RPS-BLAST 2.2.26 [Sep-21-2011]

Database: scop70_1_75 
           13,730 sequences; 2,407,596 total letters

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

Query= 011455
         (485 letters)



>d1sgva2 d.265.1.2 (A:3-235) Pseudouridine synthase II TruB
           {Mycobacterium tuberculosis [TaxId: 1773]}
          Length = 233

 Score =  142 bits (359), Expect = 3e-40
 Identities = 68/147 (46%), Positives = 95/147 (64%)

Query: 312 VLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIK 371
           V+++KP G TS  V G+ RR+   ++VGHAGTLDPMATG+L++ + +ATK++       K
Sbjct: 7   VVIDKPAGMTSHDVVGRCRRIFATRRVGHAGTLDPMATGVLVIGIERATKILGLLTAAPK 66

Query: 372 GYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGG 431
            Y+   RLG+ TST DA+  V+Q  P +H+  E I  A    RGEI QVP   SAIKVGG
Sbjct: 67  SYAATIRLGQTTSTEDAEGQVLQSVPAKHLTIEAIDAAMERLRGEIRQVPSSVSAIKVGG 126

Query: 432 EKMYDKARRGESIELSPRRISIFQFDI 458
            + Y  AR+G S++L  R I I +F++
Sbjct: 127 RRAYRLARQGRSVQLEARPIRIDRFEL 153


>d1k8wa5 d.265.1.2 (A:9-250) Pseudouridine synthase II TruB
           {Escherichia coli [TaxId: 562]}
          Length = 242

 Score =  136 bits (344), Expect = 6e-38
 Identities = 54/157 (34%), Positives = 89/157 (56%), Gaps = 1/157 (0%)

Query: 312 VLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIK 371
           +L++KP+G +S     K++R+    + GH G LDP+ATG+L +C+G+ATK         K
Sbjct: 7   LLLDKPQGMSSNDALQKVKRIYNANRAGHTGALDPLATGMLPICLGEATKFSQYLLDSDK 66

Query: 372 GYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGG 431
            Y  + RLG+ T T DAD  +++  P      E +  A  +FRG+I Q+P M+SA+K  G
Sbjct: 67  RYRVIARLGQRTDTSDADGQIVEERPV-TFSAEQLAAALDTFRGDIEQIPSMYSALKYQG 125

Query: 432 EKMYDKARRGESIELSPRRISIFQFDIERSLEDRFFF 468
           +K+Y+ AR+G  +    R I++++    R   +    
Sbjct: 126 KKLYEYARQGIEVPREARPITVYELLFIRHEGNELEL 162


>d1r3ea2 d.265.1.2 (A:10-237) Pseudouridine synthase II TruB
           {Thermotoga maritima [TaxId: 2336]}
          Length = 228

 Score =  128 bits (322), Expect = 5e-35
 Identities = 62/159 (38%), Positives = 94/159 (59%), Gaps = 1/159 (0%)

Query: 312 VLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIK 371
           ++  KPKG TS  V  ++R+ +K +KVGH GTLDP A G+LI+ V + T++++ Y+ + K
Sbjct: 6   LVAYKPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFYKDLKK 65

Query: 372 GYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGG 431
            Y    RLG  T T+D    V++     ++ +E+IR+A  SF GE  QVPP +SA K  G
Sbjct: 66  VYWVKMRLGLITETFDITGEVVEEREC-NVTEEEIREAIFSFVGEYDQVPPAYSAKKYKG 124

Query: 432 EKMYDKARRGESIELSPRRISIFQFDIERSLEDRFFFFL 470
           E++Y  AR G+ I L P+R+ IF+            F +
Sbjct: 125 ERLYKLAREGKIINLPPKRVKIFKIWDVNIEGRDVSFRV 163


>d2ey4a2 d.265.1.2 (A:8-252) Pseudouridine synthase II TruB
           {Archaeon Pyrococcus furiosus [TaxId: 2261]}
          Length = 245

