RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy8412
         (271 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 = 44.9 bits (105), Expect = 1e-06
 Identities = 23/121 (19%), Positives = 41/121 (33%), Gaps = 8/121 (6%)

Query: 17  FTDGS--KTPDSTSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIV 74
           +TDGS  +        +               +   AEL A  + L            I+
Sbjct: 11  YTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALT----DSGPKVNII 66

Query: 75  SDSKSSLTALFNIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARN 134
            DS+  +  + +    +   SK+ +      +  + +   W P+H GI GN+ VD     
Sbjct: 67  VDSQYVMGIVASQPTESE--SKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQ 124

Query: 135 A 135
            
Sbjct: 125 G 125


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

 Score = 38.8 bits (89), Expect = 1e-04
 Identities = 26/135 (19%), Positives = 42/135 (31%), Gaps = 15/135 (11%)

Query: 17  FTDGS--KTPDSTSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIV 74
           FTDG+    P     A  +    H  LL+   +  +   M +   +E +    +   + +
Sbjct: 7   FTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKEPCEVDL 66

Query: 75  SDSKSSLTALFNIRFTNPLISKVYST-------------WSFLKLNNKNVSFMWCPSHCG 121
                 L   F   +      + + T                L +    V F +   H G
Sbjct: 67  YTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGHTG 126

Query: 122 IRGNEIVDEAARNAA 136
              NE VD  AR  A
Sbjct: 127 HPENERVDREARRQA 141


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

 Score = 38.5 bits (88), Expect = 2e-04
 Identities = 24/134 (17%), Positives = 39/134 (29%), Gaps = 14/134 (10%)

Query: 17  FTDGS--KTPDSTSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIV 74
           FT GS    P        +         +   +  +   M +   + A+    +H  +I+
Sbjct: 6   FTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHAEVIL 65

Query: 75  SDSKSSLTALFNIRFTN------------PLISKVYSTWSFLKLNNKNVSFMWCPSHCGI 122
           S     +         N            P+ +          L    + + W   H G 
Sbjct: 66  STDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGH 125

Query: 123 RGNEIVDEAARNAA 136
             NE  DE AR AA
Sbjct: 126 PENERADELARAAA 139


>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 = 33.0 bits (75), Expect = 0.008
 Identities = 19/107 (17%), Positives = 34/107 (31%), Gaps = 12/107 (11%)

Query: 17  FTDGS--KTPDSTSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIV 74
           + DG+  +        +         +     +    EL AI+L L+           IV
Sbjct: 12  YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDS----GLEVNIV 67

Query: 75  SDSKSSLTALFNIRFTNPLISKVYSTWSFLKL--NNKNVSFMWCPSH 119
           +DS+        I    P  S+       ++     + V   W P+H
Sbjct: 68  TDSQ----YALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAH 110


>d1tuga1 c.78.1.1 (A:1-150,A:151-310) Aspartate carbamoyltransferase
           catalytic subunit {Escherichia coli [TaxId: 562]}
          Length = 310

 Score = 30.3 bits (67), Expect = 0.23
 Identities = 6/35 (17%), Positives = 12/35 (34%), Gaps = 4/35 (11%)

Query: 104 LKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASI 138
           L     N+  +    H   R +EI  +  +   + 
Sbjct: 254 LHNAKANMKVL----HPLPRVDEIATDVDKTPHAW 284


>d3ci0j1 d.24.1.5 (J:39-192) Pseudopilin GspJ {Escherichia coli
           [TaxId: 562]}
          Length = 154

 Score = 28.3 bits (63), Expect = 0.57
 Identities = 6/32 (18%), Positives = 13/32 (40%), Gaps = 4/32 (12%)

Query: 153 ISFLIKSEWQNQWNHIPNTNKL-KAIKPTIEH 183
           + F   + WQ  W    +   +  A++ T+  
Sbjct: 110 LQFYDGTRWQESW---SSVQAIPVAVRMTLHS 138


>d2retb1 d.24.1.5 (B:32-197) Type II secretory pathway component
           EpsJ {Vibrio vulnificus [TaxId: 672]}
          Length = 166

 Score = 27.7 bits (61), Expect = 1.0
 Identities = 8/32 (25%), Positives = 12/32 (37%), Gaps = 4/32 (12%)

Query: 153 ISFLIKSEWQNQWNHIPNTNKL-KAIKPTIEH 183
           + F    +W N+W    N   L  AI   +  
Sbjct: 119 VRFYDGKQWINEW---SNELTLPAAISVELTL 147


>d1v4pa_ d.67.1.2 (A:) Hypothetical protein PH0574 {Archaeon
           Pyrococcus horikoshii [TaxId: 53953]}
          Length = 151

 Score = 26.0 bits (56), Expect = 4.0
 Identities = 13/88 (14%), Positives = 28/88 (31%), Gaps = 3/88 (3%)

Query: 109 KNVSFMWCPSHCGIRGNEIVDEAARNAASIDPYKLCTPEDLKPFISFLIKSEWQNQWN-- 166
           + ++      +  I+  E+  E A      D Y L    +    +  ++  +W       
Sbjct: 59  ERLANEKVKENAPIKIYELPREEAEKMFGEDMYDLFPVPEDVRILKVVVIEDWNVNACNK 118

Query: 167 -HIPNTNKLKAIKPTIEHWATSNQNKRL 193
            H   T ++  IK     +  S     +
Sbjct: 119 EHTKTTGEIGPIKIRKVRFRKSKGLLEI 146


  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    0.135    0.430 

Gapped
Lambda     K      H
   0.267   0.0597    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 1,036,034
Number of extensions: 45209
Number of successful extensions: 143
Number of sequences better than 10.0: 1
Number of HSP's gapped: 143
Number of HSP's successfully gapped: 16
Length of query: 271
Length of database: 2,407,596
Length adjustment: 84
Effective length of query: 187
Effective length of database: 1,254,276
Effective search space: 234549612
Effective search space used: 234549612
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 (24.1 bits)