RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780940|ref|YP_003065353.1| ribonuclease III [Candidatus Liberibacter asiaticus str. psy62] (227 letters) >3n3w_A Ribonuclease III; nuclease domain, ribonuclase III, IDP90862, csgid, structura genomics; 2.21A {Campylobacter jejuni subsp} Length = 248 Score = 198 bits (504), Expect = 1e-51 Identities = 73/220 (33%), Positives = 121/220 (55%), Gaps = 4/220 (1%) Query: 7 STLEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSA 66 LE+ + Y F +++LL ALTH S + ERLEFLGD +L L++ LF+ F Sbjct: 29 EKLEQSLTYEFKDKNLLIHALTHKS--FKKSYNNERLEFLGDAVLDLVVGEYLFHKFAKD 86 Query: 67 KEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAAL 126 EG+LS +LV+ ++ +++A L+L FI +S + SI +D +E++I A+ Sbjct: 87 AEGDLSKLRAALVNEKSFAKIANSLNLGDFILMSVAEENNGGKEKPSILSDALEAIIGAI 146 Query: 127 YLDGGIEVAGTFVDKYWKQR--ALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPD 184 +L+ G E A T + ++ + + +D KT+LQE K G TP+Y+ GPD Sbjct: 147 HLEAGFEFAKTIALRLIEKNFPQIDAKILIKDYKTKLQEITQGKIGQTPQYETVRAFGPD 206 Query: 185 HDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREG 224 H +F + + + G A+ + SK+ A+Q+AA L++ G Sbjct: 207 HLKQFEIALMLDGKELARAIAGSKKEAQQMAAKIALEKLG 246 >1o0w_A Ribonuclease III, RNAse III; TM1102, structural genomics, JCSG, PSI, protein structure initiative, joint center for structural genomics; 2.00A {Thermotoga maritima} SCOP: a.149.1.1 d.50.1.1 Length = 252 Score = 186 bits (473), Expect = 4e-48 Identities = 71/223 (31%), Positives = 110/223 (49%), Gaps = 9/223 (4%) Query: 9 LEKRIGYAFANRSLLEKALTHSSISHSY-------QESYERLEFLGDRILGLLISTLLFN 61 +K G F N LL +AL HSS ++ ES E+LEFLGD +L L + +L+ Sbjct: 24 FQKETGINFKNEELLFRALCHSSYANEQNQAGRKDVESNEKLEFLGDAVLELFVCEILYK 83 Query: 62 HFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVES 121 + A+ G+L+ ++ S E + V+R+++L F+ + K SI AD E+ Sbjct: 84 KYPEAEVGDLARVKSAAASEEVLAMVSRKMNLGKFLFLGKGEEKTGGRDRDSILADAFEA 143 Query: 122 LIAALYLDGGIEVAGTFVDKYWKQRALKSGKFR--RDAKTELQEWAHAKFGVTPEYKVTF 179 L+AA+YLD G E ++ ++ K K D KT LQE ++ V PEY + Sbjct: 144 LLAAIYLDQGYEKIKELFEQEFEFYIEKIMKGEMLFDYKTALQEIVQSEHKVPPEYILVR 203 Query: 180 RSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKR 222 D D F V V ++G A G +K+ AE+ AA ++ Sbjct: 204 TEKNDGDRIFVVEVRVNGKTIATGKGRTKKEAEKEAARIAYEK 246 >3c4b_A Endoribonuclease dicer; RNAse, dsRNA binding protein, ATP-binding, endonuclease, helicase, hydrolase, nucleotide-binding, phosphoprotein; HET: MSE; 1.68A {Mus musculus} PDB: 3c4t_A 2eb1_A Length = 265 Score = 140 bits (353), Expect = 2e-34 Identities = 59/250 (23%), Positives = 103/250 (41%), Gaps = 37/250 (14%) Query: 6 YSTLEKRIGYAFANRSLLEKALTHSSISHSY-QESYERLEFLGDRILGLLISTLLFNHFD 64 + T EK+I Y F N++ L +A TH+S ++ + Y+RLEFLGD IL LI+ L+ Sbjct: 15 FETFEKKINYRFKNKAYLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPR 74 Query: 65 SAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSS-DLRKDVCSFM------------ 111 G L+ ++LV+ + +A + D + + S +L + F+ Sbjct: 75 QHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVKFQLEKNEMQGM 134 Query: 112 -------------------TSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQRALKSGK 152 D+ ESL A+Y+D G+ + + Y + L Sbjct: 135 DSELRRSEEDEEKEEDIEVPKAMGDIFESLAGAIYMDSGMSLEVVWQVYYPMMQPLIEKF 194 Query: 153 FRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAE 212 ++ ++E + PE + +D + V VE+ G +G+ S R A+ Sbjct: 195 SANVPRSPVRELLEME----PETAKFSPAERTYDGKVRVTVEVVGKGKFKGVGRSYRIAK 250 Query: 213 QVAAAEVLKR 222 AA L+ Sbjct: 251 SAAARRALRS 260 >2nug_A Ribonuclease III, RNAse III; dsRNA, RNA interference, endonucleolytic cleavage, hydrolase/RNA complex; 1.70A {Aquifex aeolicus} SCOP: a.149.1.1 d.50.1.1 PDB: 1yyw_A 2nue_A 2nuf_A 1yyk_A 1yz9_A 1yyo_A 2ez6_A 1rc7_A 1i4s_A 1jfz_A 1rc5_A Length = 221 Score = 138 bits (349), Expect = 6e-34 Identities = 82/219 (37%), Positives = 118/219 (53%), Gaps = 14/219 (6%) Query: 9 LEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSAKE 68 LEK++GY F ++SLLEKALTH S +S +E YE LEFLGD ++ I LL + + +E Sbjct: 7 LEKKLGYTFKDKSLLEKALTHVS--YSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKRE 64 Query: 69 GELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYL 128 G LS L+S E + +A++L+L FIR+ + I DV E+L AA+Y+ Sbjct: 65 GFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINET------IIGDVFEALWAAVYI 118 Query: 129 DGGIEVAGTFVDKYWK-----QRALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGP 183 D G + T Y A+K G+ ++D KT LQE ++ PEY++ GP Sbjct: 119 DSGRDANFTRELFYKLFKEDILSAIKEGRVKKDYKTILQEITQKRWKERPEYRLISVEGP 178 Query: 184 DHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKR 222 H +F V +I G SK+ AEQ AA E++K Sbjct: 179 HHKKKFIVEAKIKEYR-TLGEGKSKKEAEQRAAEELIKL 216 >3o2r_A Ribonuclease III; structural genomics, center for structural genomics of infec diseases, csgid, nuclease domain, ribonuclase III; HET: MLZ; 1.25A {Campylobacter jejuni subsp} PDB: 3o2r_B* Length = 170 Score = 136 bits (343), Expect = 5e-33 Identities = 47/140 (33%), Positives = 78/140 (55%), Gaps = 2/140 (1%) Query: 7 STLEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSA 66 LE+ + Y F +++LL ALTH S + ERLEFLGD +L L++ LF+ F Sbjct: 29 EKLEQSLTYEFKDKNLLIHALTHKS--FKKSYNNERLEFLGDAVLDLVVGEYLFHKFAKD 86 Query: 67 KEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAAL 126 EG+LS +LV+ ++ +++A L+L FI +S + SI +D +E++I A+ Sbjct: 87 AEGDLSKLRAALVNEKSFAKIANSLNLGDFILMSVAEENNGGKEKPSILSDALEAIIGAI 146 Query: 127 YLDGGIEVAGTFVDKYWKQR 146 +L+ G E A T + ++ Sbjct: 147 HLEAGFEFAKTIALRLIEKN 166 >2a11_A Ribonuclease III, RNAse III; nuclease domain, structural genomics, PSI, protein structure initiative; 2.10A {Mycobacterium tuberculosis} Length = 242 Score = 132 bits (332), Expect = 7e-32 Identities = 72/223 (32%), Positives = 103/223 (46%), Gaps = 9/223 (4%) Query: 7 STLEKRIGYAFANRSLLEKALTHSSISHSYQ--ESYERLEFLGDRILGLLISTLLFNHFD 64 L +G + LL ALTH S ++ + ERLEFLGD +LGL I+ LF+ Sbjct: 8 QPLLDALGVDLPDE-LLSLALTHRSYAYENGGLPTNERLEFLGDAVLGLTITDALFHRHP 66 Query: 65 SAKEGELSVRFNSLVSAETCSQVARELDLAS---FIRVSSDLRKDVCSFMTSIQADVVES 121 EG+L+ S+V+ + + VAR L + + + +SI AD +ES Sbjct: 67 DRSEGDLAKLRASVVNTQALADVARRLCAEGLGVHVLLGRGEANTGGADKSSILADGMES 126 Query: 122 LIAALYLDGGIEVAGTFVDKYWKQRALKSGKF--RRDAKTELQEWAHAKFGVTPEYKVTF 179 L+ A+YL G+E A + + + + D KT LQE A+ P Y VT Sbjct: 127 LLGAIYLQHGMEKAREVILRLFGPLLDAAPTLGAGLDWKTSLQELTAARGLGAPSYLVT- 185 Query: 180 RSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKR 222 +GPDHD FT VV + G+ SK+ AEQ K Sbjct: 186 STGPDHDKEFTAVVVVMDSEYGSGVGRSKKEAEQKXXXXXWKA 228 >2gsl_A Hypothetical protein; alpha-helical protein, structural genomics, PSI, protein structure initiative; 2.60A {Fusobacterium