (9%)

Query: 1   MRLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHGWIT 60
            R  GR+  + R  ++       A+GS LVK G+T ++     E   P      K  ++ 
Sbjct: 24  CRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPSTDAPDKG-YVV 82

Query: 61  AEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRS--------VVDLSALGSRQI 112
               + P  +         SG  G  +Q   + I   + +        +          +
Sbjct: 83  PNVDLPPLCSSRF-----RSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVL 137

Query: 113 IIDCDVIQADGGTRTAAITGAWVALHDC---------LQHMEDCSNKFQLSQVLKGHVAA 163
             D   +  DG    A       AL +             + + + K +    ++ H  A
Sbjct: 138 YCDLICLDYDGNILDACTFALLAALKNVQLPEVTINEETALAEVNLKKKSYLNIRTHPVA 197

Query: 164 ISCGMLCGYP-IVDLDYGEDSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNL 222
            S  +      IVD    E+         VM + G +  +      +  +       ++ 
Sbjct: 198 TSFAVFDDTLLIVDPTGEEEHLATGTLTIVMDEEGKLCCLHKPGG-SGLTGAKLQDCMSR 256

Query: 223 AKDRIADLIKLQKDVISN 240
           A  R  ++ KL  +VI +
Sbjct: 257 AVTRHKEVKKLMDEVIKS 274


>2nn6_F MTR3, exosome component 6; RNA, exosome, PM/SCL, phosphorolytic,
           hydrolase/transferase complex; 3.35A {Homo sapiens}
           SCOP: d.14.1.4 d.101.1.1
          Length = 272

 Score =  124 bits (311), Expect = 2e-29
 Identities = 36/255 (14%), Positives = 74/255 (29%), Gaps = 30/255 (11%)

Query: 1   MRLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTK----- 55
                R   ++R +     +   A+GS  ++ G T +L   +   +     R        
Sbjct: 26  EAPGTRDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAGAG 85

Query: 56  -------HGWITAEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALG 108
                   G +  ++   P +          +   G   +E+   +  AL   V L    
Sbjct: 86  GEAPAALRGRLLCDFRRAPFAGR-----RRRAPPGGCEERELALALQEALEPAVRLGRYP 140

Query: 109 SRQIIIDCDVIQADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGM 168
             Q+ +   +++  G    AA+T A +AL D    M D                      
Sbjct: 141 RAQLEVSALLLEDGGSALAAALTAAALALADAGVEMYDLVV----------GCGLSLAPG 190

Query: 169 LCGYPIVDLDYGEDSTIDVDANF-VMTDSGHIVEVQGSAERATFSQDHFFAMLNLAKDRI 227
                ++D    E+          +M     +  + GS E      + +   + L  +  
Sbjct: 191 PAPTWLLDPTRLEEERAAAGLTVALMPVLNQVAGLLGSGE--GGLTESWAEAVRLGLEGC 248

Query: 228 ADLIKLQKDVISNEV 242
             L  + +  +    
Sbjct: 249 QRLYPVLQQSLVRAA 263


>2ba0_I Archeal exosome RNA binding protein RRP42; RNAse PH, RNA
           degradation, exoribonuclease, S1domain, KH domain,
           archaeal; 2.70A {Archaeoglobus fulgidus} SCOP: d.14.1.4
           d.101.1.1 PDB: 2ba1_H
          Length = 259

 Score =  122 bits (307), Expect = 6e-29
 Identities = 41/240 (17%), Positives = 85/240 (35%), Gaps = 5/240 (2%)

Query: 1   MRLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHGWIT 60
            R+ GR  ++ R++ +   V + AEGS LVK GDT ++    ++     +      G I 
Sbjct: 22  ERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPG-EPYPDTPDRGVII 80

Query: 61  AEYGMLPRSTGNRVKREAVSGRQGGRS---QEIQRMIGRALRSVVDLSALGSRQIIIDCD 117
               ++P ++                    + I+      L  +V         + +D  
Sbjct: 81  VNAELVPLASPTFEPGPPDENSIELARVVDRGIRESEAVDLSKLVIEEGEKVWIVFVDIH 140

Query: 118 VIQADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLCGYPIVDL 177
            +  DG    A+   A  AL +     E           ++    +++  ++    +VD 
Sbjct: 141 ALDDDGNLLDASALAAIAALMNTKVPAERFDLGEDYLLPVRDLPVSVTSLIVGNKYLVDP 200

