RPS-BLAST 2.2.22 [Sep-27-2009]

Database: mmdb70 
           33,805 sequences; 4,956,049 total letters

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

Query= gi|254780940|ref|YP_003065353.1| ribonuclease III [Candidatus
Liberibacter asiaticus str. psy62]
         (227 letters)



>2a11_A Ribonuclease III, RNAse III; nuclease domain, structural
           genomics, PSI, protein structure initiative; 2.10A
           {Mycobacterium tuberculosis} (A:)
          Length = 242

 Score =  124 bits (311), Expect = 1e-29
 Identities = 67/223 (30%), Positives = 99/223 (44%), Gaps = 7/223 (3%)

Query: 6   YSTLEKRIGYAFANRSLLEKALTHSSISHSYQE--SYERLEFLGDRILGLLISTLLFNHF 63
              L   +G    +  LL  ALTH S ++      + ERLEFLGD +LGL I+  LF+  
Sbjct: 7   RQPLLDALGVDLPDE-LLSLALTHRSYAYENGGLPTNERLEFLGDAVLGLTITDALFHRH 65

Query: 64  DSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFM---TSIQADVVE 120
               EG+L+    S+V+ +  + VAR L            R +  +     +SI AD +E
Sbjct: 66  PDRSEGDLAKLRASVVNTQALADVARRLCAEGLGVHVLLGRGEANTGGADKSSILADGME 125

Query: 121 SLIAALYLDGGIEVAGTFVDKYWKQRALKSGKF-RRDAKTELQEWAHAKFGVTPEYKVTF 179
           SL+ A+YL  G+E A   + + +      +             +   A  G+     +  
Sbjct: 126 SLLGAIYLQHGMEKAREVILRLFGPLLDAAPTLGAGLDWKTSLQELTAARGLGAPSYLVT 185

Query: 180 RSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKR 222
            +GPDHD  FT VV +       G+  SK+ AEQ AAA   K 
Sbjct: 186 STGPDHDKEFTAVVVVMDSEYGSGVGRSKKEAEQKAAAAAWKA 228


>1o0w_A Ribonuclease III, RNAse III; TM1102, structural genomics,
           JCSG, PSI, protein structure initiative, joint center
           for structural genomics; 2.00A {Thermotoga maritima}
           (A:1-177)
          Length = 177

 Score =  114 bits (285), Expect = 1e-26
 Identities = 46/148 (31%), Positives = 75/148 (50%), Gaps = 7/148 (4%)

Query: 6   YSTLEKRIGYAFANRSLLEKALTHSSISHSYQ-------ESYERLEFLGDRILGLLISTL 58
               +K  G  F N  LL +AL HSS ++          ES E+LEFLGD +L L +  +
Sbjct: 21  VEEFQKETGINFKNEELLFRALCHSSYANEQNQAGRKDVESNEKLEFLGDAVLELFVCEI 80

Query: 59  LFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADV 118
           L+  +  A+ G+L+   ++  S E  + V+R+++L  F+ +     K       SI AD 
Sbjct: 81  LYKKYPEAEVGDLARVKSAAASEEVLAMVSRKMNLGKFLFLGKGEEKTGGRDRDSILADA 140

Query: 119 VESLIAALYLDGGIEVAGTFVDKYWKQR 146
            E+L+AA+YLD G E      ++ ++  
Sbjct: 141 FEALLAAIYLDQGYEKIKELFEQEFEFY 168


>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 (A:1-199)
          Length = 199

 Score =  114 bits (285), Expect = 1e-26
 Identities = 44/179 (24%), Positives = 70/179 (39%), Gaps = 35/179 (19%)

Query: 6   YSTLEKRIGYAFANRSLLEKALTHSSISH-SYQESYERLEFLGDRILGLLISTLLFNHFD 64
           + T EK+I Y F N++ L +A TH+S  + +  + Y+RLEFLGD IL  LI+  L+    
Sbjct: 15  FETFEKKINYRFKNKAYLLQAFTHASYHYNTITDXYQRLEFLGDAILDYLITKHLYEDPR 74

Query: 65  SAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDV----------------- 107
               G L+   ++LV+    + +A + D   + +  S     V                 
Sbjct: 75  QHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVKFQLEKNEXQGX 134

Query: 108 ---------------CSFMTSIQADVVESLIAALYLDGG--IEVAGTFVDKYWKQRALK 149
                             +     D+ ESL  A+Y D G  +EV         +    K
Sbjct: 135 DSELRRSEEDEEKEEDIEVPKAXGDIFESLAGAIYXDSGXSLEVVWQVYYPXXQPLIEK 193


>2nug_A Ribonuclease III, RNAse III; dsRNA, RNA interference,
           endonucleolytic cleavage, hydrolase/RNA complex; 1.70A
           {Aquifex aeolicus} (A:1-148)
          Length = 148

 Score =  113 bits (284), Expect = 2e-26
 Identities = 55/156 (35%), Positives = 82/156 (52%), Gaps = 13/156 (8%)

Query: 6   YSTLEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDS 65
              LEK++GY F ++SLLEKALTH S S   +E YE LEFLGD ++   I  LL  +  +
Sbjct: 4   LEQLEKKLGYTFKDKSLLEKALTHVSYSK--KEHYETLEFLGDALVNFFIVDLLVQYSPN 61

Query: 66  AKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAA 125
            +EG LS     L+S E  + +A++L+L  FIR+      +      +I  DV E+L AA
Sbjct: 62  KREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINE------TIIGDVFEALWAA 115

Query: 126 LYLDGG--IEVAGTFVDKYWKQRALKSGKFRRDAKT 159
           +Y+D G           K +K+  L      ++ + 
Sbjct: 116 VYIDSGRDANFTRELFYKLFKEDIL---SAIKEGRV 148


>2qvw_A GLP_546_48378_50642; dicer, RNAI,pseudo-merohedral twin,
           hydrolase; 3.00A {Giardia intestinalis} PDB: 2ffl_A
           (A:607-756)
          Length = 150

 Score =  106 bits (265), Expect = 3e-24
 Identities = 31/142 (21%), Positives = 52/142 (36%), Gaps = 10/142 (7%)

Query: 5   RYSTLEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFD 64
           R   +    G       LL+ ALT           Y++LE LGD  L   ++  L     
Sbjct: 14  RSLAVPIPSGTIPFLIRLLQIALTPHV--------YQKLELLGDAFLKCSLALHLHALHP 65

Query: 65  SAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIA 124
           +  EG L+    S  +     ++ +         +     K        +  D  E+++A
Sbjct: 66  TLTEGALTRMRQSAETNSVLGRLTKRFPSVVSEVIIESHPKIQPDS--KVYGDTFEAILA 123

Query: 125 ALYLDGGIEVAGTFVDKYWKQR 146
           A+ L  G E AG FV ++   +
Sbjct: 124 AILLACGEEAAGAFVREHVLPQ 145


>2gsl_A Hypothetical protein; alpha-helical protein, structural
           genomics, PSI, protein structure initiative; 2.60A
           {Fusobacterium nucleatum subsp} (A:)
          Length = 137

 Score = 96.2 bits (239), Expect = 3e-21
 Identities = 23/131 (17%), Positives = 41/131 (31%), Gaps = 14/131 (10%)

Query: 26  ALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCS 85
            +  S        S   L FLGD I  L I               L+    + V+A+  S
Sbjct: 3   NVDFSKDIR--DYSGLELAFLGDAIWELEIRKYY--LQFGYNIPTLNKYVKAKVNAKYQS 58

Query: 86  QVARELDLASFIRVSSDLRKDV----------CSFMTSIQADVVESLIAALYLDGGIEVA 135
            + +++            ++            C+     +A  +E++I A YL    E  
Sbjct: 59  LIYKKIINDLDEEFKVIGKRAKNSNIKTFPRSCTVXEYKEATALEAIIGAXYLLKKEEEI 118

Query: 136 GTFVDKYWKQR 146
              ++   K  
Sbjct: 119 KKIINIVIKGE 129


>2qvw_A GLP_546_48378_50642; dicer, RNAI,pseudo-merohedral twin,
           hydrolase; 3.00A {Giardia intestinalis} PDB: 2ffl_A
           (A:328-440)
          Length = 113

