RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy10264
         (426 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 = 1e-04
 Identities = 28/146 (19%), Positives = 44/146 (30%), Gaps = 35/146 (23%)

Query: 190 FTDGS--KTSDHTGAAYIIGDEVCSMKLNPVCSIFTAELVAIEKCLEKIKDLIRTELISE 247
           +TDGS  + S    A Y+       +K     +   AEL A    L              
Sbjct: 11  YTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALTDSG---------- 60

Query: 248 LVAIEKCLEKIKDLIRTELILQNFIICSDSKSSLQALQNVYHASPLVCNIISTIQDIREL 307
                                    I  DS+  +  + +    S     I++ I +    
Sbjct: 61  ---------------------PKVNIIVDSQYVMGIVASQPTESE--SKIVNQIIEEMIK 97

Query: 308 GTRVSFFWIPSHLGIRENENVDHAAR 333
              +   W+P+H GI  N+ VDH   
Sbjct: 98  KEAIYVAWVPAHKGIGGNQEVDHLVS 123


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

 Score = 32.6 bits (73), Expect = 0.042
 Identities = 27/149 (18%), Positives = 50/149 (33%), Gaps = 22/149 (14%)

Query: 190 FTDGSKTSD--HTGAAYII---GDEVCSMKLNPVCSIFTAELVAIEKCLEKIKDLIRTEL 244
           FTDG+   +    G A ++     E          +    EL A  + L+ +K+    +L
Sbjct: 7   FTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKEPCEVDL 66

Query: 245 ISELVAIEKCLEKIKDLIRTELILQNFIICSDSKSSLQALQNVYHASPLVCNIISTIQDI 304
            ++   ++K               + ++     +    A         L   ++  +   
Sbjct: 67  YTDSHYLKKAFT------------EGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPH 114

Query: 305 RELGTRVSFFWIPSHLGIRENENVDHAAR 333
           R       F ++  H G  ENE VD  AR
Sbjct: 115 RV-----RFHFVKGHTGHPENERVDREAR 138


>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 = 30.7 bits (69), Expect = 0.090
 Identities = 20/132 (15%), Positives = 39/132 (29%), Gaps = 35/132 (26%)

Query: 190 FTDGS--KTSDHTGAAYIIGDEVCSMKLNPVCSIFTAELVAIEKCLEKIKDLIRTELISE 247
           + DG+  + +    A Y+       +      +    EL AI   L+             
Sbjct: 12  YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSG---------- 61

Query: 248 LVAIEKCLEKIKDLIRTELILQNFIICSDSKSSLQALQNVYHASPLVCNIISTIQDIREL 307
                                    I +DS+ +L  +Q     S     +++ I +    
Sbjct: 62  ---------------------LEVNIVTDSQYALGIIQAQPDQSES--ELVNQIIEQLIK 98

Query: 308 GTRVSFFWIPSH 319
             +V   W+P+H
Sbjct: 99  KEKVYLAWVPAH 110


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

 Score = 30.0 bits (66), Expect = 0.29
 Identities = 9/23 (39%), Positives = 12/23 (52%)

Query: 311 VSFFWIPSHLGIRENENVDHAAR 333
           + + W+  H G  ENE  D  AR
Sbjct: 114 IKWEWVKGHAGHPENERADELAR 136


>d1ab4a_ e.11.1.1 (A:) DNA Gyrase A {Escherichia coli [TaxId: 562]}
          Length = 493

 Score = 26.8 bits (59), Expect = 5.9
 Identities = 13/39 (33%), Positives = 25/39 (64%), Gaps = 2/39 (5%)

Query: 229 IEKCLEKIKDLIRTELISELVAIEKCLEKIKDLIRTELI 267
            EK L++ K+L+  + I+EL+ I    +++ ++IR EL 
Sbjct: 442 HEKLLDEYKELL--DQIAELLRILGSADRLMEVIREELE 478


>d1usub_ d.83.2.1 (B:) Activator of Hsp90 ATPase, Aha1 {Baker's
           yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
          Length = 142

 Score = 25.5 bits (56), Expect = 8.8
 Identities = 12/36 (33%), Positives = 19/36 (52%), Gaps = 2/36 (5%)

Query: 230 EKCLEKIKDLIRTELISELVAIEKCLEKIKDLIRTE 265
              L + K LIR+EL+ +L   +   +  KDL+ T 
Sbjct: 106 TSELSEAKPLIRSELLPKLR--QIFQQFGKDLLATH 139


  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
   0.322    0.136    0.405 

Gapped
Lambda     K      H
   0.267   0.0499    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 1,574,209
Number of extensions: 73780
Number of successful extensions: 200
Number of sequences better than 10.0: 1
Number of HSP's gapped: 200
Number of HSP's successfully gapped: 9
Length of query: 426
Length of database: 2,407,596
Length adjustment: 88
Effective length of query: 338
Effective length of database: 1,199,356
Effective search space: 405382328
Effective search space used: 405382328
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: 54 (25.1 bits)