Query: 178 DYGEDSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNLAKDRIADLIKLQKDV 237
              E S  D           ++V +Q S       +  F  +L+++ +    L +  K++
Sbjct: 201 SREEMSVGDTTLTITTDKDDNVVAMQKSGG-YLLDEKLFDELLDVSINCARKLREKFKEI 259


>2je6_A RRP42, exosome complex exonuclease 2; nuclease, hydrolase,
           exonuclease, phosphorolytic, exoribonuclease, RNA
           degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus}
           SCOP: d.14.1.4 d.101.1.1 PDB: 2jea_A* 2jeb_A* 2br2_A
           2c37_A* 2c38_A* 2c39_A*
          Length = 277

 Score =  120 bits (301), Expect = 3e-28
 Identities = 54/250 (21%), Positives = 86/250 (34%), Gaps = 15/250 (6%)

Query: 1   MRLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHG--- 57
           +R  GR+    R +S+T   +K A+GS LVK G T +L    LE   P      +     
Sbjct: 29  IRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYEDTPNQGNLIV 88

Query: 58  -WITAEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDC 116
                         G   +      R   RS   +      L  +V         + +D 
Sbjct: 89  NVELLPLAYETFEPGPPDENAIELARVVDRSL--RDSKALDLTKLVIEPGKSVWTVWLDV 146

Query: 117 DVIQADGGTRTAAITGAWVALHDCLQHMED--------CSNKFQLSQVLKGHVAAISCGM 168
            V+   G    A    +  AL++   +  +          N+      L   V  IS   
Sbjct: 147 YVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGISVNKNEVVGKLPLNYPVVTISVAK 206

Query: 169 LCGYPIVDLDYGEDSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNLAKDRIA 228
           +  Y +VD D  E+S +D   +F  T    IV +Q S +  + S        N A+    
Sbjct: 207 VDKYLVVDPDLDEESIMDAKISFSYTPDLKIVGIQKSGK-GSMSLQDIDQAENTARSTAV 265

Query: 229 DLIKLQKDVI 238
            L++  K  +
Sbjct: 266 KLLEELKKHL 275


>2ba0_F Archeal exosome RNA binding protein RRP41; RNAse PH, RNA
           degradation, exoribonuclease, S1domain, KH domain,
           archaeal; 2.70A {Archaeoglobus fulgidus} SCOP: d.14.1.4
           d.101.1.1 PDB: 2ba1_E
          Length = 258

 Score =  119 bits (298), Expect = 6e-28
 Identities = 57/242 (23%), Positives = 94/242 (38%), Gaps = 20/242 (8%)

Query: 1   MRLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLE-EKVPMWIRNTKHGWI 59
           +RL GR+ +++R I +   V K A+GSC ++ G   ++       E  P  +++     I
Sbjct: 16  LRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPRHLQDPSKAII 75

Query: 60  TAEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDVI 119
              Y M P S   R +          RS EI ++   A  +V+         I I  +V+
Sbjct: 76  RYRYNMAPFSVEERKRPG-----PDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVL 130

Query: 120 QADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLCGYPIVDLDY 179
           QAD G+RTA +  A VAL D    M+                     G   G  ++D   
Sbjct: 131 QADAGSRTACLNAASVALVDAGVPMKGMITSVA-------------VGKADGQLVLDPMK 177

Query: 180 GEDSTIDVDANFVMTDSGH-IVEVQGSAERATFSQDHFFAMLNLAKDRIADLIKLQKDVI 238
            ED+  + D  F        I  +         ++D     + LAK     + ++Q++ I
Sbjct: 178 EEDNFGEADMPFAFLIRNGKIESIALLQMDGRMTRDEVKQAIELAKKGALQIYEMQREAI 237

Query: 239 SN 240
             
Sbjct: 238 LR 239


>2po1_A Probable exosome complex exonuclease 1; RNAse PH,
           hydrolase/hydrolase/RNA complex; 1.94A {Pyrococcus
           abyssi} PDB: 2po0_A* 2pnz_A 2po2_A*
          Length = 249

 Score =  119 bits (298), Expect = 7e-28
 Identities = 61/243 (25%), Positives = 100/243 (41%), Gaps = 23/243 (9%)

Query: 2   RLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLE-EKVPMWIRNTKHGWIT 60
           R+ GR++ ++R I +   V K A GS  +++G   ++       E  P  ++      + 
Sbjct: 17  RIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGPRELHPKHLQRPDRAILR 76

Query: 61  AEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDVIQ 120
             Y M P S   R K          RS EI ++I  AL   + L       I +  +V+Q
Sbjct: 77  VRYNMAPFSVEERKKPG-----PDRRSIEISKVIKGALEPALILEMFPRTAIDVFIEVLQ 131

