RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy4967
         (354 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 = 60.3 bits (145), Expect = 5e-12
 Identities = 29/134 (21%), Positives = 51/134 (38%), Gaps = 16/134 (11%)

Query: 140 PDSTVVYTDAS--KNDVAVSSAFCSQDTKFSSRLHPLLSICNAELTAILFAIHFSISAHL 197
           P +   YTD S  +      + + +   K   +     +   AEL A   A+  S     
Sbjct: 5   PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALTDSGPKV- 63

Query: 198 NNVNRAYLVICSDSLSALQTLQN--IFSLNPIAGEIRDLILTNKSKLNVRFIWVPSHVGI 255
                    I  DS   +  + +    S + I  +I + ++  +    +   WVP+H GI
Sbjct: 64  --------NIIVDSQYVMGIVASQPTESESKIVNQIIEEMIKKE---AIYVAWVPAHKGI 112

Query: 256 AGNEEADRLAKEAL 269
            GN+E D L  + +
Sbjct: 113 GGNQEVDHLVSQGI 126


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

 Score = 47.6 bits (112), Expect = 2e-07
 Identities = 21/136 (15%), Positives = 38/136 (27%), Gaps = 11/136 (8%)

Query: 144 VVYTD--ASKNDVAVSSAFCSQD---TKFSSRLHPLLSICNAELTAILFAIHFSISAHLN 198
            ++TD     N      A   +     K  S      +    EL A +  +         
Sbjct: 5   ALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKEPCEV 64

Query: 199 NVNRAY------LVICSDSLSALQTLQNIFSLNPIAGEIRDLILTNKSKLNVRFIWVPSH 252
           ++                     +  +          ++ + +L   +   VRF +V  H
Sbjct: 65  DLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGH 124

Query: 253 VGIAGNEEADRLAKEA 268
            G   NE  DR A+  
Sbjct: 125 TGHPENERVDREARRQ 140


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

 Score = 44.2 bits (103), Expect = 3e-06
 Identities = 11/26 (42%), Positives = 15/26 (57%)

Query: 243 NVRFIWVPSHVGIAGNEEADRLAKEA 268
            +++ WV  H G   NE AD LA+ A
Sbjct: 113 QIKWEWVKGHAGHPENERADELARAA 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 = 39.2 bits (91), Expect = 9e-05
 Identities = 22/117 (18%), Positives = 40/117 (34%), Gaps = 16/117 (13%)

Query: 140 PDSTVVYTDAS--KNDVAVSSAFCSQDTKFSSRLHPLLSICNAELTAILFAIHFSISAHL 197
             +   Y D +  +      + + +   +         +    EL AI  A+  S     
Sbjct: 6   VGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLE-- 63

Query: 198 NNVNRAYLVICSDSLSALQTLQNIF--SLNPIAGEIRDLILTNKSKLNVRFIWVPSH 252
                  + I +DS  AL  +Q     S + +  +I + +     K  V   WVP+H
Sbjct: 64  -------VNIVTDSQYALGIIQAQPDQSESELVNQIIEQL---IKKEKVYLAWVPAH 110


>d1m6ia1 c.3.1.5 (A:128-263,A:401-477) Apoptosis-inducing factor
          (AIF) {Human (Homo sapiens) [TaxId: 9606]}
          Length = 213

 Score = 28.9 bits (63), Expect = 0.81
 Identities = 15/86 (17%), Positives = 29/86 (33%), Gaps = 2/86 (2%)

Query: 4  GVRLALGAFKSSPIPSILSEAGEPPLSYRREILTCNYLFNTQRNPKHFLSPLLTDDSLQQ 63
              A       P   +L  + +P L Y R  L+    F+   N    L     +   + 
Sbjct: 16 AFAAARSIRARDPGARVLIVSEDPELPYMRPPLSKELWFSDDPNVTKTLRFKQWNGKERS 75

Query: 64 LYERKSSYEKPLRIRGKLLLEKYGID 89
          +Y +  S+   +  +    +E  G+ 
Sbjct: 76 IYFQPPSFY--VSAQDLPHIENGGVA 99


>d1eeja1 c.47.1.9 (A:61-216) Disulfide bond isomerase, DsbC,
           C-terminal domain {Escherichia coli [TaxId: 562]}
          Length = 156

 Score = 25.9 bits (56), Expect = 5.6
 Identities = 12/84 (14%), Positives = 30/84 (35%), Gaps = 5/84 (5%)

Query: 129 NISFQELLQK---TPDSTVVYTDASKNDVAVSSAFCSQDTKFSSRLHPLLSICNAELTAI 185
           N++ + LL++        +VY   +  +  V + F      +  +LH  ++  NA    +
Sbjct: 1   NVTNKMLLKQLNALEKEMIVY--KAPQEKHVITVFTDITCGYCHKLHEQMADYNALGITV 58

Query: 186 LFAIHFSISAHLNNVNRAYLVICS 209
            +          +       + C+
Sbjct: 59  RYLAFPRQGLDSDAEKEMKAIWCA 82


>d1r9da_ c.7.1.1 (A:) Glycerol dehydratase DhaB1 {Clostridium
           butyricum [TaxId: 1492]}
          Length = 786

 Score = 26.3 bits (58), Expect = 6.5
 Identities = 17/85 (20%), Positives = 35/85 (41%), Gaps = 4/85 (4%)

Query: 205 LVICSDSLSALQTLQNIFSLNPIA-GEIRDLILTN-KSKLNVRFIWVPSHVGIAGNEEAD 262
           +    DSL A++ +  +F  N I   E++  +  + K+   ++ +   +       +E D
Sbjct: 552 VANIGDSLVAVKKI--VFDENKITPSELKKTLNNDFKNSEEIQALLKNAPKFGNDIDEVD 609

Query: 263 RLAKEALTSTHPTINKIPIPDYKAY 287
            LA+E        +NK   P    +
Sbjct: 610 NLAREGALVYCREVNKYTNPRGGNF 634


>d1ufaa1 a.8.3.3 (A:413-517) Hypothetical protein TT1467, domain 2
           {Thermus thermophilus [TaxId: 274]}
          Length = 105

 Score = 24.8 bits (54), Expect = 9.5
 Identities = 6/31 (19%), Positives = 8/31 (25%)

Query: 193 ISAHLNNVNRAYLVICSDSLSALQTLQNIFS 223
              H             + L AL+   N F 
Sbjct: 66  YEEHARAFFHLLKGASPEELRALEERDNPFP 96


  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
   0.317    0.134    0.395 

Gapped
Lambda     K      H
   0.267   0.0645    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 1,298,688
Number of extensions: 59979
Number of successful extensions: 133
Number of sequences better than 10.0: 1
Number of HSP's gapped: 133
Number of HSP's successfully gapped: 8
Length of query: 354
Length of database: 2,407,596
Length adjustment: 86
Effective length of query: 268
Effective length of database: 1,226,816
Effective search space: 328786688
Effective search space used: 328786688
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: 53 (24.4 bits)