RPS-BLAST 2.2.26 [Sep-21-2011]

Database: pdb70 
           27,921 sequences; 6,701,793 total letters

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

Query= psy11234
         (98 letters)



>1f3u_A Transcription initiation factor IIF, beta subunit; general
          transcription initiation and elongation factor, RNA
          polymerase II; 1.70A {Homo sapiens} SCOP: b.65.1.1
          Length = 118

 Score = 28.1 bits (62), Expect = 0.30
 Identities = 9/29 (31%), Positives = 13/29 (44%), Gaps = 2/29 (6%)

Query: 19 VWLLLCPAHLSHDWQFGSIPLVTSLGDVR 47
          VWL+  P +LS  W          +G +R
Sbjct: 17 VWLVKVPKYLSQQWA--KASGRGEVGKLR 43


>1ems_A Nitfhit, NIT-fragIle histidine triad fusion protein; WORM,
           nitrilase, nucleotide-binding protein, cancer; 2.80A
           {Caenorhabditis elegans} SCOP: d.13.1.1 d.160.1.1
          Length = 440

 Score = 27.4 bits (61), Expect = 0.77
 Identities = 7/39 (17%), Positives = 11/39 (28%), Gaps = 11/39 (28%)

Query: 17  FNVWLLLCPAHLSHDWQFGSIPLVTSLGDVRNFATCLLF 55
            N+WL L           G +           + T L+ 
Sbjct: 88  HNIWLSL-----------GGLHHKDPSDAAHPWNTHLII 115


>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription
           factor, RNA polymerase recycling, activator,
           ATP-binding, DNA-binding; 3.20A {Escherichia coli K12}
          Length = 968

 Score = 26.2 bits (57), Expect = 2.4
 Identities = 5/13 (38%), Positives = 7/13 (53%)

Query: 21  LLLCPAHLSHDWQ 33
           L++ P  L H W 
Sbjct: 204 LIIVPETLQHQWL 216


>4epz_A Transcription anti-terminator antagonist UPXZ; transcription
           regulation, antagonist of transcription anti-
           termination; HET: MSE; 1.68A {Bacteroides uniformis atcc
           8492}
          Length = 162

 Score = 24.9 bits (54), Expect = 4.7
 Identities = 5/13 (38%), Positives = 8/13 (61%)

Query: 6   CRLLTFCYLAVFN 18
            RLLT+ Y   ++
Sbjct: 105 MRLLTWGYSETYD 117


  Database: pdb70
    Posted date:  Sep 4, 2012  3:40 AM
  Number of letters in database: 6,701,793
  Number of sequences in database:  27,921
  
Lambda     K      H
   0.334    0.142    0.488 

Gapped
Lambda     K      H
   0.267   0.0593    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,412,001
Number of extensions: 64875
Number of successful extensions: 135
Number of sequences better than 10.0: 1
Number of HSP's gapped: 135
Number of HSP's successfully gapped: 5
Length of query: 98
Length of database: 6,701,793
Length adjustment: 64
Effective length of query: 34
Effective length of database: 4,914,849
Effective search space: 167104866
Effective search space used: 167104866
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.6 bits)
S2: 51 (23.7 bits)