Query: 121 ADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLCGYPIVDLDYG 180
           AD GTR A IT A +AL D    M D              VAA + G + G  ++DL+  
Sbjct: 132 ADAGTRVAGITAASLALADAGIPMRDL-------------VAACAAGKIEGEIVLDLNKE 178

Query: 181 EDSTIDVDANFVMTDS-GHIVEVQGSAERATFSQDHFFAMLNLAKDRIADLIKLQKDVIS 239
           ED+  + D    +      I  +Q        ++D F   + LA      + + Q++ + 
Sbjct: 179 EDNYGEADVPVAIMPLKNDITLLQMD---GYLTKDEFIEAVKLAIKGAKAVYQKQREALK 235

Query: 240 NEV 242
            + 
Sbjct: 236 EKY 238


>2wp8_B Exosome complex component SKI6; nucleus, hydrolase, cytoplasm,
           RNA-binding, RNA binding, mitochondrion, rRNA
           processing; 3.00A {Saccharomyces cerevisiae}
          Length = 246

 Score =  111 bits (279), Expect = 1e-25
 Identities = 45/241 (18%), Positives = 87/241 (36%), Gaps = 21/241 (8%)

Query: 1   MRLSGRQENQMREISLTR-RVSKYAEGSCLVKFGDTHLLTTATLE-EKVPMWIRNTKHGW 58
           +RL GR+ N++R    +       A+GS  ++ G+  ++T      E       +T    
Sbjct: 12  LRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKAL 71

Query: 59  ITAEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDV 118
           +     +   S   R K    S +   R  EIQ  + R     V L+      I I+  V
Sbjct: 72  LNVSVNINKFSKFERSKS---SHKNERRVLEIQTSLVRMFEKNVMLNIYPRTVIDIEIHV 128

Query: 119 IQADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLCGYPIVDLD 178
           ++ DGG   + I G  +AL D    M               +++ IS G+    P++D +
Sbjct: 129 LEQDGGIMGSLINGITLALIDAGISM-------------FDYISGISVGLYDTTPLLDTN 175

Query: 179 YGEDSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNLAKDRIADLIKLQKDVI 238
             E++ +       +      + +    ++     D    +L +       +  L  + +
Sbjct: 176 SLEENAMS-TVTLGVVGKSEKLSLLLVEDKIPL--DRLENVLAIGIAGAHRVRDLMDEEL 232

Query: 239 S 239
            
Sbjct: 233 R 233


>2je6_B RRP41, exosome complex exonuclease 1; nuclease, hydrolase,
           exonuclease, phosphorolytic, exoribonuclease, RNA
           degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus}
           SCOP: d.14.1.4 d.101.1.1 PDB: 2jea_B* 2jeb_B* 2br2_B
           2c37_B* 2c38_B* 2c39_B*
          Length = 250

 Score =  105 bits (261), Expect = 1e-23
 Identities = 56/241 (23%), Positives = 99/241 (41%), Gaps = 23/241 (9%)

Query: 2   RLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATL-EEKVPMWIRNTKHGWIT 60
           R  GR+ +++R I +   V K A+GS + + G+T  +      +E  P  +       + 
Sbjct: 21  RTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLR 80

Query: 61  AEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDVIQ 120
             Y M P ST  R            R  E+ ++I  AL S V +       I +  +++Q
Sbjct: 81  VRYHMTPFSTDERKNP-----APSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQ 135

Query: 121 ADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLCGYPIVDLDYG 180
           AD G+R  ++  A +AL D    M D              +A ++ G   G  I+DL+  
Sbjct: 136 ADAGSRLVSLMAASLALADAGIPMRDL-------------IAGVAVGKADGVIILDLNET 182

Query: 181 EDSTIDVDANFVMTDSGH-IVEVQGSAERATFSQDHFFAMLNLAKDRIADLIKLQKDVIS 239
           E    + D    M  S + +   Q +    + + D F    +LA   I  +  L+++ + 
Sbjct: 183 EAMWGEADMPIAMMPSLNQVTLFQLN---GSMTPDEFRQAFDLAVKGINIIYNLEREALK 239

Query: 240 N 240
           +
Sbjct: 240 S 240


>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA
           degradation, kinase, transferase; 2.60A {Escherichia
           coli} PDB: 1sro_A
          Length = 723

 Score =  104 bits (262), Expect = 1e-23
 Identities = 49/246 (19%), Positives = 92/246 (37%), Gaps = 24/246 (9%)

