RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy12122
         (412 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 = 27.6 bits (60), Expect = 1.3
 Identities = 6/16 (37%), Positives = 7/16 (43%)

Query: 53  HVGIAGNEAADREAKS 68
           H GI GN+  D     
Sbjct: 109 HKGIGGNQEVDHLVSQ 124


>d1d4ua2 g.39.1.5 (A:1-36) DNA repair factor XPA DNA- and
           RPA-binding domain, N-terminal subdomain {Human (Homo
           sapiens) [TaxId: 9606]}
          Length = 36

 Score = 25.5 bits (56), Expect = 1.3
 Identities = 7/15 (46%), Positives = 8/15 (53%)

Query: 150 SFLFRREDPPVCDKC 164
           S+L    D P CD C
Sbjct: 18  SYLMDHFDLPTCDDC 32


>d1t47a2 d.32.1.3 (A:179-377) 4-hydroxyphenylpyruvate dioxygenase,
           HppD {Streptomyces avermitilis [TaxId: 33903]}
          Length = 199

 Score = 28.0 bits (62), Expect = 1.5
 Identities = 29/134 (21%), Positives = 43/134 (32%), Gaps = 33/134 (24%)

Query: 148 THSFLFRREDPPVCDKCNVPLTVEHIVLSCRKMRFRPNSFLN------STLSDVLKDDPD 201
              +L       V     + L    IV + R MR     FL+       TL + + D   
Sbjct: 78  IDEYLEFYGGAGVQH---IALNTGDIVETVRTMRAAGVQFLDTPDSYYDTLGEWVGDTRV 134

Query: 202 SVATLMRF---LKRNN-------FPKELYRRSGLYPGSPGFYRGEDLKRVQSVMYRGYEG 251
            V TL        R+        F K +  R  +      F+  E ++R       G  G
Sbjct: 135 PVDTLRELKILADRDEDGYLLQIFTKPVQDRPTV------FF--EIIER------HGSMG 180

Query: 252 VGAPNFRRPSHSKE 265
            G  NF+    + E
Sbjct: 181 FGKGNFKALFEAIE 194


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

 Score = 27.6 bits (60), Expect = 1.7
 Identities = 8/15 (53%), Positives = 9/15 (60%)

Query: 53  HVGIAGNEAADREAK 67
           H G   NE  DREA+
Sbjct: 124 HTGHPENERVDREAR 138


>d1udxa3 d.242.1.1 (A:341-416) Obg GTP-binding protein C-terminal
           domain {Thermus thermophilus [TaxId: 274]}
          Length = 76

 Score = 25.7 bits (57), Expect = 2.5
 Identities = 7/31 (22%), Positives = 11/31 (35%), Gaps = 1/31 (3%)

Query: 198 DDPDSVATLMRFLKRNNFPKELYRRSGLYPG 228
           D  ++   L    +R      L R  G+  G
Sbjct: 31  DLMEAAGYLQEVFRRQGVEAAL-RAKGVRAG 60


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

 Score = 26.1 bits (56), Expect = 5.1
 Identities = 7/15 (46%), Positives = 8/15 (53%)

Query: 53  HVGIAGNEAADREAK 67
           H G   NE AD  A+
Sbjct: 122 HAGHPENERADELAR 136


>d1a8ra_ d.96.1.1 (A:) GTP cyclohydrolase I {Escherichia coli
           [TaxId: 562]}
          Length = 221

 Score = 26.5 bits (58), Expect = 5.5
 Identities = 9/57 (15%), Positives = 27/57 (47%), Gaps = 2/57 (3%)

Query: 160 VCDKCNVPLTVE--HIVLSCRKMRFRPNSFLNSTLSDVLKDDPDSVATLMRFLKRNN 214
           +    NV ++++  H  +  R +R   ++   ++L  + K   ++    +R ++ +N
Sbjct: 165 LLGTNNVAVSIDAVHYCVKARGIRDATSATTTTSLGGLFKSSQNTRHEFLRAVRHHN 221


  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    0.137    0.425 

Gapped
Lambda     K      H
   0.267   0.0743    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 1,559,379
Number of extensions: 71927
Number of successful extensions: 160
Number of sequences better than 10.0: 1
Number of HSP's gapped: 160
Number of HSP's successfully gapped: 7
Length of query: 412
Length of database: 2,407,596
Length adjustment: 88
Effective length of query: 324
Effective length of database: 1,199,356
Effective search space: 388591344
Effective search space used: 388591344
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: 54 (24.6 bits)