 Score = 93.5 bits (232), Expect = 2e-20
 Identities = 27/110 (24%), Positives = 47/110 (42%), Gaps = 6/110 (5%)

Query: 38  ESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFI 97
           + ++RLE LGD +LG +++  L   F  A  G L      LV  E  + + + L L    
Sbjct: 5   DVFQRLELLGDAVLGFIVTARLLCLFPDASVGTLVELKMELVRNEALNYLVQTLGLPQLA 64

Query: 98  RVSSDLRKDVCSFMTSIQADVVESLIAALYLD-GGIEVAGTFVDKYWKQR 146
             S++L        +   AD+ E ++ +++    GI     F+ K     
Sbjct: 65  EFSNNLVA-----KSKTWADMYEEIVGSIFTGPNGIYGCEEFLAKTLMSP 109


>1u61_A Hypothetical protein; structural genomics, PSI, protein
           structure initiative, midwest center for structural
           genomics, MCSG, unknown function; 2.15A {Bacillus
           cereus} (A:)
          Length = 138

 Score = 84.7 bits (209), Expect = 1e-17
 Identities = 23/122 (18%), Positives = 36/122 (29%), Gaps = 13/122 (10%)

Query: 37  QESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASF 96
           Q +   L + GD +    I   L       +  +L     S VSA+  ++V   L   +F
Sbjct: 9   QLNSLALAYXGDAVYEQYIRYHLLQKGK-VRPNQLHRLGTSFVSAKAQAKVVYHLLETAF 67

Query: 97  IRVS------------SDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWK 144
           +               S          T   +   E+LI   +L    E     V K   
Sbjct: 68  LTEEEEAVLRRGRNANSGTVPKNTDVQTYRHSTAFEALIGYHHLLNNRERLDEIVYKAIA 127

Query: 145 QR 146
             
Sbjct: 128 VL 129


>1whn_A Hypothetical protein riken cDNA 2310016K04; double-stranded
           RNA binding domain, DSRBD, DSRM, riken structural
           genomics/proteomics initiative, RSGI; NMR {Mus musculus}
           (A:)
          Length = 128

 Score = 80.1 bits (197), Expect = 2e-16
 Identities = 22/95 (23%), Positives = 34/95 (35%), Gaps = 12/95 (12%)

Query: 129 DGGIEVAGTFVDKYWKQRALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPR 188
            G I++A  F  + +  +           K  L EW   +    P Y+         D  
Sbjct: 8   SGIIKMAIRFDRRAYPPQ--------ITPKMCLLEWCRREKLPQPVYETV---QRTIDRM 56

Query: 189 FTVVVEISGLAPAQGMDC-SKRAAEQVAAAEVLKR 222
           F  VV ++       +   SK+ AEQ AA   L+ 
Sbjct: 57  FCSVVTVAEQKYQSTLWDKSKKLAEQTAAIVCLRS 91


>1o0w_A Ribonuclease III, RNAse III; TM1102, structural genomics,
           JCSG, PSI, protein structure initiative, joint center
           for structural genomics; 2.00A {Thermotoga maritima}
           (A:178-252)
          Length = 75

 Score = 78.0 bits (192), Expect = 1e-15
 Identities = 23/67 (34%), Positives = 33/67 (49%)

Query: 156 DAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVA 215
           D KT LQE   ++  V PEY +      D D  F V V ++G   A G   +K+ AE+ A
Sbjct: 3   DYKTALQEIVQSEHKVPPEYILVRTEKNDGDRIFVVEVRVNGKTIATGKGRTKKEAEKEA 62

Query: 216 AAEVLKR 222
           A    ++
Sbjct: 63  ARIAYEK 69


>2nug_A Ribonuclease III, RNAse III; dsRNA, RNA interference,
           endonucleolytic cleavage, hydrolase/RNA complex; 1.70A
           {Aquifex aeolicus} (A:149-221)
          Length = 73

 Score = 77.5 bits (191), Expect = 2e-15
 Identities = 25/69 (36%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 154 RRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQ 213
           ++D KT LQE    ++   PEY++    GP H  +F V  +I       G   SK+ AEQ
Sbjct: 1   KKDYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYR-TLGEGKSKKEAEQ 59

