RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy12035
         (251 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 = 39.1 bits (90), Expect = 9e-05
 Identities = 16/84 (19%), Positives = 27/84 (32%), Gaps = 1/84 (1%)

Query: 28  TIHHMGIRLISRALKSSP-VNSLYAESAILPLSVRRRLLFSNIIAKQEYYFASTNGSQIS 86
           T     +   + AL  S    ++  +S  +   V  +   S      +          I 
Sbjct: 43  TNQQAELEAFAMALTDSGPKVNIIVDSQYVMGIVASQPTESESKIVNQIIEEMIKKEAIY 102

Query: 87  FMWIPSHSNIALNDKADQLAKNSI 110
             W+P+H  I  N + D L    I
Sbjct: 103 VAWVPAHKGIGGNQEVDHLVSQGI 126


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

 Score = 38.1 bits (87), Expect = 3e-04
 Identities = 11/43 (25%), Positives = 23/43 (53%)

Query: 74  EYYFASTNGSQISFMWIPSHSNIALNDKADQLAKNSINSKLLD 116
           +   A+    QI + W+  H+    N++AD+LA+ +  +  L+
Sbjct: 103 QRLDAALGQHQIKWEWVKGHAGHPENERADELARAAAMNPTLE 145


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

 Score = 37.2 bits (85), Expect = 5e-04
 Identities = 6/38 (15%), Positives = 17/38 (44%)

Query: 76  YFASTNGSQISFMWIPSHSNIALNDKADQLAKNSINSK 113
              +    ++ F ++  H+    N++ D+ A+    S+
Sbjct: 107 LLLAMAPHRVRFHFVKGHTGHPENERVDREARRQAQSQ 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 = 27.3 bits (60), Expect = 0.78
 Identities = 12/85 (14%), Positives = 27/85 (31%), Gaps = 1/85 (1%)

Query: 10  YGCSIFMNANKKYLSHLDTIHHMGIRLISRALKSSPVN-SLYAESAILPLSVRRRLLFSN 68
            G        K       T     ++ I  AL+ S +  ++  +S      ++ +   S 
Sbjct: 26  AGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDQSE 85

Query: 69  IIAKQEYYFASTNGSQISFMWIPSH 93
                +         ++   W+P+H
Sbjct: 86  SELVNQIIEQLIKKEKVYLAWVPAH 110


  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
   0.321    0.134    0.394 

Gapped
Lambda     K      H
   0.267   0.0659    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 917,580
Number of extensions: 41351
Number of successful extensions: 103
Number of sequences better than 10.0: 1
Number of HSP's gapped: 103
Number of HSP's successfully gapped: 9
Length of query: 251
Length of database: 2,407,596
Length adjustment: 83
Effective length of query: 168
Effective length of database: 1,268,006
Effective search space: 213025008
Effective search space used: 213025008
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 (21.9 bits)
S2: 52 (24.0 bits)