nucleatum subsp} Length = 137 Score = 90.4 bits (224), Expect = 3e-19 Identities = 23/118 (19%), Positives = 40/118 (33%), Gaps = 12/118 (10%) Query: 37 QESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASF 96 S L FLGD I L I L+ + V+A+ S + +++ Sbjct: 12 DYSGLELAFLGDAIWELEIRKYYLQFG--YNIPTLNKYVKAKVNAKYQSLIYKKIINDLD 69 Query: 97 I----------RVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWK 144 + C+ M +A +E++I A+YL E ++ K Sbjct: 70 EEFKVIGKRAKNSNIKTFPRSCTVMEYKEATALEAIIGAMYLLKKEEEIKKIINIVIK 127 >2khx_A Ribonuclease 3; drosha, RNA binding domain, hydrolase, gene regulation, nuclear protein; NMR {Homo sapiens} Length = 85 Score = 84.2 bits (208), Expect = 2e-17 Identities = 22/72 (30%), Positives = 30/72 (41%), Gaps = 5/72 (6%) Query: 156 DAKTELQEWAH-----AKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRA 210 D K++LQ+ K P YK GP H +TV V G G S + Sbjct: 2 DPKSQLQQCCLTLRTEGKEPDIPLYKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQ 61 Query: 211 AEQVAAAEVLKR 222 AE AA + L++ Sbjct: 62 AEMGAAMDALEK 73 >1u61_A Hypothetical protein; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG, unknown function; 2.15A {Bacillus cereus} SCOP: a.149.1.1 Length = 138 Score = 84.3 bits (208), Expect = 2e-17 Identities = 23/121 (19%), Positives = 37/121 (30%), Gaps = 13/121 (10%) Query: 37 QESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASF 96 Q + L ++GD + I L + +L S VSA+ ++V L +F Sbjct: 9 QLNSLALAYMGDAVYEQYIRYHLLQKGK-VRPNQLHRLGTSFVSAKAQAKVVYHLLETAF 67 Query: 97 IRVS------------SDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWK 144 + S T + E+LI +L E V K Sbjct: 68 LTEEEEAVLRRGRNANSGTVPKNTDVQTYRHSTAFEALIGYHHLLNNRERLDEIVYKAIA 127 Query: 145 Q 145 Sbjct: 128 V 128 >3adj_A F21M12.9 protein; HYL1, miRNA processing, RNA binding protein, gene regulation; 3.00A {Arabidopsis thaliana} PDB: 2l2m_A Length = 76 Score = 76.9 bits (189), Expect = 4e-15 Identities = 18/65 (27%), Positives = 24/65 (36%) Query: 158 KTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAA 217 K LQE+A P Y+ +FT VEI G+ +K+ AE A Sbjct: 7 KNLLQEYAQKMNYAIPLYQCQKVETLGRVTQFTCTVEIGGIKYTGAATRTKKDAEISAGR 66 Query: 218 EVLKR 222 L Sbjct: 67 TALLA 71 >3adl_A RISC-loading complex subunit tarbp2; TRBP2, miRNA processing, gene regulation-RNA complex; 2.20A {Homo sapiens} Length = 88 Score = 75.3 bits (185), Expect = 1e-14 Identities = 24/68 (35%), Positives = 31/68 (45%), Gaps = 1/68 (1%) Query: 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQV 214 LQE K PEY VT SGP H FT+ + G SK+ A++ Sbjct: 15 SHEVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVERFI-EIGSGTSKKLAKRN 73 Query: 215 AAAEVLKR 222 AAA++L R Sbjct: 74 AAAKMLLR 81 >1qu6_A Protein kinase PKR; dsRNA-binding domain, solution structure, transferase; NMR {Homo sapiens} SCOP: d.50.1.1 d.50.1.1 Length = 179 Score = 72.9 bits (178), Expect = 5e-14 Identities = 23/68 (33%), Positives = 31/68 (45%), Gaps = 1/68 (1%) Query: 154 RRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQ 213 EL + K GV +Y+ SGP HD RFT V I G +G SK+ A+ Sbjct: 12 AGFFMEELNTYRQ-KQGVVLKYQELPNSGPPHDRRFTFQVIIDGREFPEGEGRSKKEAKN 70 Query: 214 VAAAEVLK 221 AA ++ Sbjct: 71 AAAKLAVE 78 Score = 53.3 bits (127), Expect = 4e-08 Identities = 16/103 (15%), Positives = 33/103 (32%), Gaps = 2/103 (1%) Query: 120 