RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy11904
         (199 letters)



>d1k3xa3 g.39.1.8 (A:223-262) Endonuclease VIII {Escherichia coli
           [TaxId: 562]}
          Length = 40

 Score = 26.5 bits (59), Expect = 0.32
 Identities = 7/35 (20%), Positives = 14/35 (40%), Gaps = 5/35 (14%)

Query: 100 RFNPYTQKFESCKIC-----RQKVHQVGSHYCQAC 129
           RF  + +  E C+ C     +  +     ++C  C
Sbjct: 4   RFKVFHRDGEPCERCGSIIEKTTLSSRPFYWCPGC 38


>d1r2za3 g.39.1.8 (A:229-274) DNA repair protein MutM (Fpg)
           {Bacillus stearothermophilus [TaxId: 1422]}
          Length = 46

 Score = 25.8 bits (57), Expect = 0.72
 Identities = 9/35 (25%), Positives = 14/35 (40%), Gaps = 5/35 (14%)

Query: 100 RFNPYTQKFESCKICRQKVHQV-----GSHYCQAC 129
               Y ++   CK C   + +      G+HYC  C
Sbjct: 10  HLYVYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRC 44


>d1ee8a3 g.39.1.8 (A:211-266) DNA repair protein MutM (Fpg) {Thermus
           thermophilus [TaxId: 274]}
          Length = 56

 Score = 25.2 bits (55), Expect = 1.2
 Identities = 9/35 (25%), Positives = 15/35 (42%), Gaps = 5/35 (14%)

Query: 100 RFNPYTQKFESCKICRQKVHQV-----GSHYCQAC 129
           R   Y ++   C  C + V +      G+H+C  C
Sbjct: 17  RHAVYGREGLPCPACGRPVERRVVAGRGTHFCPTC 51


>d1tdza3 g.39.1.8 (A:225-271) DNA repair protein MutM (Fpg)
           {Lactococcus lactis [TaxId: 1358]}
          Length = 47

 Score = 25.0 bits (55), Expect = 1.4
 Identities = 8/35 (22%), Positives = 15/35 (42%), Gaps = 5/35 (14%)

Query: 100 RFNPYTQKFESCKICRQKVHQV-----GSHYCQAC 129
               Y +  E C  C  ++ ++     G+H+C  C
Sbjct: 10  ELQVYGKTGEKCSRCGAEIQKIKVAGRGTHFCPVC 44


>d1k82a3 g.39.1.8 (A:225-268) DNA repair protein MutM (Fpg)
           {Escherichia coli [TaxId: 562]}
          Length = 44

 Score = 24.6 bits (54), Expect = 1.6
 Identities = 8/35 (22%), Positives = 14/35 (40%), Gaps = 5/35 (14%)

Query: 100 RFNPYTQKFESCKICRQKVHQV-----GSHYCQAC 129
               Y +K E C++C   +         + YC+ C
Sbjct: 8   ELQVYGRKGEPCRVCGTPIVATKHAQRATFYCRQC 42


>d2o3ga1 d.145.1.4 (A:180-255) Putative protein NMB1485 {Neisseria
           meningitidis [TaxId: 487]}
          Length = 76

 Score = 24.3 bits (53), Expect = 3.6
 Identities = 8/37 (21%), Positives = 15/37 (40%)

Query: 143 DPEKGDKFALISGEHLVLVTADPEKGDKFAFDNHAFK 179
             E+   F  ++G  +  +   P+ GD   F    F+
Sbjct: 22  QQEEDADFHTVAGLIMEELQTIPDVGDFADFHGWRFE 58


>d1dszb_ g.39.1.2 (B:) Retinoid X receptor (RXR-alpha) DNA-binding
           domain {Human (Homo sapiens) [TaxId: 9606]}
          Length = 84

 Score = 24.1 bits (52), Expect = 6.2
 Identities = 6/34 (17%), Positives = 11/34 (32%)

Query: 100 RFNPYTQKFESCKICRQKVHQVGSHYCQACAYKK 133
           R       +         + +   + CQ C Y+K
Sbjct: 34  RTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQK 67


  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
   0.318    0.133    0.402 

Gapped
Lambda     K      H
   0.267   0.0642    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 765,656
Number of extensions: 34868
Number of successful extensions: 153
Number of sequences better than 10.0: 1
Number of HSP's gapped: 150
Number of HSP's successfully gapped: 22
Length of query: 199
Length of database: 2,407,596
Length adjustment: 81
Effective length of query: 118
Effective length of database: 1,295,466
Effective search space: 152864988
Effective search space used: 152864988
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 (21.7 bits)
S2: 50 (23.2 bits)