Query: 214 VAAAEVLKR 222
            AA E++K 
Sbjct: 60  RAAEELIKL 68


>1t4o_A Ribonuclease III; RNT1P, DSRBD, RNA-binding, hydrolase;
           2.50A {Saccharomyces cerevisiae} (A:)
          Length = 117

 Score = 77.4 bits (190), Expect = 2e-15
 Identities = 12/75 (16%), Positives = 22/75 (29%), Gaps = 1/75 (1%)

Query: 148 LKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCS 207
           +K+ K   +AK +L         +   Y    +                G     G+  +
Sbjct: 1   MKTDKLDMNAKRQLYSLIGYA-SLRLHYVTVKKPTAVDPNSIVECRVGDGTVLGTGVGRN 59

Query: 208 KRAAEQVAAAEVLKR 222
            + A   AA   L+ 
Sbjct: 60  IKIAGIRAAENALRD 74


>1qu6_A Protein kinase PKR; dsRNA-binding domain, solution
           structure, transferase; NMR {Homo sapiens} (A:1-92)
          Length = 92

 Score = 76.9 bits (189), Expect = 2e-15
 Identities = 23/68 (33%), Positives = 31/68 (45%), Gaps = 1/68 (1%)

Query: 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQV 214
                EL  +   K GV  +Y+    SGP HD RFT  V I G    +G   SK+ A+  
Sbjct: 13  GFFMEELNTYRQ-KQGVVLKYQELPNSGPPHDRRFTFQVIIDGREFPEGEGRSKKEAKNA 71

Query: 215 AAAEVLKR 222
           AA   ++ 
Sbjct: 72  AAKLAVEI 79


>1x49_A Interferon-induced, double-stranded RNA- activated protein
           kinase; structure genomics, DSRM domain, structural
           genomics, NPPSFA; NMR {Mus musculus} (A:)
          Length = 97

 Score = 76.1 bits (187), Expect = 3e-15
 Identities = 20/68 (29%), Positives = 26/68 (38%), Gaps = 1/68 (1%)

Query: 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQV 214
                +L ++     GV   YK    SGP HD RFT  V I      +    SK+ A   
Sbjct: 14  GFYMDKLNKYRQ-MHGVAITYKELSTSGPPHDRRFTFQVLIDEKEFPEAKGRSKQEARNA 72

Query: 215 AAAEVLKR 222
           AA   +  
Sbjct: 73  AAKLAVDI 80


>1x48_A Interferon-induced, double-stranded RNA- activated protein
           kinase; structure genomics, DSRM domain, structural
           genomics, NPPSFA; NMR {Mus musculus} (A:)
          Length = 88

 Score = 76.1 bits (187), Expect = 4e-15
 Identities = 13/68 (19%), Positives = 26/68 (38%), Gaps = 2/68 (2%)

Query: 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQV 214
                 +  +A  K  ++  Y+       +   RF    +I       G   +K+ A+Q+
Sbjct: 6   SGYIGLVNSFAQ-KKKLSVNYEQC-EPNSELPQRFICKCKIGQTMYGTGSGVTKQEAKQL 63

Query: 215 AAAEVLKR 222
           AA E  ++
Sbjct: 64  AAKEAYQK 71


>1t4n_A Ribonuclease III; DSRBD, RNA-binding, hydrolase; NMR
           {Saccharomyces cerevisiae} (A:)
          Length = 94

 Score = 75.7 bits (186), Expect = 5e-15
 Identities = 10/68 (14%), Positives = 18/68 (26%), Gaps = 1/68 (1%)

Query: 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQV 214
            +AK +L         +   Y    +                G     G+  + + A   
Sbjct: 6   MNAKRQLYSLIGYA-SLRLHYVTVKKPTAVDPNSIVECRVGDGTVLGTGVGRNIKIAGIR 64

Query: 215 AAAEVLKR 222
           AA   L+ 
Sbjct: 65  AAENALRD 72


>1qu6_A Protein kinase PKR; dsRNA-binding domain, solution
           structure, transferase; NMR {Homo sapiens} (A:93-179)
          Length = 87

 Score = 74.9 bits (184), Expect = 9e-15
 Identities = 14/76 (18%), Positives = 26/76 (34%), Gaps = 2/76 (2%)