Query: 1   MRLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNT----KH 56
            R+ GR+++ +R + +   V     GS L   G+T  L TATL       + +     + 
Sbjct: 320 PRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGERT 379

Query: 57  GWITAEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDC 116
                 Y   P S G         G    R     R+  R + +V+         + +  
Sbjct: 380 DTFLFHYNFPPYSVGETGMV----GSPKRREIGHGRLAKRGVLAVMPDMDKFPYTVRVVS 435

Query: 117 DVIQADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLCGY--PI 174
           ++ +++G +  A++ GA +AL D                 +K  VA I+ G++      +
Sbjct: 436 EITESNGSSSMASVCGASLALMDA-------------GVPIKAAVAGIAMGLVKEGDNYV 482

Query: 175 VDLDYGEDSTIDVDANFVMTDSGH-IVEVQGSAERATFSQDHFFAMLNLAKDRIADLIKL 233
           V  D   D     D +F +  S   I  +Q   +    +++     LN AK     ++ +
Sbjct: 483 VLSDILGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQAKGARLHILGV 542

Query: 234 QKDVIS 239
            +  I+
Sbjct: 543 MEQAIN 548



 Score = 46.3 bits (110), Expect = 6e-06
 Identities = 43/246 (17%), Positives = 84/246 (34%), Gaps = 55/246 (22%)

Query: 12  REISL-TRRVSKYAEGSCLVKFGDTHLLTTATLEEKV-------PMWIRNTKHGWITAEY 63
             ++L T  +++ A  + +V   DT +  T   ++K        P+          T  Y
Sbjct: 20  HTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPL----------TVNY 69

Query: 64  -------GMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDC 116
                  G +P   G+  +RE   GR       I R+I R +R +     +   Q+I   
Sbjct: 70  QERTYAAGRIP---GSFFRRE---GRPSEGETLIARLIDRPIRPLFPEGFVNEVQVI--A 121

Query: 117 DVIQADGGTRT--AAITGAWVALHDCLQHMEDCSNKFQLSQV-LKGHVAAISCGMLCGYP 173
            V+  +        A+ GA  AL               LS +   G + A   G +    
Sbjct: 122 TVVSVNPQVNPDIVAMIGASAAL--------------SLSGIPFNGPIGAARVGYINDQY 167

Query: 174 IVDLDYGEDSTIDVDANFVMTDSGHIVEVQGSAERATF-SQDHFFAMLNLAKDRIADLIK 232
           +++    E      ++   +  +G    V      A   S+D     +    ++   +I+
Sbjct: 168 VLNPTQDELK----ESKLDLVVAGTEAAVLMVESEAQLLSEDQMLGAVVFGHEQQQVVIQ 223

Query: 233 LQKDVI 238
              +++
Sbjct: 224 NINELV 229


>2nn6_B Exosome complex exonuclease RRP41; RNA, exosome, PM/SCL,
           phosphorolytic, hydrolase/transferase complex; 3.35A
           {Homo sapiens} SCOP: d.14.1.4 d.101.1.1
          Length = 249

 Score =  104 bits (260), Expect = 2e-23
 Identities = 56/241 (23%), Positives = 91/241 (37%), Gaps = 23/241 (9%)

Query: 2   RLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATL--EEKVPMWIRNTKHGWI 59
           R+ GR+  ++R+I     V   A+GS  ++ G+T  L       E +            +
Sbjct: 17  RVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALV 76

Query: 60  TAEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDVI 119
             +Y     STG R +R         +S E+   + +   + +        QI I   V+
Sbjct: 77  NCQYSSATFSTGERKRRP----HGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVL 132

Query: 120 QADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLCGYPIVDLDY 179
           QADGGT  A +  A +A+ D    M D              V A S G + G  + DL +
Sbjct: 133 QADGGTYAACVNAATLAVLDAGIPMRDF-------------VCACSAGFVDGTALADLSH 179

Query: 180 GEDSTIDVDANFVMT-DSGHIVEVQGSAERATFSQDHFFAMLNLAKDRIADLIKLQKDVI 238
            E++         +   SG I  ++  A      +DH   +L  A     D+  L   V+
Sbjct: 180 VEEAAGGPQLALALLPASGQIALLEMDAR---LHEDHLERVLEAAAQAARDVHTLLDRVV 236

Query: 239 S 239
            
Sbjct: 237 R 237


>2nn6_D Exosome complex exonuclease RRP46; RNA, exosome, PM/SCL,
           phosphorolytic, hydrolase/transferase complex; 3.35A
           {Homo sapiens} SCOP: d.14.1.4 d.101.1.1
          Length = 237

