RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy15277
         (269 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 = 48.4 bits (114), Expect = 6e-08
 Identities = 25/124 (20%), Positives = 49/124 (39%), Gaps = 8/124 (6%)

Query: 7   DSVVCFSDGS--KTPNSTSCAYSIDKQIHSFNLNKVNSVFSAELMAILLCIKNLKFLPHN 64
            +   ++DGS  +        Y  D+        +  +   AEL A  + + +       
Sbjct: 6   GAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALTD----SGP 61

Query: 65  KFIIISDSMSALQAISNLNSNNSLVPKIYSHWLDLKSCGKNLCFLWCPSHCGIKGNESVD 124
           K  II DS   +  +++  + +    KI +  ++     + +   W P+H GI GN+ VD
Sbjct: 62  KVNIIVDSQYVMGIVASQPTES--ESKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVD 119

Query: 125 NAAR 128
           +   
Sbjct: 120 HLVS 123


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

 Score = 41.9 bits (97), Expect = 2e-05
 Identities = 25/136 (18%), Positives = 46/136 (33%), Gaps = 15/136 (11%)

Query: 9   VVCFSDGSKTPNSTSCAYS--IDKQIHSFNLNKVNSVFSAELMAILLCIKNLKFLPHNKF 66
           V  F+DG+   N     ++  +    H   L+   +  +   M +   I+ LK L     
Sbjct: 4   VALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKEPCE 63

Query: 67  III-SDSMSALQAISNL-------NSNNSLVPKIYSHWLDLKSCGKNL-----CFLWCPS 113
           + + +DS    +A +             +   K   +    ++    +      F +   
Sbjct: 64  VDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKG 123

Query: 114 HCGIKGNESVDNAARN 129
           H G   NE VD  AR 
Sbjct: 124 HTGHPENERVDREARR 139


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

 Score = 33.5 bits (75), Expect = 0.011
 Identities = 23/141 (16%), Positives = 37/141 (26%), Gaps = 18/141 (12%)

Query: 9   VVCFSDGSKTPNSTSCAYSI-----DKQIHSFNLNKVNSVFSAELMAILL------CIKN 57
           V  F+ GS   N     Y        ++          +    ELMA ++          
Sbjct: 3   VEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHAE 62

Query: 58  LKFLPHNKFIIISDSMSALQAISNLNSNNSLVPK---IYSHWLDLKSCGKNLCFLWCPSH 114
           +     ++++    +                 P         LD       + + W   H
Sbjct: 63  VILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGH 122

Query: 115 CGIKGNESVDN----AARNPN 131
            G   NE  D     AA NP 
Sbjct: 123 AGHPENERADELARAAAMNPT 143


>d1h5ya_ c.1.2.1 (A:) Cyclase subunit (or domain) of
           imidazoleglycerolphosphate synthase HisF {Archaeon
           Pyrobaculum aerophilum [TaxId: 13773]}
          Length = 252

 Score = 30.8 bits (69), Expect = 0.13
 Identities = 19/147 (12%), Positives = 42/147 (28%), Gaps = 8/147 (5%)

Query: 88  LVPKIYSHWLDLKSCGKNLCFLWCPSHCGIKGNESVDNAARNPNYNTTLRKCTSDDFRP- 146
            V ++          G  +  L   +     G + V +       N  L    + +F   
Sbjct: 67  SVKRVAEAVSIPVLVGGGVRSLEDATTLFRAGADKV-SVNTAAVRNPQLVALLAREFGSQ 125

Query: 147 -IISTIIMKNWQTSWDNITNNKLKNIKPKIEEWVSSNRDSRYEEIVITRL-----RIGHT 200
             +  I  K     ++       +       +W     +    EI++T +      +G+ 
Sbjct: 126 STVVAIDAKWNGEYYEVYVKGGREATGLDAVKWAKEVEELGAGEILLTSIDRDGTGLGYD 185

Query: 201 RLTHEFLFNKTPRPSCSCGEPLSVQHL 227
                 + +    P  + G    V+H 
Sbjct: 186 VELIRRVADSVRIPVIASGGAGRVEHF 212


>d1thfd_ c.1.2.1 (D:) Cyclase subunit (or domain) of
           imidazoleglycerolphosphate synthase HisF {Thermotoga
           maritima [TaxId: 2336]}
          Length = 253

 Score = 28.6 bits (63), Expect = 0.76
 Identities = 28/154 (18%), Positives = 51/154 (33%), Gaps = 14/154 (9%)

Query: 85  NNSLVPKIYSHWLDLKSCGKNLCFLWCPSHCGIKGNESV---DNAARNPNYNTTLRKCTS 141
              LV K+        + G  +      S   ++G + V     A  NP+    L    +
Sbjct: 62  MLELVEKVAEQIDIPFTVGGGIHDFETASELILRGADKVSINTAAVENPS----LITQIA 117

Query: 142 DDFRPIISTIIM--KNWQTSWDNITNNKLKNIKPKIEEWVSSNRDSRYEEIVITRL---- 195
             F      + +  K     +   T +  KN    + +WV         EI++T +    
Sbjct: 118 QTFGSQAVVVAIDAKRVDGEFMVFTYSGKKNTGILLRDWVVEVEKRGAGEILLTSIDRDG 177

Query: 196 -RIGHTRLTHEFLFNKTPRPSCSCGEPLSVQHLL 228
            + G+      F+   T  P  + G    ++H L
Sbjct: 178 TKSGYDTEMIRFVRPLTTLPIIASGGAGKMEHFL 211


>d1sx5a_ c.52.1.2 (A:) Restriction endonuclease EcoRV {Escherichia
           coli [TaxId: 562]}
          Length = 244

 Score = 26.0 bits (57), Expect = 5.1
 Identities = 12/51 (23%), Positives = 20/51 (39%), Gaps = 9/51 (17%)

Query: 22  TSCAYSIDKQIHSFNLNKVNSVFSAELMAILLCIKNLKFLPHNKFIIISDS 72
           T  A      + ++N+N        EL  I    K +K    +K++I  D 
Sbjct: 138 TRVATRKS-SLKTYNIN--------ELNEIPKPYKGVKVFLQDKWVIAGDL 179


>d2ayja1 g.41.8.7 (A:1-56) Ribosomal protein L40e {Sulfolobus
           solfataricus [TaxId: 2287]}
          Length = 56

 Score = 23.6 bits (51), Expect = 6.7
 Identities = 8/20 (40%), Positives = 10/20 (50%)

Query: 127 ARNPNYNTTLRKCTSDDFRP 146
           A NP   T  R+C S + R 
Sbjct: 27  ALNPIRATKCRRCHSTNLRL 46


  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
   0.319    0.132    0.409 

Gapped
Lambda     K      H
   0.267   0.0651    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 991,927
Number of extensions: 44235
Number of successful extensions: 92
Number of sequences better than 10.0: 1
Number of HSP's gapped: 92
Number of HSP's successfully gapped: 16
Length of query: 269
Length of database: 2,407,596
Length adjustment: 84
Effective length of query: 185
Effective length of database: 1,254,276
Effective search space: 232041060
Effective search space used: 232041060
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 (21.8 bits)
S2: 52 (24.0 bits)