RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy9745
         (570 letters)



>d1mu2a1 c.55.3.1 (A:430-555) HIV RNase H (Domain of reverse
           transcriptase) {Human immunodeficiency virus type 2
           [TaxId: 11709]}
          Length = 126

 Score = 42.2 bits (98), Expect = 2e-05
 Identities = 25/124 (20%), Positives = 41/124 (33%), Gaps = 13/124 (10%)

Query: 379 FTDGS--KTTDHTGAAFIIRDEICSMKLNPICSIFTAELIAIEKCLEKIKDVVTHDLVTQ 436
           +TDGS  + +    A ++       +K     +   AEL A    L              
Sbjct: 11  YTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALTDSG---------P 61

Query: 437 NFIICSDSKSSLQALQNVYHVSPLVCDIISTIQDIRDLGTRVSFLWIPSHLGIRENDNVD 496
              I  DS+  +  + +    S          + I+     +   W+P+H GI  N  VD
Sbjct: 62  KVNIIVDSQYVMGIVASQPTESESKIVNQIIEEMIKK--EAIYVAWVPAHKGIGGNQEVD 119

Query: 497 HAAR 500
           H   
Sbjct: 120 HLVS 123


>d1wdua_ d.151.1.1 (A:) Endonuclease domain of TRAS1 retrotransposon
           (ORF2) {Silkworm (Bombyx mori) [TaxId: 7091]}
          Length = 228

 Score = 35.8 bits (81), Expect = 0.008
 Identities = 23/90 (25%), Positives = 37/90 (41%), Gaps = 3/90 (3%)

Query: 89  IKRQLPRPYIICSDMNAHNTIWGGSKIDSNGVQVEKFLLENDDVCLLNTNEATHFNSSNG 148
            ++  P+  I   D NA +T WG  + D+ G Q+   L E     L   +  T      G
Sbjct: 124 ERKMGPKRLIFGGDANAKSTWWGSKEDDARGDQLMGTLGELGLHILNEGDVPTFDTIRGG 183

Query: 149 TF--SAIDLTLASRSITPDLK-WSVHDDLY 175
               S +D+T  +  +   +  W V +DL 
Sbjct: 184 KRYQSRVDVTFCTEDMLDLIDGWRVDEDLV 213


>d1rila_ c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermophilus
           [TaxId: 274]}
          Length = 147

 Score = 34.2 bits (77), Expect = 0.015
 Identities = 25/133 (18%), Positives = 41/133 (30%), Gaps = 12/133 (9%)

Query: 379 FTDGSKTTD--HTGAAFIIRD---EICSMKLNPICSIFTAELIA------IEKCLEKIKD 427
           FTDG+   +    G A ++R    E          +    EL A        K   ++  
Sbjct: 7   FTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKEPCEVDL 66

Query: 428 VVTHDLVTQNFIICSDSKSSLQALQNVYHVSPLVCDIISTIQDIRDLGTRVSFLWIPSHL 487
                 + + F          +  +          D+   +        RV F ++  H 
Sbjct: 67  YTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMA-PHRVRFHFVKGHT 125

Query: 488 GIRENDNVDHAAR 500
           G  EN+ VD  AR
Sbjct: 126 GHPENERVDREAR 138


>d1hhsa_ e.8.1.6 (A:) dsRNA phage RNA-dependent RNA-polymerase
           {Bacteriophage PHI-6 [TaxId: 10879]}
          Length = 664

 Score = 33.4 bits (76), Expect = 0.084
 Identities = 16/81 (19%), Positives = 30/81 (37%), Gaps = 17/81 (20%)

Query: 1   TVHSEEITINSPLQVVAARVRSPVLSCPLTVCCLYIS----HDRKITKDEIYNIKRQLPR 56
           T       +N+P+  VA  VR+ + S        Y        R   ++++         
Sbjct: 271 TAMGGPFALNAPIMAVAQPVRNKIYS-------KYAYTFHHTTRLNKEEKVKEWS----- 318

Query: 57  PYIICSDMNAHNTIWGGSKID 77
              + +D++ H+T W G   D
Sbjct: 319 -LCVATDVSDHDTFWPGWLRD 338


>d1jl1a_ c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli [TaxId:
           562]}
          Length = 152

 Score = 31.1 bits (69), Expect = 0.15
 Identities = 19/132 (14%), Positives = 37/132 (28%), Gaps = 11/132 (8%)

Query: 379 FTDGS--KTTDHTGAAFIIRDE----ICSMKLNPICSIFTAELIAIEKCLEKIKDVVTHD 432
           FT GS        G   I+R        S       +     + AI       +      
Sbjct: 6   FTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHAEVIL 65

Query: 433 LVTQNFIICSDSKSSLQALQNVYHVS----PLVCDIISTIQDIRDLGTRVSFLWIPSHLG 488
                ++    ++      +  +  +        D+   +        ++ + W+  H G
Sbjct: 66  STDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG-QHQIKWEWVKGHAG 124

Query: 489 IRENDNVDHAAR 500
             EN+  D  AR
Sbjct: 125 HPENERADELAR 136


>d1vr9a3 d.37.1.1 (A:1-121) Hypothetical protein TM0892, CBS tandem
           {Thermotoga maritima [TaxId: 2336]}
          Length = 121

 Score = 26.0 bits (56), Expect = 6.9
 Identities = 14/100 (14%), Positives = 25/100 (25%), Gaps = 6/100 (6%)

Query: 424 KIKDVVTHDLVTQN------FIICSDSKSSLQALQNVYHVSPLVCDIISTIQDIRDLGTR 477
           K+K  VT D             +    +                  +        DL + 
Sbjct: 2   KVKKWVTQDFPMVEESATVRECLHRMRQYQTNECIVKDREGHFRGVVNKEDLLDLDLDSS 61

Query: 478 VSFLWIPSHLGIRENDNVDHAARHCNDVPITKVCISDDHK 517
           V          + E DN+ HA     +     + + D+  
Sbjct: 62  VFNKVSLPDFFVHEEDNITHALLLFLEHQEPYLPVVDEEM 101


>d2bcqa2 a.60.12.1 (A:329-385) DNA polymerase lambda {Human (Homo
           sapiens) [TaxId: 9606]}
          Length = 57

 Score = 24.2 bits (53), Expect = 8.6
 Identities = 7/36 (19%), Positives = 14/36 (38%), Gaps = 5/36 (13%)

Query: 442 SDSKSSLQALQNVYHVSP-----LVCDIISTIQDIR 472
           S+S   L+   N++                +++DIR
Sbjct: 1   SESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIR 36


  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
   0.320    0.135    0.407 

Gapped
Lambda     K      H
   0.267   0.0552    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 2,134,301
Number of extensions: 100277
Number of successful extensions: 229
Number of sequences better than 10.0: 1
Number of HSP's gapped: 227
Number of HSP's successfully gapped: 8
Length of query: 570
Length of database: 2,407,596
Length adjustment: 90
Effective length of query: 480
Effective length of database: 1,171,896
Effective search space: 562510080
Effective search space used: 562510080
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)