 Score =  100 bits (249), Expect = 3e-22
 Identities = 32/245 (13%), Positives = 67/245 (27%), Gaps = 32/245 (13%)

Query: 1   MRLSGRQEN-QMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHGWI 59
              S R     +R  +  + +    +GS     GDT +L       +V +          
Sbjct: 19  TGSSPRGPGCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSK-------- 70

Query: 60  TAEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDVI 119
              +         R K     G  G   +  +R+I     +VV  +      I +   V+
Sbjct: 71  -EIFNKATLEVILRPKI----GLPGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVV 125

Query: 120 QADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLCGY-PIVDLD 178
              G      +  A +AL D    M                   ++C +      ++D  
Sbjct: 126 SDAGSLLACCLNAACMALVDAGVPMRALFCG-------------VACALDSDGTLVLDPT 172

Query: 179 YGEDSTIDVDANFVMT-DSGHIVEVQGSAERATFSQDHFFAMLNLAKDRIADLIKLQKDV 237
             ++        F +      ++          +S       L  A+     + +  ++ 
Sbjct: 173 SKQEKEARAVLTFALDSVERKLLMSSTKGL---YSDTELQQCLAAAQAASQHVFRFYRES 229

Query: 238 ISNEV 242
           +    
Sbjct: 230 LQRRY 234


>2wdx_A Putative hexose oxidase; oxidoreductase-antibiotic complex; HET:
           FAD GHP 3MY 3FG OMY D3P BMA NAG BDP T55; 2.30A
           {Nonomuraea SP} PDB: 2wdw_A*
          Length = 523

 Score = 26.1 bits (56), Expect = 8.5
 Identities = 16/121 (13%), Positives = 32/121 (26%), Gaps = 12/121 (9%)

Query: 101 VVDLSALGSRQIIIDCDVIQADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGH 160
           ++D+S L         +    + G   + +        +       C         + GH
Sbjct: 105 IIDMSLLTEIAYDPSMNAFLIEPGNTLSEVYEKLYLGWNVTIPGGVCG-----GVGVGGH 159

Query: 161 VAAISCGMLCGYPIVDLDYGEDSTIDVDANFVM-TDSGHIVEVQGSAERATFSQDHFFAM 219
           +     G L         +G           V+    G    +  + ER     D ++A 
Sbjct: 160 ICGGGYGPLSRQ------FGSVVDYLYAVEVVVVNKQGKARVIVATRERDDPHHDLWWAH 213

Query: 220 L 220
            
Sbjct: 214 T 214


>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
            acyl-carrier-protein, beta-ketoacyl reductase,
            beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces
            cerevisiae}
          Length = 2006

 Score = 25.7 bits (56), Expect = 9.0
 Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 8/55 (14%)

Query: 196  SGHIVE-VQGSAERATF-------SQDHFFAMLNLAKDRIADLIKLQKDVISNEV 242
            +G +VE V  + E   +       + D    +LN  K +  D+I+LQK +   EV
Sbjct: 1837 TGWLVEIVNYNVENQQYVAAGDLRALDTVTNVLNFIKLQKIDIIELQKSLSLEEV 1891


>2wqp_A Polysialic acid capsule biosynthesis protein SIAC; NEUB, inhibitor,
           TIM barrel, sialic acid synthase, transferase; HET: WQP;
           1.75A {Neisseria meningitidis} PDB: 2zdr_A 1xuz_A*
           1xuu_A 3cm4_A
          Length = 349

 Score = 25.7 bits (55), Expect = 9.4
 Identities = 8/31 (25%), Positives = 18/31 (58%)

Query: 212 SQDHFFAMLNLAKDRIADLIKLQKDVISNEV 242
           S    F M++ A +  A+++K Q  ++ +E+
Sbjct: 33  SLKTAFEMVDAAYNAGAEVVKHQTHIVEDEM 63


  Database: pdb70
    Posted date:  Jan 26, 2011 11:21 AM
  Number of letters in database: 5,693,230
  Number of sequences in database:  24,244
  
Lambda     K      H
   0.321    0.134    0.393 

Gapped
Lambda     K      H
   0.267   0.0472    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,995,200
Number of extensions: 88161
Number of successful extensions: 339
Number of sequences better than 10.0: 1
Number of HSP's gapped: 270
Number of HSP's successfully gapped: 43
Length of query: 242
Length of database: 5,693,230
Length adjustment: 90
Effective length of query: 152
Effective length of database: 3,511,270
Effective search space: 533713040
Effective search space used: 533713040
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.6 bits)