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)