Query: 147 ALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDC 206
               G    +    +   A  K  +T  Y+    SG      F    ++     + G   
Sbjct: 4   NSSEGLSMGNYIGLINRIAQKK-RLTVNYEQC-ASGVHGPEGFHYKCKMGQKEYSIGTGS 61

Query: 207 SKRAAEQVAAAEVLKR 222
           +K+ A+Q+AA     +
Sbjct: 62  TKQEAKQLAAKLAYLQ 77


>2b7t_A Double-stranded RNA-specific editase 1; RNA editing,
           RNA-binding protein, hydrolase; NMR {Rattus norvegicus}
           (A:)
          Length = 73

 Score = 74.8 bits (184), Expect = 9e-15
 Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 6/72 (8%)

Query: 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQV 214
           ++A  +L E          +Y +  ++GP H P F + VE++G    +G   +K+ A+  
Sbjct: 7   KNALMQLNEIKP-----GLQYMLLSQTGPVHAPLFVMSVEVNGQ-VFEGSGPTKKKAKLH 60

Query: 215 AAAEVLKREGIW 226
           AA + L+    +
Sbjct: 61  AAEKALRSFVQF 72


>1uil_A Double-stranded RNA-binding motif; structural genomics,
           DSRM, riken structural genomics/proteomics initiative,
           RSGI RNA binding protein; NMR {Mus musculus} (A:)
          Length = 113

 Score = 74.7 bits (183), Expect = 1e-14
 Identities = 21/105 (20%), Positives = 36/105 (34%), Gaps = 12/105 (11%)

Query: 133 EVAGTFVDKYWKQR--ALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFT 190
               + ++         L       +AK  L ++   +  +  EYK T + GPDH+  F 
Sbjct: 2   SSGSSGLESEEVDLNAGLHGNWTLENAKARLNQYFQKE-KIQGEYKYT-QVGPDHNRSFI 59

Query: 191 VVVEISGL-----APAQGMDCSKRAAEQVAAA---EVLKREGIWT 227
             + I          A+    +K+ A Q  A      L   G+  
Sbjct: 60  AEMTIYIKQLGRRIFAREHGSNKKLAAQSCALSLVRQLYHLGVIE 104


>1uhz_A Staufen (RNA binding protein) homolog 2; DSRM, staufen
           homolog 2, structural genomics, riken structural
           genomics/proteomics initiative, RSGI; NMR {Mus musculus}
           (A:)
          Length = 89

 Score = 74.2 bits (182), Expect = 1e-14
 Identities = 15/73 (20%), Positives = 29/73 (39%), Gaps = 1/73 (1%)

Query: 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQV 214
               + L +   A+    P+Y +    G      F + V++     A G   +K+ A++ 
Sbjct: 6   SGPISRLAQIQQARKEKEPDYILLSERGMPRRREFVMQVKVGNE-VATGTGPNKKIAKKN 64

Query: 215 AAAEVLKREGIWT 227
           AA  +L + G   
Sbjct: 65  AAEAMLLQLGYKA 77


>1ekz_A DSRBDIII, maternal effect protein (staufen); structure,
           protein/RNA, protein DSRBD, RNA hairpin; NMR {Drosophila
           melanogaster} (A:)
          Length = 76

 Score = 73.7 bits (181), Expect = 2e-14
 Identities = 13/68 (19%), Positives = 29/68 (42%), Gaps = 2/68 (2%)

Query: 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQV 214
           +   +++ E    +  +T  +KV    GP H   F     +  +   +G    K+ +++ 
Sbjct: 7   KSPISQVHEIGIKR-NMTVHFKVLREEGPAHMKNFITACIVGSI-VTEGEGNGKKVSKKR 64

Query: 215 AAAEVLKR 222
           AA ++L  
Sbjct: 65  AAEKMLVE 72


>1di2_A XLRBPA, double stranded RNA binding protein A; protein-RNA
           complex, protein-RNA interactions, RNA-bining protein;
           1.90A {Xenopus laevis} (A:)
          Length = 69

 Score = 73.3 bits (180), Expect = 2e-14
 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


