RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy2182
         (67 letters)



>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX,
           paired domain, DNA-binding protein, gene regulation/DNA
           complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP:
           a.4.1.5
          Length = 128

 Score = 77.8 bits (191), Expect = 9e-21
 Identities = 33/60 (55%), Positives = 44/60 (73%)

Query: 7   YYETGSIKPRAIGGSKPRVATNGVVTKIADYKRECPSIFAWEIRDRLLAEGVCNNDNIPS 66
           Y ETGSI+P  IGGSKPR+AT  +  +I +YKR  P +F+WEIR++L+ EGVC+    PS
Sbjct: 57  YQETGSIRPGVIGGSKPRIATPEIENRIEEYKRSSPGMFSWEIREKLIREGVCDRSTAPS 116


>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription
           factor, transcription/DNA complex; 2.25A {Homo sapiens}
           SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A
          Length = 149

 Score = 76.4 bits (187), Expect = 5e-20
 Identities = 45/60 (75%), Positives = 52/60 (86%)

Query: 7   YYETGSIKPRAIGGSKPRVATNGVVTKIADYKRECPSIFAWEIRDRLLAEGVCNNDNIPS 66
           YYETGSIKP  IGGSKP+VAT  VV KIA+YKR+ P++FAWEIRDRLLAE VC+ND +PS
Sbjct: 72  YYETGSIKPGVIGGSKPKVATPKVVEKIAEYKRQNPTMFAWEIRDRLLAERVCDNDTVPS 131


>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple
           frequency, 3D NMR, induced FIT, alternative splicing,
           developmental protein; NMR {Homo sapiens}
          Length = 159

 Score = 76.4 bits (187), Expect = 7e-20
 Identities = 45/60 (75%), Positives = 52/60 (86%)

Query: 7   YYETGSIKPRAIGGSKPRVATNGVVTKIADYKRECPSIFAWEIRDRLLAEGVCNNDNIPS 66
           YYETGSI+P  IGGSKP+VAT  VV KI DYKR+ P++FAWEIRDRLLAEGVC+ND +PS
Sbjct: 65  YYETGSIRPGVIGGSKPKVATPKVVEKIGDYKRQNPTMFAWEIRDRLLAEGVCDNDTVPS 124


>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation,
          DNA-binding, POU domain, diabetes, disease mutation,
          MODY3, transcription/DNA comple; 2.60A {Homo sapiens}
          SCOP: a.4.1.1 a.35.1.1
          Length = 194

 Score = 39.5 bits (91), Expect = 1e-05
 Identities = 4/36 (11%), Positives = 12/36 (33%)

Query: 32 TKIADYKRECPSIFAWEIRDRLLAEGVCNNDNIPSL 67
            +    +E P   A  ++  L    +   + + + 
Sbjct: 18 AVVETLLQEDPWRVAKMVKSYLQQHNIPQREVVDTT 53


>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU,
          homeo, protein-DNA, human disease; 3.20A {Homo sapiens}
          Length = 221

 Score = 35.0 bits (79), Expect = 5e-04
 Identities = 4/28 (14%), Positives = 9/28 (32%)

Query: 32 TKIADYKRECPSIFAWEIRDRLLAEGVC 59
           ++     E P   A  I+  +    + 
Sbjct: 19 AEVDRMLSEDPWRAAKMIKGYMQQHNIP 46


>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
          photosynthetic reaction center, peripheral antenna;
          HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
          Length = 154

 Score = 28.8 bits (63), Expect = 0.096
 Identities = 6/22 (27%), Positives = 9/22 (40%), Gaps = 1/22 (4%)

Query: 10 TGSIKPRAIGGSKPRVATNGVV 31
            S+K  A   S P +A    +
Sbjct: 26 QASLKLYA-DDSAPALAIKATM 46


>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex,
          helix-turn-helix (HTH), DNA-binding, homeobox, nucleus,
          transcription regulation; 2.51A {Homo sapiens}
          Length = 151

 Score = 25.0 bits (54), Expect = 1.8
 Identities = 5/18 (27%), Positives = 8/18 (44%)

Query: 45 FAWEIRDRLLAEGVCNND 62
          FA   + R L+ G+    
Sbjct: 9  FAKNFKIRRLSLGLTQTQ 26


>3k92_A NAD-GDH, NAD-specific glutamate dehydrogenase; ROCG,
           oxidoreductase; 2.30A {Bacillus subtilis} PDB: 3k8z_A
          Length = 424

 Score = 24.0 bits (53), Expect = 4.5
 Identities = 12/30 (40%), Positives = 15/30 (50%), Gaps = 4/30 (13%)

Query: 2   YSE-EGYYETGSI--KPRAIGGSKPRV-AT 27
           YS    +   G I  KP  +GGS+ R  AT
Sbjct: 171 YSRLREFDSPGFITGKPLVLGGSQGRETAT 200


>3aoe_E Glutamate dehydrogenase; rossmann fold, NADH, oxidoreductase; 2.60A
           {Thermus thermophilus}
          Length = 419

 Score = 23.6 bits (52), Expect = 5.1
 Identities = 12/30 (40%), Positives = 15/30 (50%), Gaps = 4/30 (13%)

Query: 2   YSE-EGYYETGSI--KPRAIGGSKPRV-AT 27
           YS   G    G +  KP A+GGS+ R  A 
Sbjct: 168 YSMTVGSTVPGVVTGKPHALGGSEGRDDAA 197


  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
   0.316    0.136    0.411 

Gapped
Lambda     K      H
   0.267   0.0828    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,065,729
Number of extensions: 47493
Number of successful extensions: 87
Number of sequences better than 10.0: 1
Number of HSP's gapped: 87
Number of HSP's successfully gapped: 9
Length of query: 67
Length of database: 6,701,793
Length adjustment: 38
Effective length of query: 29
Effective length of database: 5,640,795
Effective search space: 163583055
Effective search space used: 163583055
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 51 (23.2 bits)