ESLIAALYLDGGIEVAGTFVDKYWKQRALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTF 179 ++ A L ++ + G + + A K +T Y+ Sbjct: 69 KNAAAKLAVEILNKEKKAVSPLLLTTTNSSEGLSMGNYIGLINRIAQ-KKRLTVNYEQC- 126 Query: 180 RSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKR 222 SG F ++ + G +K+ A+Q+AA + Sbjct: 127 ASGVHGPEGFHYKCKMGQKEYSIGTGSTKQEAKQLAAKLAYLQ 169 >1di2_A XLRBPA, double stranded RNA binding protein A; protein-RNA complex, protein-RNA interactions, RNA-bining protein; 1.90A {Xenopus laevis} SCOP: d.50.1.1 Length = 69 Score = 69.9 bits (171), Expect = 4e-13 Identities = 23/65 (35%), Positives = 31/65 (47%), Gaps = 1/65 (1%) Query: 158 KTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAA 217 LQE A K PEY V SGP H FT+ + G SK+ A++VAA Sbjct: 3 VGSLQELAVQKGWRLPEYTVAQESGPPHKREFTITCRVETFV-ETGSGTSKQVAKRVAAE 61 Query: 218 EVLKR 222 ++L + Sbjct: 62 KLLTK 66 >2l2n_A Hyponastic leave 1; DSRBD, miRNA, RNA binding protein, plant protein; NMR {Arabidopsis thaliana} Length = 103 Score = 69.2 bits (169), Expect = 8e-13 Identities = 21/68 (30%), Positives = 32/68 (47%), Gaps = 2/68 (2%) Query: 156 DAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDC-SKRAAEQV 214 K+ LQE+A TP Y++ + GP H F V + G+ +++AAEQ Sbjct: 18 VFKSRLQEYAQKYKLPTPVYEIV-KEGPSHKSLFQSTVILDGVRYNSLPGFFNRKAAEQS 76 Query: 215 AAAEVLKR 222 AA L+ Sbjct: 77 AAEVALRE 84 >3adg_A F21M12.9 protein; HYL1, miRNA processing mechanism, RNA binding protein, gene regulation; 1.70A {Arabidopsis thaliana} PDB: 3adi_A Length = 73 Score = 69.0 bits (169), Expect = 8e-13 Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 2/66 (3%) Query: 158 KTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLA-PAQGMDCSKRAAEQVAA 216 K+ LQE+A TP Y++ + GP H F V + G+ + +++AAEQ AA Sbjct: 6 KSRLQEYAQKYKLPTPVYEIV-KEGPSHKSLFQSTVILDGVRYNSLPGFFNRKAAEQSAA 64 Query: 217 AEVLKR 222 L+ Sbjct: 65 EVALRE 70 >2l33_A Interleukin enhancer-binding factor 3; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, DRBM; NMR {Homo sapiens} Length = 91 Score = 68.3 bits (167), Expect = 1e-12 Identities = 22/74 (29%), Positives = 34/74 (45%), Gaps = 9/74 (12%) Query: 149 KSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSK 208 K GK + EL E +Y++ +G HD RF + VE+ G QG +K Sbjct: 14 KHGK---NPVMELNEKRRG-----LKYELISETGGSHDKRFVMEVEVDGQ-KFQGAGSNK 64 Query: 209 RAAEQVAAAEVLKR 222 + A+ AA L++ Sbjct: 65 KVAKAYAALAALEK 78 >2yt4_A Protein DGCR8; DSRBD, RNA binding domain, RNA binding protein; 2.60A {Homo sapiens} Length = 232 Score = 68.2 bits (166), Expect = 2e-12 Identities = 17/68 (25%), Positives = 23/68 (33%), Gaps = 2/68 (2%) Query: 154 RRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQ 213 + L E+ V P Y P F V I G+ G SK+ A+ Sbjct: 21 GKSEVCILHEYMQRVLKVRPVYNFFECENPSEP--FGASVTIDGVTYGSGTASSKKLAKN 78 Query: 214 VAAAEVLK 221 AA L+ Sbjct: 79 KAARATLE 86 Score = 48.9 bits (116), Expect = 8e-07 Identities = 12/62 (19%), Positives = 26/62 (41%), Gaps = 2/62 (3%) Query: 161 LQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVL 220 L E G+ + + F P + + V+ +G +KR +Q+A+ ++L Sbjct: 136 LHECLKRNHGM-GDTSIKFEVVPGKNQKSEYVMACGKHT-VRGWCKNKRVGKQLASQKIL 193 Query: 221 KR 222 + Sbjct: 194 QL 195 >1t4o_A Ribonuclease III; RNT1P, DSRBD, RNA-binding, hydrolase; 2.50A {Saccharomyces cerevisiae} SCOP: d.50.1.1 PDB: 1t4l_B Length = 117 Score = 67.8 bits (165), Expect = 2e-12 Identities = 12/78 (15%), Positives = 24/78 (30%), Gaps = 1/78 (1%) Query: 148 LKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCS 207 +K+ K +AK +L + Y + G G+ + Sbjct: 1 MKTDKLDMNAKRQLYSLI-GYASLRLHYVTVKKPTAVDPNSIVECRVGDGTVLGTGVGRN 59 Query: 208 KRAAEQVAAAEVLKREGI 225 + A AA L+ + + Sbjct: 60 IKIAGIRAAENALRDKKM 77 >1ekz_A DSRBDIII, maternal effect protein (staufen); structure, protein/RNA, protein DSRBD, RNA hairpin; NMR {Drosophila melanogaster} SCOP: d.50.1.1 PDB: 1stu_A Length = 76 Score = 66.8 bits (163), Expect = 3e-12 Identities = 14/68 (20%), Positives = 29/68 (42%), Gaps = 2/68 (2%) Query: 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQV 214 + +++ E + +T +KV GP H F + G +G K+ +++ Sbjct: 7 KSPISQVHEIGIKR-NMTVHFKVLREEGPAHMKNFITACIV-GSIVTEGEGNGKKVSKKR 64 Query: 215 AAAEVLKR 222 AA ++L Sbjct: 65 AAEKMLVE 72 >2b7t_A Double-stranded RNA-specific editase 1; RNA editing, RNA-binding protein, hydrolase; NMR {Rattus norvegicus} SCOP: d.50.1.1 Length = 73 Score = 66.9 bits (163), Expect = 4e-12 Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 3/67 (4%) Query: 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQV 214 K L + K G +Y + ++GP H P F + VE++G +G +K+ A+ Sbjct: 4 VLPKNALMQLNEIKPG--LQYMLLSQTGPVHAPLFVMSVEVNGQ-VFEGSGPTKKKAKLH 60 Query: 215 AAAEVLK 221 AA + L+ Sbjct: 61 AAEKALR 67 >1x49_A Interferon-induced, double-stranded RNA- activated protein kinase; structure genomics, DSRM domain, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.50.1.1 Length = 97 Score = 65.5 bits (159), Expect = 9e-12 Identities = 20/67 (29%), Positives = 26/67 (38%), Gaps = 1/67 (1%) Query: 156 DAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVA 215 +L ++ GV YK SGP HD RFT V I + SK+ A A Sbjct: 15 FYMDKLNKYRQ-MHGVAITYKELSTSGPPHDRRFTFQVLIDEKEFPEAKGRSKQEARNAA 73 Query: 216 AAEVLKR 222 A + Sbjct: 74 AKLAVDI 80 >2dmy_A Spermatid perinuclear RNA-binding protein; DSRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.50.1.1 Length = 97 Score = 64.6 bits (157), Expect = 2e-11 Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 3/70 (4%) Query: 156 DAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVA 215 D L + G +YK+ +SGP H P FT+ V++ G + SK+ A+ Sbjct: 17 DLMNALMRLNQIRPG--LQYKLLSQSGPVHAPVFTMSVDVDGT-TYEASGPSKKTAKLHV 73 Query: 216 AAEVLKREGI 225 A +VL+ G Sbjct: 74 AVKVLQAMGY 83 >2b7v_A Double-stranded RNA-specific editase 1; RNA editing, RNA-binding protein, hydrolase; NMR {Rattus norvegicus} SCOP: d.50.1.1 Length = 71 Score = 62.1 bits (151), Expect = 1e-10 Identities = 15/68 (22%), Positives = 24/68 (35%), Gaps = 6/68 (8%) Query: 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQV 214 ++ L E +Y SG H F + V + G +G +K+ A+ Sbjct: 4 KNPVMILNELRPG-----LKYDFLSESGESHAKSFVMSVVVDGQ-FFEGSGRNKKLAKAR 57 Query: 215 AAAEVLKR 222 AA L Sbjct: 58 AAQSALAT 65 >1t4n_A Ribonuclease III; DSRBD, RNA-binding, hydrolase; NMR {Saccharomyces cerevisiae} SCOP: d.50.1.1 Length = 94 Score = 61.2 bits (148), Expect = 2e-10 Identities = 10/71 (14%), Positives = 20/71 (28%), Gaps = 1/71 (1%) Query: 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQV 214 +AK +L + Y + G G+ + + A Sbjct: 6 MNAKRQLYSLI-GYASLRLHYVTVKKPTAVDPNSIVECRVGDGTVLGTGVGRNIKIAGIR 64 Query: 215 AAAEVLKREGI 225 AA L+ + + Sbjct: 65 AAENALRDKKM 75 >2l3j_A