RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy5287
         (65 letters)



>d1ne3a_ b.40.4.5 (A:) Ribosomal protein S28e {Archaeon
          Methanobacterium thermoautotrophicum [TaxId: 145262]}
          Length = 68

 Score = 93.5 bits (233), Expect = 4e-28
 Identities = 30/64 (46%), Positives = 40/64 (62%), Gaps = 2/64 (3%)

Query: 4  QVVLARVIKTLGRTGSQGQCTQVKVEFIG--DQNRTIIRNVKGPVREGDILTLLESEREA 61
              A VI+ L RTG  G+  QVK   +   D+ R + RNV GP+REGDIL LL++ REA
Sbjct: 3  DATPAEVIEVLKRTGMTGEVMQVKCRILDGRDKGRILTRNVMGPIREGDILMLLDTIREA 62

Query: 62 RRLR 65
          + +R
Sbjct: 63 KEIR 66


>d1ny4a_ b.40.4.5 (A:) Ribosomal protein S28e {Archaeon Pyrococcus
          horikoshii [TaxId: 53953]}
          Length = 71

 Score = 90.5 bits (225), Expect = 5e-27
 Identities = 34/67 (50%), Positives = 45/67 (67%), Gaps = 2/67 (2%)

Query: 1  MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIG--DQNRTIIRNVKGPVREGDILTLLESE 58
           + +   A VI+ +GRTG+ G  TQVKV  +   D+ R I RNV+GPVR GDIL L E+E
Sbjct: 2  AEDEGYPAEVIEIIGRTGTTGDVTQVKVRILEGRDKGRVIRRNVRGPVRVGDILILRETE 61

Query: 59 REARRLR 65
          REAR ++
Sbjct: 62 REAREIK 68


>d2d30a1 c.97.1.1 (A:1-124) mono-domain cytidine deaminase {Bacillus
           anthracis [TaxId: 1392]}
          Length = 124

 Score = 26.1 bits (57), Expect = 0.19
 Identities = 12/35 (34%), Positives = 17/35 (48%)

Query: 21  GQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLL 55
           G C QV VE      +  + N+ G V+E  +  LL
Sbjct: 87  GACRQVMVELCKQDTKVYLSNLHGDVQETTVGELL 121


>d1uwza_ c.97.1.1 (A:) mono-domain cytidine deaminase {Bacillus
           subtilis [TaxId: 1423]}
          Length = 130

 Score = 25.4 bits (55), Expect = 0.45
 Identities = 10/35 (28%), Positives = 17/35 (48%)

Query: 21  GQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLL 55
           G C QV  E        ++ N++G ++E  +  LL
Sbjct: 87  GACRQVISELCTKDVIVVLTNLQGQIKEMTVEELL 121


>d1w36b2 c.37.1.19 (B:486-880) Exodeoxyribonuclease V beta chain
          (RecB), N-terminal domain {Escherichia coli [TaxId:
          562]}
          Length = 395

 Score = 24.2 bits (51), Expect = 1.3
 Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 12/58 (20%)

Query: 8  ARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESEREARRLR 65
          A  I+   + G +G+   +     GD  R        PVR  DI  L+ S +EA ++R
Sbjct: 38 AAQIRDWLQAGQRGEALLMN----GDDAR--------PVRASDISVLVRSRQEAAQVR 83


>d1a6db2 c.8.5.2 (B:216-367) Thermosome, A-domain {Archaeon
           Thermoplasma acidophilum, beta chain [TaxId: 2303]}
          Length = 152

 Score = 22.7 bits (48), Expect = 3.9
 Identities = 6/25 (24%), Positives = 11/25 (44%)

Query: 21  GQCTQVKVEFIGDQNRTIIRNVKGP 45
           G   +V+   +G+   T +   K P
Sbjct: 128 GTAERVEQVKVGEDYMTFVTGCKNP 152


>d1q3qa2 c.8.5.2 (A:217-369) Thermosome, A-domain {Archaeon
           Thermococcus sp. ks-1, alpha chain [TaxId: 79679]}
          Length = 153

 Score = 22.2 bits (47), Expect = 5.5
 Identities = 5/25 (20%), Positives = 9/25 (36%)

Query: 21  GQCTQVKVEFIGDQNRTIIRNVKGP 45
           G    V+   +  +N   +   K P
Sbjct: 129 GYAEVVEERKLAGENMIFVEGCKNP 153


>d1assa_ c.8.5.2 (A:) Thermosome, A-domain {Archaeon Thermoplasma
           acidophilum, alpha chain [TaxId: 2303]}
          Length = 152

 Score = 21.9 bits (46), Expect = 9.5
 Identities = 7/23 (30%), Positives = 10/23 (43%)

Query: 21  GQCTQVKVEFIGDQNRTIIRNVK 43
           G+   V+   IGD   T +   K
Sbjct: 130 GEAETVEERKIGDDRMTFVMGCK 152


  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    0.138    0.373 

Gapped
Lambda     K      H
   0.267   0.0561    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 214,399
Number of extensions: 7517
Number of successful extensions: 23
Number of sequences better than 10.0: 1
Number of HSP's gapped: 21
Number of HSP's successfully gapped: 9
Length of query: 65
Length of database: 2,407,596
Length adjustment: 34
Effective length of query: 31
Effective length of database: 1,940,776
Effective search space: 60164056
Effective search space used: 60164056
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: 47 (22.3 bits)