RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy11794
         (325 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 = 36.0 bits (82), Expect = 0.001
 Identities = 26/119 (21%), Positives = 42/119 (35%), Gaps = 7/119 (5%)

Query: 77  TDTAYRLQENRYSCCYLGTLVGPGPRYFNLTTIYLAELLALYLCLKEISEFHSSSRIAII 136
           TD +   Q       Y+        +    TT   AEL A  + L +     +     II
Sbjct: 12  TDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALTDSGPKVN-----II 66

Query: 137 SDSLSVLSALGNICFSHPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAAN 195
            DS  V+  + +             + ++I      +   W P+H GI GN+ VD   +
Sbjct: 67  VDSQYVMGIVASQPTESESKIVNQIIEEMIKKE--AIYVAWVPAHKGIGGNQEVDHLVS 123


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

 Score = 32.2 bits (72), Expect = 0.034
 Identities = 11/46 (23%), Positives = 15/46 (32%)

Query: 150 CFSHPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAAN 195
               P  ++      L+      V F +   H G   NE VD  A 
Sbjct: 93  AEGKPVKNRDLWEALLLAMAPHRVRFHFVKGHTGHPENERVDREAR 138


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

 Score = 29.6 bits (65), Expect = 0.31
 Identities = 7/23 (30%), Positives = 9/23 (39%)

Query: 173 VVFLWCPSHCGIDGNEAVDSAAN 195
           + + W   H G   NE  D  A 
Sbjct: 114 IKWEWVKGHAGHPENERADELAR 136


>d1m9la_ c.10.3.1 (A:) Outer arm dynein light chain 1 {Green algae
           (Chlamydomonas reinhardtii) [TaxId: 3055]}
          Length = 198

 Score = 26.6 bits (57), Expect = 3.2
 Identities = 18/149 (12%), Positives = 38/149 (25%), Gaps = 6/149 (4%)

Query: 121 LKEISEFHSSSRIAIISDSLSVLSALGNICFSHPFISKIYQLWKLIVTRGTDVVFLWCPS 180
            +++        I  +  +LS L A  ++  S   I KI  L  +   R   +       
Sbjct: 25  AEKVELHGMIPPIEKMDATLSTLKACKHLALSTNNIEKISSLSGMENLRILSLGRNLIKK 84

Query: 181 HCGIDGNEAVDSAANHHTHPRHVNLCSTDDLKPWIKAIVKKDIVDMWNSIPPSNKLKRIK 240
              +D             +           +   +  +    I +       +   K   
Sbjct: 85  IENLDAVADTLEELWISYNQIASLSGIEKLVNLRVLYMSNNKITNWGEIDKLAALDKLED 144

Query: 241 PTVDSW------TSSFRNNRYEEVVLTRL 263
             +           +   + Y   V+ RL
Sbjct: 145 LLLAGNPLYNDYKENNATSEYRIEVVKRL 173


>d1im4a_ e.8.1.7 (A:) DinB homolog (DBH) {Archaeon Sulfolobus
           solfataricus [TaxId: 2287]}
          Length = 209

 Score = 25.9 bits (56), Expect = 6.2
 Identities = 5/52 (9%), Positives = 19/52 (36%), Gaps = 3/52 (5%)

Query: 176 LWCPSHCGIDGNEAVDSAANHHTHPRHVNLCSTDDLKPWIKAIVKKDIVDMW 227
                  G+  N+ +       + P  + +    +++ ++  +   DI ++ 
Sbjct: 141 EKITVTVGVAPNKILAKIIADKSKPNGLGVIRPTEVQDFLNEL---DIDEIP 189


>d2r8oa3 c.48.1.1 (A:528-663) Transketolase (TK), C-domain
           {Escherichia coli [TaxId: 562]}
          Length = 136

 Score = 25.2 bits (54), Expect = 8.0
 Identities = 8/87 (9%), Positives = 19/87 (21%)

Query: 149 ICFSHPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHPRHVNLCST 208
              +   +      ++ +   G     +  PS    D  +A    +              
Sbjct: 27  FIATGSEVELAVAAYEKLTAEGVKARVVSMPSTDAFDKQDAAYRESVLPKAVTARVAVEA 86

Query: 209 DDLKPWIKAIVKKDIVDMWNSIPPSNK 235
                W K +     +    +   S  
Sbjct: 87  GIADYWYKYVGLNGAIVGMTTFGESAP 113


  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
   0.324    0.138    0.443 

Gapped
Lambda     K      H
   0.267   0.0516    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 1,280,498
Number of extensions: 59634
Number of successful extensions: 166
Number of sequences better than 10.0: 1
Number of HSP's gapped: 166
Number of HSP's successfully gapped: 11
Length of query: 325
Length of database: 2,407,596
Length adjustment: 86
Effective length of query: 239
Effective length of database: 1,226,816
Effective search space: 293209024
Effective search space used: 293209024
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 53 (24.7 bits)