Double-stranded RNA-specific editase 1; editing, dsRNA recognition, DSRBM, hydrolase-RNA complex; NMR {Rattus norvegicus} Length = 236 Score = 59.9 bits (144), Expect = 5e-10 Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 3/66 (4%) Query: 156 DAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVA 215 K L + K G +Y + ++GP H P F + VE++G +G +K+ A+ A Sbjct: 5 LPKNALMQLNEIKPG--LQYMLLSQTGPVHAPLFVMSVEVNGQV-FEGSGPTKKKAKLHA 61 Query: 216 AAEVLK 221 A + L+ Sbjct: 62 AEKALR 67 Score = 59.1 bits (142), Expect = 8e-10 Identities = 16/103 (15%), Positives = 27/103 (26%), Gaps = 6/103 (5%) Query: 120 ESLIAALYLDGGIEVAGTFVDKYWKQRALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTF 179 + V + ++ L E +Y Sbjct: 126 SFSSSGDVSLSASPVPASLTQPPLPIPPPFPPPSGKNPVMILNELRPG-----LKYDFLS 180 Query: 180 RSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKR 222 SG H F + V + G +G +K+ A+ AA L Sbjct: 181 ESGESHAKSFVMSVVVDGQ-FFEGSGRNKKLAKARAAQSALAT 222 >1x48_A Interferon-induced, double-stranded RNA- activated protein kinase; structure genomics, DSRM domain, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.50.1.1 Length = 88 Score = 56.6 bits (136), Expect = 5e-09 Identities = 12/67 (17%), Positives = 24/67 (35%), Gaps = 2/67 (2%) Query: 156 DAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVA 215 + +A K ++ + RF +I G +K+ A+Q+A Sbjct: 7 GYIGLVNSFAQ-KKKLSV-NYEQCEPNSELPQRFICKCKIGQTMYGTGSGVTKQEAKQLA 64 Query: 216 AAEVLKR 222 A E ++ Sbjct: 65 AKEAYQK 71 >1whn_A Hypothetical protein riken cDNA 2310016K04; double-stranded RNA binding domain, DSRBD, DSRM, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.50.1.1 Length = 128 Score = 56.3 bits (135), Expect = 5e-09 Identities = 22/97 (22%), Positives = 38/97 (39%), Gaps = 4/97 (4%) Query: 130 GGIEVAGTFVDKYWKQRALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRF 189 G +G+ + K + ++ + K L EW + P Y+ D F Sbjct: 1 GSSGSSGSGIIKMAIRFDRRAYPPQITPKMCLLEWCRREKLPQPVYETVQ---RTIDRMF 57 Query: 190 TVVVEISGLAPAQGMDC-SKRAAEQVAAAEVLKREGI 225 VV ++ + SK+ AEQ AA L+ +G+ Sbjct: 58 CSVVTVAEQKYQSTLWDKSKKLAEQTAAIVCLRSQGL 94 >2dix_A Interferon-inducible double stranded RNA- dependent protein kinase activator A; structure genomics, DSRM domain, hypothetical protein PRKRA; NMR {Homo sapiens} SCOP: d.50.1.1 Length = 84 Score = 56.3 bits (135), Expect = 5e-09 Identities = 18/73 (24%), Positives = 25/73 (34%), Gaps = 2/73 (2%) Query: 150 SGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKR 209 SG + L E+ K P Y+ H P FT V + G SK+ Sbjct: 3 SGSSGKTPIQVLHEYGM-KTKNIPVYECERSDVQIHVPTFTFRVTVGD-ITCTGEGTSKK 60 Query: 210 AAEQVAAAEVLKR 222 A+ AA + Sbjct: 61 LAKHRAAEAAINI 73 >1x47_A DGCR8 protein; structural genomics, DSRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.50.1.1 Length = 98 Score = 54.4 bits (130), Expect = 2e-08 Identities = 17/69 (24%), Positives = 23/69 (33%), Gaps = 2/69 (2%) Query: 154 RRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQ 213 + L E+ V P Y P F V I G+ G SK+ A+ Sbjct: 15 GKSEVCILHEYMQRVLKVRPVYNFFECENPSEP--FGASVTIDGVTYGSGTASSKKLAKN 72 Query: 214 VAAAEVLKR 222 AA L+ Sbjct: 73 KAARATLEI 81 >2cpn_A TAR RNA-binding protein 2; double-stranded RNA binding domain, DSRBD, DSRM., structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.50.1.1 Length = 89 Score = 54.1 bits (129), Expect = 