RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy9180
         (491 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 = 47.2 bits (111), Expect = 3e-07
 Identities = 25/119 (21%), Positives = 46/119 (38%), Gaps = 8/119 (6%)

Query: 153 YTDGSKTMNTT--SCAFSIDDLISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIV 210
           YTDGS    +      +  D      +     +   AEL A  + L         +  I+
Sbjct: 11  YTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALT----DSGPKVNII 66

Query: 211 SDSRSALAALSNVSFTNPLVSKVYSCWDLLRSRNKVVHFLWCPSHCGIRGNEAVDEAAR 269
            DS+  +  +++    +   SK+ +       + + ++  W P+H GI GN+ VD    
Sbjct: 67  VDSQYVMGIVASQPTESE--SKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVS 123


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

 Score = 41.1 bits (95), Expect = 5e-05
 Identities = 25/133 (18%), Positives = 42/133 (31%), Gaps = 15/133 (11%)

Query: 153 YTDGSKTMNTTSCAFSI-----DDLISSSQLNPVNSIFSAELIAIYLCLEA------ITV 201
           +TDG+   N     ++            S      +    EL A    L+A      + +
Sbjct: 7   FTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKEPCEVDL 66

Query: 202 HPSDQFLIVSDSRSAL----AALSNVSFTNPLVSKVYSCWDLLRSRNKVVHFLWCPSHCG 257
           +    +L  + +   L          +   P+ ++      LL      V F +   H G
Sbjct: 67  YTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGHTG 126

Query: 258 IRGNEAVDEAARN 270
              NE VD  AR 
Sbjct: 127 HPENERVDREARR 139


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

 Score = 38.5 bits (88), Expect = 5e-04
 Identities = 24/131 (18%), Positives = 39/131 (29%), Gaps = 14/131 (10%)

Query: 153 YTDGSKTMNTTSCAFSI-----DDLISSSQLNPVNSIFSAELIAIYLCLEA------ITV 201
           +T GS   N     +           + S      +    EL+A  + LEA      + +
Sbjct: 6   FTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHAEVIL 65

Query: 202 HPSDQFLIVSDSRSALAALSNVS-FTNPLVSKVYSCWDLLR--SRNKVVHFLWCPSHCGI 258
               Q++    ++             +    K    W  L        + + W   H G 
Sbjct: 66  STDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGH 125

Query: 259 RGNEAVDEAAR 269
             NE  DE AR
Sbjct: 126 PENERADELAR 136


>d2b0la1 a.4.5.66 (A:167-257) GTP-sensing transcriptional
           pleiotropic repressor CodY, C-terminal domain {Bacillus
           subtilis [TaxId: 1423]}
          Length = 91

 Score = 25.5 bits (56), Expect = 5.9
 Identities = 13/25 (52%), Positives = 16/25 (64%), Gaps = 6/25 (24%)

Query: 387 LSKLHNSGVVESRS------YTKVL 405
           L KL ++GV+ESRS      Y KVL
Sbjct: 55  LRKLESAGVIESRSLGMKGTYIKVL 79


  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    0.398 

Gapped
Lambda     K      H
   0.267   0.0654    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 1,791,533
Number of extensions: 81022
Number of successful extensions: 194
Number of sequences better than 10.0: 1
Number of HSP's gapped: 194
Number of HSP's successfully gapped: 5
Length of query: 491
Length of database: 2,407,596
Length adjustment: 89
Effective length of query: 402
Effective length of database: 1,185,626
Effective search space: 476621652
Effective search space used: 476621652
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: 55 (25.1 bits)