>2yt4_A Protein DGCR8; DSRBD, RNA binding domain, RNA binding
           protein; 2.60A {Homo sapiens} (A:22-104)
          Length = 83

 Score = 73.4 bits (180), Expect = 2e-14
 Identities = 16/68 (23%), Positives = 23/68 (33%), Gaps = 2/68 (2%)

Query: 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQV 214
           +     L E+      V P Y        +    F   V I G+    G   SK+ A+  
Sbjct: 1   KSEVCILHEYMQRVLKVRPVYNFF--ECENPSEPFGASVTIDGVTYGSGTASSKKLAKNK 58

Query: 215 AAAEVLKR 222
           AA   L+ 
Sbjct: 59  AARATLEI 66


>2dix_A Interferon-inducible double stranded RNA- dependent protein
           kinase activator A; structure genomics, DSRM domain,
           hypothetical protein PRKRA; NMR {Homo sapiens} (A:)
          Length = 84

 Score = 72.2 bits (177), Expect = 5e-14
 Identities = 15/68 (22%), Positives = 23/68 (33%), Gaps = 2/68 (2%)

Query: 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQV 214
           +     L E+        P Y+        H P FT  V +  +    G   SK+ A+  
Sbjct: 8   KTPIQVLHEYGMKT-KNIPVYECERSDVQIHVPTFTFRVTVGDI-TCTGEGTSKKLAKHR 65

Query: 215 AAAEVLKR 222
           AA   +  
Sbjct: 66  AAEAAINI 73


>2cpn_A TAR RNA-binding protein 2; double-stranded RNA binding
           domain, DSRBD, DSRM., structural genomics, NPPSFA; NMR
           {Homo sapiens} (A:)
          Length = 89

 Score = 72.2 bits (177), Expect = 6e-14
 Identities = 24/76 (31%), Positives = 34/76 (44%), Gaps = 1/76 (1%)

Query: 147 ALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDC 206
            +   +   +    LQE    K    PEY VT  SGP H   FT+   +       G   
Sbjct: 8   PVSPQQSECNPVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVERFI-EIGSGT 66

Query: 207 SKRAAEQVAAAEVLKR 222
           SK+ A++ AAA++L R
Sbjct: 67  SKKLAKRNAAAKMLLR 82


>2dmy_A Spermatid perinuclear RNA-binding protein; DSRM domain,
           structural genomics, NPPSFA, national project on protein
           structural and functional analyses; NMR {Homo sapiens}
           (A:)
          Length = 97

 Score = 71.9 bits (176), Expect = 7e-14
 Identities = 19/68 (27%), Positives = 31/68 (45%), Gaps = 3/68 (4%)

Query: 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQV 214
            D    L      +     +YK+  +SGP H P FT+ V++ G    +    SK+ A+  
Sbjct: 16  IDLMNALMRLNQIR--PGLQYKLLSQSGPVHAPVFTMSVDVDGT-TYEASGPSKKTAKLH 72

Query: 215 AAAEVLKR 222
            A +VL+ 
Sbjct: 73  VAVKVLQA 80


>2b7v_A Double-stranded RNA-specific editase 1; RNA editing,
           RNA-binding protein, hydrolase; NMR {Rattus norvegicus}
           (A:)
          Length = 71

 Score = 72.1 bits (177), Expect = 7e-14
 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


>1x47_A DGCR8 protein; structural genomics, DSRM domain, NPPSFA,
           national project on protein structural and functional
           analyses; NMR {Homo sapiens} (A:)
          Length = 98

 Score = 71.5 bits (175), Expect = 1e-13
 Identities = 17/68 (25%), Positives = 23/68 (33%), Gaps = 2/68 (2%)

Query: 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQV 214
           +     L E+      V P Y       P     F   V I G+    G   SK+ A+  
Sbjct: 16  KSEVCILHEYMQRVLKVRPVYNFFECENPSE--PFGASVTIDGVTYGSGTASSKKLAKNK 73

Query: 215 AAAEVLKR 222
           AA   L+ 
Sbjct: 74  AARATLEI 81


>1whq_A RNA helicase A; double-stranded RNA binding domain, DSRBD,
           DSRM, riken structural genomics/proteomics initiative,
           RSGI, structural genomics; NMR {Mus musculus} (A:)
          Length = 99