2e-08 Identities = 24/67 (35%), Positives = 32/67 (47%), Gaps = 1/67 (1%) Query: 156 DAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVA 215 + LQE K PEY VT SGP H FT+ + G SK+ A++ A Sbjct: 17 NPVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVER-FIEIGSGTSKKLAKRNA 75 Query: 216 AAEVLKR 222 AA++L R Sbjct: 76 AAKMLLR 82 >1uil_A Double-stranded RNA-binding motif; structural genomics, DSRM, riken structural genomics/proteomics initiative, RSGI RNA binding protein; NMR {Mus musculus} SCOP: d.50.1.1 Length = 113 Score = 53.6 bits (128), Expect = 4e-08 Identities = 19/73 (26%), Positives = 33/73 (45%), Gaps = 7/73 (9%) Query: 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAP-----AQGMDCSKR 209 +AK L ++ K + EYK T + GPDH+ F + I A+ +K+ Sbjct: 26 ENAKARLNQYFQ-KEKIQGEYKYT-QVGPDHNRSFIAEMTIYIKQLGRRIFAREHGSNKK 83 Query: 210 AAEQVAAAEVLKR 222 A Q A ++++ Sbjct: 84 LAAQSCALSLVRQ 96 >1whq_A RNA helicase A; double-stranded RNA binding domain, DSRBD, DSRM, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Mus musculus} SCOP: d.50.1.1 Length = 99 Score = 52.9 bits (126), Expect = 6e-08 Identities = 14/76 (18%), Positives = 22/76 (28%), Gaps = 4/76 (5%) Query: 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQV 214 K L W + +TP Y++ + V G +K+ A+ Sbjct: 6 SGIKNFLYAWCGKR-KMTPAYEIRAVGNKNRQKFMCEVRVEGFNYAGMGNSTNKKDAQSN 64 Query: 215 AAA---EVLKREGIWT 227 AA L R Sbjct: 65 AARDFVNYLVRINEVK 80 >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 = 52.6 bits (126), Expect = 6e-08 Identities = 34/190 (17%), Positives = 58/190 (30%), Gaps = 53/190 (27%) Query: 16 AFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSAKEG---ELS 72 A++ R L L+H S+ H LL+ T F +E L Sbjct: 3 AYSTRPL---TLSHGSLEHV-----------------LLVPTASFFIASQLQEQFNKILP 42 Query: 73 VRFNSLVSAETCSQVARELDLASFIR-VSSDLRKDVCSFMTSI--------------QAD 117 + + + A EL + F+ VSS + + D Sbjct: 43 EPTEGFAADDEPTTPA-EL-VGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGND 100 Query: 118 VVESLIAAL--YLDGGIEVAGTFVDKYWKQRALKSGKFRRDAKTELQEWA---HAK---- 168 + +L A L D + + Y R + F + + + L +A+ Sbjct: 101 -IHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAI 159 Query: 169 F---GVTPEY 175 F G T +Y Sbjct: 160 FGGQGNTDDY 169 Score = 33.4 bits (76), Expect = 0.039 Identities = 25/130 (19%), Positives = 43/130 (33%), Gaps = 51/130 (39%) Query: 15 YAFANRSLLE-KA---LTHSSISHSYQESYER-LEFLGDRILGLLISTLLFNHFDSAKEG 69 Y N +L + KA L S I S ER L+F N F Sbjct: 387 YGL-NLTLRKAKAPSGLDQSRIPFS-----ERKLKF--------------SNRF------ 420 Query: 70 EL--SVRFNS--LVSAETCSQVARELDLASFIRVSSDLR---------KDVCSFMTSIQA 116 L + F+S LV A + ++L + + D++ D + + Sbjct: 421 -LPVASPFHSHLLVPAS--DLINKDLVKNNVSFNAKDIQIPVYDTFDGSD----LRVLSG 473 Query: 117 DVVESLIAAL 126 + E ++ + Sbjct: 474 SISERIVDCI 483 >1uhz_A Staufen (RNA binding protein) homolog 2; DSRM, staufen homolog 2, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.50.1.1 Length = 89 Score = 52.6 bits (125), Expect = 7e-08 Identities = 14/70 (20%), Positives = 28/70 (40%), Gaps = 1/70 (1%) Query: 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQV 214 + L + A+ P+Y + G F + V++ G +K+ A++ Sbjct: 6 SGPISRLAQIQQARKEKEPDYILLSERGMPRRREFVMQVKVGNEVA-TGTGPNKKIAKKN 64 Query: 215 AAAEVLKREG 224 AA +L + G Sbjct: 65 AAEAMLLQLG 74 >2qvw_A GLP_546_48378_50642; dicer, RNAI,pseudo-merohedral