RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy3902
         (181 letters)



>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain
           (RecD) {Escherichia coli [TaxId: 562]}
          Length = 359

 Score = 52.6 bits (125), Expect = 3e-09
 Identities = 23/103 (22%), Positives = 33/103 (32%), Gaps = 14/103 (13%)

Query: 66  FTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGP----TVFSKLGQQLE--- 118
               V+DEA     P +   I  L  D+  V+  GD  QL       V   +        
Sbjct: 262 LDVLVVDEASMIDLPMMSRLIDAL-PDHARVIFLGDRDQLASVEAGAVLGDICAYANAGF 320

Query: 119 --LRISLLERLTGRFLYSRDMSRFYATGGYDPRLVTRLVNNYR 159
              R   L RLTG  + +   +            +  L  +YR
Sbjct: 321 TAERARQLSRLTGTHVPAGTGT----EAASLRDSLCLLQKSYR 359



 Score = 41.4 bits (96), Expect = 2e-05
 Identities = 14/63 (22%), Positives = 22/63 (34%), Gaps = 1/63 (1%)

Query: 6   FTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELSTPSGY 65
               V+DEA     P +   I  L  D+  V+  GD  QL       +   +     +G+
Sbjct: 262 LDVLVVDEASMIDLPMMSRLIDAL-PDHARVIFLGDRDQLASVEAGAVLGDICAYANAGF 320

Query: 66  FTH 68
              
Sbjct: 321 TAE 323


>d1w36b1 c.37.1.19 (B:1-485) Exodeoxyribonuclease V beta chain
           (RecB), N-terminal domain {Escherichia coli [TaxId:
           562]}
          Length = 485

 Score = 33.5 bits (75), Expect = 0.012
 Identities = 20/111 (18%), Positives = 39/111 (35%), Gaps = 27/111 (24%)

Query: 64  GYFTHCVIDEAGQATEPEVLVPISLL--HRDNGHVVLAGDPLQLGPTVFSKLGQQLELRI 121
             F   +IDE  Q T+P+       +  H+    ++L GDP Q    +++  G  +   +
Sbjct: 376 TRFPVAMIDEF-QDTDPQQYRIFRRIWHHQPETALLLIGDPKQ---AIYAFRGADIFTYM 431

Query: 122 SLLERLTGRFLYSRDMSRFYATGGYDPRLVTRLVNNYRTMPEILKISSDLF 172
                +   +                      L  N+R+ P ++   + LF
Sbjct: 432 KARSEVHAHY---------------------TLDTNWRSAPGMVNSVNKLF 461


>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia
           coli, RepD [TaxId: 562]}
          Length = 306

 Score = 30.1 bits (66), Expect = 0.13
 Identities = 9/27 (33%), Positives = 14/27 (51%)

Query: 146 YDPRLVTRLVNNYRTMPEILKISSDLF 172
           +    V +L  NYR+   ILK ++ L 
Sbjct: 264 FPALKVIKLEQNYRSSGRILKAANILI 290


>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus
           stearothermophilus, PcrA [TaxId: 1422]}
          Length = 318

 Score = 27.7 bits (60), Expect = 0.85
 Identities = 15/70 (21%), Positives = 22/70 (31%), Gaps = 12/70 (17%)

Query: 115 QQLELRISLLERLTGRFLYSRDMSRFYATGGYDPRL------------VTRLVNNYRTMP 162
            Q  L   L ER              Y   G D +             V  L  NYR+  
Sbjct: 231 AQYTLVKKLAERFQNICAVGDADQSIYRWRGADIQNILSFERDYPNAKVILLEQNYRSTK 290

Query: 163 EILKISSDLF 172
            IL+ ++++ 
Sbjct: 291 RILQAANEVI 300


>d2py5a1 c.55.3.5 (A:5-187) Exonuclease domain of phi29 DNA
           polymerase {Bacteriophage phi-29 [TaxId: 10756]}
          Length = 183

 Score = 25.7 bits (56), Expect = 3.3
 Identities = 10/52 (19%), Positives = 18/52 (34%), Gaps = 3/52 (5%)

Query: 41  DPLQLGPTVFSKLGQQLELSTPSGYFTHCVIDEAGQATEPEVLVPISLLHRD 92
           D L+  P    K+ +  +L+   G   +      G    PE     + +  D
Sbjct: 117 DSLKKLPFPVKKIAKDFKLTVLKGDIDYHKERPVGYKITPEE---YAYIKND 165


>d1pm3a_ b.41.1.2 (A:) MTH1895 {Archaeon Methanobacterium
           thermoautotrophicum [TaxId: 145262]}
          Length = 78

 Score = 23.7 bits (51), Expect = 5.9
 Identities = 9/50 (18%), Positives = 20/50 (40%), Gaps = 5/50 (10%)

Query: 57  LELSTPSGYFTHCVIDEAGQATEP-----EVLVPISLLHRDNGHVVLAGD 101
           +E+   S      V+ + G +        E +VP  ++ +    ++L G 
Sbjct: 27  VEVDIESQAIESLVLGKGGISEGLGLSKGETIVPYEMVKKIGDKILLKGP 76


>d2bhga1 b.47.1.4 (A:7-205) 3C cysteine protease (picornain 3C)
           {Foot-and-mouth disease virus FMDV [TaxId: 12110]}
          Length = 199

 Score = 24.7 bits (53), Expect = 6.0
 Identities = 12/90 (13%), Positives = 27/90 (30%)

Query: 22  VLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELSTPSGYFTHCVIDEAGQATEPE 81
            LVP  L       ++L G  +        +   +++           V+    +  +  
Sbjct: 35  YLVPRHLFAEKYDKIMLDGRAMTDSDYRVFEFEIKVKGQDMLSDAALMVLHRGNKVRDIT 94

Query: 82  VLVPISLLHRDNGHVVLAGDPLQLGPTVFS 111
                +   +    VV   +   +G  +FS
Sbjct: 95  KHFRDTARMKKGTPVVGVVNNADVGRLIFS 124


>d2ab0a1 c.23.16.2 (A:2-196) Protein ThiJ (YajL) {Escherichia coli
           [TaxId: 562]}
          Length = 195

 Score = 24.3 bits (52), Expect = 9.1
 Identities = 12/47 (25%), Positives = 16/47 (34%)

Query: 79  EPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELRISLLE 125
           E E +  I LL R    V  A         +    G +L     L+E
Sbjct: 14  ETEAVTTIDLLVRGGIKVTTASVASDGNLAITCSRGVKLLADAPLVE 60


  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
   0.320    0.140    0.415 

Gapped
Lambda     K      H
   0.267   0.0576    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 670,654
Number of extensions: 29224
Number of successful extensions: 67
Number of sequences better than 10.0: 1
Number of HSP's gapped: 65
Number of HSP's successfully gapped: 9
Length of query: 181
Length of database: 2,407,596
Length adjustment: 80
Effective length of query: 101
Effective length of database: 1,309,196
Effective search space: 132228796
Effective search space used: 132228796
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: 50 (23.4 bits)