RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy4748
         (136 letters)



>d1qypa_ g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {Archaeon
           Thermococcus celer [TaxId: 2264]}
          Length = 57

 Score = 53.6 bits (129), Expect = 1e-11
 Identities = 17/47 (36%), Positives = 26/47 (55%)

Query: 90  KDKTEIADGPIVERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136
             + ++   P  +  C +C NDT  +  +Q R+ DE  TIF+ CTKC
Sbjct: 3   HMEQDLKTLPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKC 49


>d1twfi2 g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase II
           {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
          Length = 72

 Score = 50.3 bits (120), Expect = 5e-10
 Identities = 11/38 (28%), Positives = 18/38 (47%)

Query: 99  PIVERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136
           P  +R+C +C++    +   Q R  D    +FF C  C
Sbjct: 20  PRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSC 57


>d1tfia_ g.41.3.1 (A:) Transcriptional factor SII, C-terminal domain
           {Human (Homo sapiens) [TaxId: 9606]}
          Length = 50

 Score = 48.2 bits (115), Expect = 2e-09
 Identities = 13/33 (39%), Positives = 17/33 (51%)

Query: 104 KCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136
            C +C     +Y  +Q RSADE  T F  C +C
Sbjct: 11  TCGKCKKKNCTYTQVQTRSADEPMTTFVVCNEC 43


>d1pvma3 g.41.13.1 (A:143-178) Hypothetical protein Ta0289
          C-terminal domain {Archaeon Thermoplasma acidophilum
          [TaxId: 2303]}
          Length = 36

 Score = 24.2 bits (52), Expect = 1.3
 Identities = 9/25 (36%), Positives = 16/25 (64%), Gaps = 2/25 (8%)

Query: 13 FCSKCGT--ILPLFDFKGDVKCYVC 35
           C KCG   + P+++ KG++K + C
Sbjct: 3  LCPKCGVGVLEPVYNEKGEIKVFRC 27


>d2bvla1 c.68.1.22 (A:1-542) Toxin B {Clostridium difficile
          [TaxId: 1496]}
          Length = 542

 Score = 25.3 bits (55), Expect = 3.2
 Identities = 6/30 (20%), Positives = 9/30 (30%)

Query: 57 KRFKGHFNLFLAVFEEIKAEYTIHFNTVEK 86
           R K        +  E+      +   VEK
Sbjct: 67 GRNKALKKFKEYLVTEVLELKNNNLTPVEK 96


>d1na6a2 c.52.1.22 (A:179-398) Restriction endonuclease EcoRII,
          C-terminal domain {Escherichia coli [TaxId: 562]}
          Length = 220

 Score = 23.7 bits (51), Expect = 8.4
 Identities = 9/29 (31%), Positives = 14/29 (48%)

Query: 49 LGPDILFLKRFKGHFNLFLAVFEEIKAEY 77
          L PD   L R +  +++FL V E    + 
Sbjct: 34 LDPDEQLLDRRRVEYDIFLLVEELHVLDI 62


>d1s5qb_ a.59.1.1 (B:) Sin3A {Mouse (Mus musculus) [TaxId: 10090]}
          Length = 89

 Score = 23.0 bits (49), Expect = 9.5
 Identities = 9/61 (14%), Positives = 16/61 (26%), Gaps = 7/61 (11%)

Query: 41 TQEQQPLLLGPDILFLKRFKGHF-------NLFLAVFEEIKAEYTIHFNTVEKEKQKDKT 93
           Q  QP+     I ++ + K  F         FL +    + E                 
Sbjct: 2  LQNNQPVEFNHAINYVNKIKNRFQGQPDIYKAFLEILHTYQKEQRNAKEAGGNYTPALTE 61

Query: 94 E 94
          +
Sbjct: 62 Q 62


  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
   0.323    0.138    0.425 

Gapped
Lambda     K      H
   0.267   0.0579    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 500,873
Number of extensions: 21823
Number of successful extensions: 76
Number of sequences better than 10.0: 1
Number of HSP's gapped: 76
Number of HSP's successfully gapped: 10
Length of query: 136
Length of database: 2,407,596
Length adjustment: 76
Effective length of query: 60
Effective length of database: 1,364,116
Effective search space: 81846960
Effective search space used: 81846960
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 (21.9 bits)
S2: 48 (22.6 bits)