twin, hydrolase; 3.00A {Giardia intestinalis} PDB: 2ffl_A Length = 756 Score = 40.8 bits (95), Expect = 2e-04 Identities = 24/93 (25%), Positives = 44/93 (47%), Gaps = 5/93 (5%) Query: 35 SYQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLA 94 S+ + ++RLE LGD +LG +++ L F A G L LV E + + + L L Sbjct: 329 SHTDVFQRLELLGDAVLGFIVTARLLCLFPDASVGTLVELKMELVRNEALNYLVQTLGLP 388 Query: 95 SFIRVSSDLRKDVCSFMTSIQADVVESLIAALY 127 S++L + AD+ E ++ +++ Sbjct: 389 QLAEFSNNLVAK-----SKTWADMYEEIVGSIF 416 Score = 33.1 bits (75), Expect = 0.047 Identities = 30/124 (24%), Positives = 51/124 (41%), Gaps = 16/124 (12%) Query: 22 LLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSA 81 LL+ ALT Y++LE LGD L ++ L + EG L+ S + Sbjct: 637 LLQIALT--------PHVYQKLELLGDAFLKCSLALHLHALHPTLTEGALTRMRQSAETN 688 Query: 82 ETCSQVARELD---LASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTF 138 ++ + I ++ D + + D E+++AA+ L G E AG F Sbjct: 689 SVLGRLTKRFPSVVSEVIIESHPKIQPD-----SKVYGDTFEAILAAILLACGEEAAGAF 743 Query: 139 VDKY 142 V ++ Sbjct: 744 VREH 747 >3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190 Score = 32.2 bits (72), Expect = 0.11 Identities = 12/62 (19%), Positives = 25/62 (40%), Gaps = 17/62 (27%) Query: 132 IEVAGTFVDKYWKQRALKSGKFRRDAKTELQEWAHAKFGVTPEYKV-------TFRSGPD 184 ++ A +++ W+++A K +L+EW + + K+ F PD Sbjct: 101 LDAASKVMEQEWREKA----------KKDLEEWNQRQSEQVEKNKINNRIADKAFYQQPD 150 Query: 185 HD 186 D Sbjct: 151 AD 152 >1wdd_A Ribulose bisphosphate carboxylase large chain; rubisco, photosynthesis, alpha/beta barrel, N- methylmethionine, post-translational modification; HET: KCX CAP; 1.35A {Oryza sativa} SCOP: c.1.14.1 d.58.9.1 PDB: 1rlc_L* 4rub_A* 3rub_L 1ej7_L 1aa1_L* 1aus_L 1rbo_L* 1rco_L* 1rcx_L* 1rxo_L* 1gk8_A* 1ir2_A* 1uzd_A* 1uzh_A* 2v69_A* 1uwa_A* 2v63_A* 2v67_A* 8ruc_A* 1upm_B* ... Length = 477 Score = 29.4 bits (66), Expect = 0.74 Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 3/59 (5%) Query: 158 KTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAA 216 +TE + K GV +YK+T+ + P+++ + T ++ + P G+ + A VAA Sbjct: 4 QTETKASVGFKAGVK-DYKLTYYT-PEYETKDTDILAAFRVTPQPGVP-PEEAGAAVAA 59 >3evf_A RNA-directed RNA polymerase NS5; NS5 methyltransferase, RNA CAP binding, ATP-binding, capsid protein, cleavage on PAIR of basic residues; HET: GTA SAH; 1.45A {Yellow fever virus 17D} PDB: 3evb_A* 3evc_A* 3evd_A* 3eve_A* 3eva_A* Length = 277 Score = 26.4 bits (58), Expect = 5.4 Identities = 9/49 (18%), Positives = 18/49 (36%), Gaps = 1/49 (2%) Query: 129 DGGIEVAGTFVDKYWKQRALKSGKFRRDAKTELQEWAHAKFGVTPEYKV 177 +EV ++ + + +G +L W H + V E +V Sbjct: 31 TDIVEVDRDTARRHLAEGKVDTGVAVSRGTAKL-RWFHERGYVKLEGRV 78 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 0.319 0.132 0.377 Gapped Lambda K H 0.267 0.0545 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 1,874,019 Number of extensions: 82240 Number of successful extensions: 241 Number of sequences better than 10.0: 1 Number of HSP's gapped: 195 Number of HSP's successfully gapped: 46 Length of query: 227 Length of database: 5,693,230 Length adjustment: 89 Effective length of query: 138 Effective length of database: 3,535,514 Effective search space: 487900932 Effective search space used: 487900932 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 (21.8 bits) S2: 55 (25.4 bits)