RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy3058
         (244 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 = 45.3 bits (106), Expect = 6e-07
 Identities = 16/85 (18%), Positives = 33/85 (38%), Gaps = 2/85 (2%)

Query: 17  AFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKNILIHDIQVACHKLILKGNNV 76
               E+    +        + I  DS+ ++  +     ++      Q+    +  +   +
Sbjct: 44  NQQAELEAFAMALTDSGPKVNIIVDSQYVMGIVASQPTESESKIVNQIIEEMIKKE--AI 101

Query: 77  KIIWIPSHCGIAGNEEVDKAAQSFI 101
            + W+P+H GI GN+EVD      I
Sbjct: 102 YVAWVPAHKGIGGNQEVDHLVSQGI 126


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

 Score = 39.9 bits (92), Expect = 6e-05
 Identities = 17/104 (16%), Positives = 38/104 (36%), Gaps = 12/104 (11%)

Query: 13  FTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKN------------ILIH 60
            T     ++  ++ L     P  + ++TDS  L  +  + + +              + +
Sbjct: 41  TTNNRMELKAAIEGLKALKEPCEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKN 100

Query: 61  DIQVACHKLILKGNNVKIIWIPSHCGIAGNEEVDKAAQSFINAQ 104
                   L +  + V+  ++  H G   NE VD+ A+    +Q
Sbjct: 101 RDLWEALLLAMAPHRVRFHFVKGHTGHPENERVDREARRQAQSQ 144


>d1s1ta1 c.55.3.1 (A:430-539) HIV RNase H (Domain of reverse
           transcriptase) {Human immunodeficiency virus type 1
           [TaxId: 11676]}
          Length = 110

 Score = 32.6 bits (74), Expect = 0.012
 Identities = 14/75 (18%), Positives = 33/75 (44%), Gaps = 7/75 (9%)

Query: 10  SSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKNILIHDIQVACHKL 69
           +++   E  A+ + L +         + I TDS+  +  +Q    ++      Q+   + 
Sbjct: 43  TTNQKTELQAIYLALQDS-----GLEVNIVTDSQYALGIIQAQPDQSESELVNQII--EQ 95

Query: 70  ILKGNNVKIIWIPSH 84
           ++K   V + W+P+H
Sbjct: 96  LIKKEKVYLAWVPAH 110


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

 Score = 33.1 bits (74), Expect = 0.013
 Identities = 10/51 (19%), Positives = 19/51 (37%), Gaps = 1/51 (1%)

Query: 55  KNILIHDIQVACHKLILKGNNVKIIWIPSHCGIAGNEEVDKAAQSFINAQN 105
           K +   D+       +   + +K  W+  H G   NE  D+ A++      
Sbjct: 94  KPVKNVDLWQRLDAAL-GQHQIKWEWVKGHAGHPENERADELARAAAMNPT 143


>d1jh6a_ d.61.1.1 (A:) tRNA splicing product Appr>p cyclic
           nucleotide phosphodiesterase {Thale cress (Arabidopsis
           thaliana) [TaxId: 3702]}
          Length = 181

 Score = 29.1 bits (64), Expect = 0.31
 Identities = 10/119 (8%), Positives = 31/119 (26%), Gaps = 2/119 (1%)

Query: 80  WIPSHCGIAGNEEVDKAAQSFINAQNYSLITHVDLKAFLKNEFKKKWQIWWDNIQPPNKI 139
               H  +A +  +       +       +          +     +Q  +  +Q   ++
Sbjct: 38  RFVPHVTVAVSAYLTADEAKKMFESACDGLKAYTATVDRVSTGTFFFQCVFLLLQTTPEV 97

Query: 140 KDTVKEWQTSNRNSRKEEII--LSRLRIGHTRLTHGFLMERTDPPQCEVCNVTITVKHI 196
            +  +  +     S     +  LS L    T        E+       +  ++  +  +
Sbjct: 98  MEAGEHCKNHFNCSTTTPYMPHLSLLYAELTEEEKKNAQEKAYTLDSSLDGLSFRLNRL 156


>d1m32a_ c.67.1.3 (A:) 2-aminoethylphosphonate transaminase
           {Salmonella typhimurium [TaxId: 90371]}
          Length = 361

 Score = 26.7 bits (57), Expect = 3.1
 Identities = 12/138 (8%), Positives = 31/138 (22%), Gaps = 6/138 (4%)

Query: 1   MSTYRLNSLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKS------LISSMQQLFC 54
           M                  +   L  L         ++   S S      L S++     
Sbjct: 19  MLFDSCTWDDDYNIGVVEQIRQQLTALATASEGYTSVLLQGSGSYAVEAVLGSALGPQDK 78

Query: 55  KNILIHDIQVACHKLILKGNNVKIIWIPSHCGIAGNEEVDKAAQSFINAQNYSLITHVDL 114
             I+ +    A    +     +             + +   A  +     ++  + H + 
Sbjct: 79  VLIVSNGAYGARMVEMAGLMGIAHHAYDCGEVARPDVQAIDAILNADPTISHIAMVHSET 138

Query: 115 KAFLKNEFKKKWQIWWDN 132
              + N   +   +    
Sbjct: 139 TTGMLNPIDEVGALAHRY 156


>d2i00a2 d.108.1.10 (A:10-300) Putative acetyltransferase EF2353
           {Enterococcus faecalis [TaxId: 1351]}
          Length = 291

 Score = 25.7 bits (55), Expect = 5.7
 Identities = 5/25 (20%), Positives = 10/25 (40%)

Query: 213 NNLQIKDILGDNPRTIDLLFRFLKD 237
               IK++   N    + L+ F+  
Sbjct: 227 EVFHIKEMFYLNQEARNGLWNFITA 251


  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
   0.323    0.136    0.421 

Gapped
Lambda     K      H
   0.267   0.0660    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 934,787
Number of extensions: 43311
Number of successful extensions: 163
Number of sequences better than 10.0: 1
Number of HSP's gapped: 162
Number of HSP's successfully gapped: 18
Length of query: 244
Length of database: 2,407,596
Length adjustment: 83
Effective length of query: 161
Effective length of database: 1,268,006
Effective search space: 204148966
Effective search space used: 204148966
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 52 (24.0 bits)