 Score = 70.4 bits (172), Expect = 2e-13
 Identities = 15/69 (21%), Positives = 27/69 (39%), Gaps = 3/69 (4%)

Query: 155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLA-PAQGMDCSKRAAEQ 213
              K  L  W   +  +TP Y++    G  +  +F   V + G      G   +K+ A+ 
Sbjct: 6   SGIKNFLYAWCGKR-KMTPAYEIR-AVGNKNRQKFMCEVRVEGFNYAGMGNSTNKKDAQS 63

Query: 214 VAAAEVLKR 222
            AA + +  
Sbjct: 64  NAARDFVNY 72


>2khx_A Ribonuclease 3; drosha, RNA binding domain, hydrolase, gene
           regulation, nuclear protein; NMR {Homo sapiens}
           (A:29-85)
          Length = 57

 Score = 59.0 bits (143), Expect = 6e-10
 Identities = 14/48 (29%), Positives = 19/48 (39%)

Query: 180 RSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREGIWT 227
             GP H   +TV V   G     G   S + AE  AA + L++     
Sbjct: 3   TVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEKYNFPQ 50


>2qyf_B MAD2L1-binding protein; MAD2 family, spindle assembly
           checkpoint, cell cycle, cell division, mitosis, nucleus,
           phosphorylation; 2.30A {Homo sapiens} (B:)
          Length = 240

 Score = 25.9 bits (57), Expect = 4.5
 Identities = 13/52 (25%), Positives = 16/52 (30%), Gaps = 16/52 (30%)

Query: 71  LSVRFNSLVSAETCSQVAREL----------------DLASFIRVSSDLRKD 106
           + V F   VS E C Q   EL                 L  F R  S   ++
Sbjct: 22  VPVVFPGPVSQEGCCQFTCELLKHIXYQRQQLPLPYEQLKHFYRKPSPQAEE 73


>2qx5_A Nucleoporin NIC96; mRNA transport, nuclear pore complex,
           nucleus, protein transport, translocation, transport,
           transport protein; 2.50A {Saccharomyces cerevisiae} PDB:
           2rfo_A (A:89-295)
          Length = 207

 Score = 25.2 bits (55), Expect = 7.6
 Identities = 16/74 (21%), Positives = 25/74 (33%), Gaps = 14/74 (18%)

Query: 151 GKFRRDAKTELQEWAHAKFGVTP---------EYKVTFRSGPDHDPRFTVVVEISGLAPA 201
            K  +   T  + +A +K    P         EY    +S  D DP    V ++ G    
Sbjct: 95  KKVEQSFLTYFKAYASSKDHGLPVEYSTKLHTEYNQHIKSSLDGDPYRLAVYKLIG---- 150

Query: 202 QGMDCSKRAAEQVA 215
              D S++    V 
Sbjct: 151 -RCDLSRKNIPAVT 163


>1pzx_A Hypothetical protein APC36103; structural genomics, two
          domains containing mixed alpha/beta structures, PSI;
          HET: PLM; 2.00A {Geobacillus stearothermophilus}
          (A:1-29,A:66-158)
          Length = 122

 Score = 24.9 bits (54), Expect = 8.6
 Identities = 5/32 (15%), Positives = 11/32 (34%)

Query: 36 YQESYERLEFLGDRILGLLISTLLFNHFDSAK 67
           +E +          L +  S+ L   + +A 
Sbjct: 34 MKELFLPYAKENRPCLYIAFSSKLSGTYQTAM 65


  Database: mmdb70
    Posted date:  Jun 20, 2010  3:12 AM
  Number of letters in database: 4,956,049
  Number of sequences in database:  33,805
  
Lambda     K      H
   0.319    0.132    0.377 

Gapped
Lambda     K      H
   0.267   0.0491    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 1,657,772
Number of extensions: 70522
Number of successful extensions: 204
Number of sequences better than 10.0: 1
Number of HSP's gapped: 161
Number of HSP's successfully gapped: 35
Length of query: 227
Length of database: 4,956,049
Length adjustment: 85
Effective length of query: 142
Effective length of database: 2,082,624
Effective search space: 295732608
Effective search space used: 295732608
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: 53 (24.8 bits)