RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy5302
         (333 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 = 54.5 bits (130), Expect = 5e-10
 Identities = 26/131 (19%), Positives = 47/131 (35%), Gaps = 12/131 (9%)

Query: 97  DSTVIYTDAS--KTDVAVSSAFCSQDIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLN 154
            +   YTD S  +      + + +   K   +     +   AEL +              
Sbjct: 6   GAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFA---------MAL 56

Query: 155 EHTQACFVICSDSLSALQTLQNVFSLNPIASEIRNLILENKSKLSIRFIWVPSHVGIAGN 214
             +     I  DS   +  + +  +    +  +  +I E   K +I   WVP+H GI GN
Sbjct: 57  TDSGPKVNIIVDSQYVMGIVASQPT-ESESKIVNQIIEEMIKKEAIYVAWVPAHKGIGGN 115

Query: 215 EEADRLAKEAL 225
           +E D L  + +
Sbjct: 116 QEVDHLVSQGI 126


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

 Score = 45.7 bits (107), Expect = 1e-06
 Identities = 20/136 (14%), Positives = 42/136 (30%), Gaps = 11/136 (8%)

Query: 100 VIYTDASKTD---VAVSSAFCSQD--IKFSTRLHSLLSICNAELTSILFAIHFLLSSCL- 153
            ++TD +          +A        K  +   +  +    EL + +  +  L   C  
Sbjct: 5   ALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKEPCEV 64

Query: 154 -----NEHTQACFVICSDSLSALQTLQNVFSLNPIASEIRNLILENKSKLSIRFIWVPSH 208
                + + +  F          +  +          ++   +L   +   +RF +V  H
Sbjct: 65  DLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGH 124

Query: 209 VGIAGNEEADRLAKEA 224
            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 = 43.5 bits (101), Expect = 6e-06
 Identities = 12/25 (48%), Positives = 15/25 (60%)

Query: 200 IRFIWVPSHVGIAGNEEADRLAKEA 224
           I++ WV  H G   NE AD LA+ A
Sbjct: 114 IKWEWVKGHAGHPENERADELARAA 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 = 29.6 bits (66), Expect = 0.21
 Identities = 21/118 (17%), Positives = 46/118 (38%), Gaps = 18/118 (15%)

Query: 96  VDSTVIYTDAS---KTDVAVSSAFCSQDIKFSTRLHSLLSICNAELTSILFAIHFLLSSC 152
           V +   Y D +   +T +   + + +   +      +  +    EL +I  A+       
Sbjct: 6   VGAETFYVDGAANRETKLG-KAGYVTNRGRQKVVTLTDTTNQKTELQAIYLAL------- 57

Query: 153 LNEHTQACFVICSDSLSALQTLQNVF--SLNPIASEIRNLILENKSKLSIRFIWVPSH 208
             + +     I +DS  AL  +Q     S + + ++I   +++   K  +   WVP+H
Sbjct: 58  --QDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIK---KEKVYLAWVPAH 110


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

 Score = 28.3 bits (63), Expect = 1.7
 Identities = 21/95 (22%), Positives = 36/95 (37%), Gaps = 4/95 (4%)

Query: 164 CSDSLSALQTLQNVFSLNPIASE--IRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLA 221
             DSL A++ +  VF  N I      + L  + K+   I+ +   +       +E D LA
Sbjct: 555 IGDSLVAVKKI--VFDENKITPSELKKTLNNDFKNSEEIQALLKNAPKFGNDIDEVDNLA 612

Query: 222 KEALTSTHPTINKIPIPDYKAYSKRKILTSWNSEW 256
           +E        +NK   P    +      +S N  +
Sbjct: 613 REGALVYCREVNKYTNPRGGNFQPGLYPSSINVYF 647


  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    0.133    0.400 

Gapped
Lambda     K      H
   0.267   0.0636    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 1,213,983
Number of extensions: 55505
Number of successful extensions: 148
Number of sequences better than 10.0: 1
Number of HSP's gapped: 148
Number of HSP's successfully gapped: 7
Length of query: 333
Length of database: 2,407,596
Length adjustment: 86
Effective length of query: 247
Effective length of database: 1,226,816
Effective search space: 303023552
Effective search space used: 303023552
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: 53 (24.4 bits)