 Score =  115 bits (289), Expect = 4e-30
 Identities = 35/124 (28%), Positives = 57/124 (45%), Gaps = 18/124 (14%)

Query: 312 VLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIK 371
           + ++KP G TS  V   +++++ ++K GH GTLDP  +G+L V + KAT++V       K
Sbjct: 45  INLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPVALEKATRVVQALLPAGK 104

Query: 372 GYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGG 431
            Y  +  L                     + ++ I +    F GEI Q PP+ SA+K   
Sbjct: 105 EYVALMHL------------------HGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRRL 146

Query: 432 EKMY 435
               
Sbjct: 147 RTRK 150


>d2apoa2 d.265.1.2 (A:17-246) Pseudouridine synthase II TruB
           {Archaeon Methanococcus jannaschii [TaxId: 2190]}
          Length = 230

 Score =  100 bits (249), Expect = 8e-25
 Identities = 41/148 (27%), Positives = 68/148 (45%), Gaps = 23/148 (15%)

Query: 312 VLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIK 371
           V+V+KP+G TS  V   +++++ + K GH GTLDP  TG+L V + +ATK +  +    K
Sbjct: 32  VVVDKPRGPTSHEVSTWVKKILNLDKAGHGGTLDPKVTGVLPVALERATKTIPMWHIPPK 91

Query: 372 GYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGG 431
            Y  +  L                       +EDI +    F G I+Q PP+ +A+    
Sbjct: 92  EYVCLMHL------------------HRDASEEDILRVFKEFTGRIYQRPPLKAAV---- 129

Query: 432 EKMYDKARRGESIELSPRRISIFQFDIE 459
            K   + R+   +EL  +      F ++
Sbjct: 130 -KRRLRIRKIHELELLDKDGKDVLFRVK 156


>d1c3ya_ a.39.2.1 (A:) Thp12-carrier protein {Yellow mealworm
           (Tenebrio molitor) [TaxId: 7067]}
          Length = 108

 Score = 28.4 bits (63), Expect = 0.67
 Identities = 16/76 (21%), Positives = 29/76 (38%), Gaps = 6/76 (7%)

Query: 207 DPSADQNVKK----MRKKAGGKSEEKKYNKEDDKRLVFFDDQEKKSEKDSILGEDVNVKG 262
           +   D  +K+    + K+AG      ++    D     F +  +  EK   L     VK 
Sbjct: 32  EEVDDPKLKEHAFCILKRAGFIDASGEFQL--DHIKTKFKENSEHPEKVDDLVAKCAVKK 89

Query: 263 EVSEKKVEEFFKCLKK 278
           +  +    +FFKC+  
Sbjct: 90  DTPQHSSADFFKCVHD 105


>d1nc7a_ b.123.1.1 (A:) Hypothetical protein TM1070 {Thermotoga
           maritima [TaxId: 2336]}
          Length = 116

 Score = 25.4 bits (56), Expect = 7.4
 Identities = 7/27 (25%), Positives = 11/27 (40%)

Query: 154 PEVVEFNRLHKREEELYFYDTFAYPWE 180
           P V++ +RL   +       T  Y  E
Sbjct: 89  PVVMQLSRLDVGKNHYTLMTTIGYWEE 115


  Database: scop70_1_75
    Posted date:  Mar 27, 2010  6:21 PM
  Number of letters in database: 2,407,596
  Number of sequences in database:  13,730
  
Lambda     K      H
   0.316    0.135    0.397 

Gapped
Lambda     K      H
   0.267   0.0578    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 1,848,737
Number of extensions: 90360
Number of successful extensions: 213
Number of sequences better than 10.0: 1
Number of HSP's gapped: 209
Number of HSP's successfully gapped: 18
Length of query: 485
Length of database: 2,407,596
Length adjustment: 89
Effective length of query: 396
Effective length of database: 1,185,626
Effective search space: 469507896
Effective search space used: 469507896
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.3 bits)