RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy8266
         (68 letters)



>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins,
          transcription-activato; 2.27A {Mus musculus}
          Length = 387

 Score = 82.7 bits (204), Expect = 5e-21
 Identities = 18/54 (33%), Positives = 34/54 (62%)

Query: 14 KSNPSKRHRERLNAELDTLANLLPFEQNILSKLDRLSILRLSVSYLRTKSYFQE 67
           S   KR R+++N+ +D LA+L+P    +  KLD+L++LR++V +++T      
Sbjct: 17 HSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATN 70


>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH,
          PAS, circadian rhythm proteins, transcription-activato;
          2.27A {Mus musculus}
          Length = 361

 Score = 80.4 bits (198), Expect = 4e-20
 Identities = 13/62 (20%), Positives = 29/62 (46%), Gaps = 3/62 (4%)

Query: 5  KPPPKDGVTKSNPSKRHRERLNAELDTLANLLPFEQNILSKLDRLSILRLSVSYLRTKSY 64
                 V+++   K+ R++ N  +  L ++LP       K+D+ ++L+ S+ +LR    
Sbjct: 7  DKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNA---RKMDKSTVLQKSIDFLRKHKE 63

Query: 65 FQ 66
            
Sbjct: 64 TT 65


>1an4_A Protein (upstream stimulatory factor); protein-DNA complex,
          double helix, overhanging base, transcription/DNA
          complex; HET: DNA; 2.90A {Homo sapiens} SCOP: a.38.1.1
          Length = 65

 Score = 31.9 bits (73), Expect = 0.002
 Identities = 9/44 (20%), Positives = 21/44 (47%), Gaps = 2/44 (4%)

Query: 19 KRHRERLNAELDTLANLLPFEQNIL--SKLDRLSILRLSVSYLR 60
          +R R+++N  +  L+ ++P        S   +  IL  +  Y++
Sbjct: 14 RRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQ 57


>1am9_A Srebp-1A, protein (sterol regulatory element binding protein 1A);
          basic-helix-loop- helix-leucine zipper, transcription
          factor; HET: DNA; 2.30A {Homo sapiens} SCOP: a.38.1.1
          PDB: 1ukl_C
          Length = 82

 Score = 28.5 bits (64), Expect = 0.048
 Identities = 12/42 (28%), Positives = 27/42 (64%), Gaps = 3/42 (7%)

Query: 19 KRHRERLNAELDTLANLLPFEQNILSKLDRLSILRLSVSYLR 60
          KR+R  +N ++  L +L+   +   +KL++ ++LR ++ Y+R
Sbjct: 15 KRYRSSINDKIIELKDLVVGTE---AKLNKSAVLRKAIDYIR 53


>1hlo_A Protein (transcription factor MAX); transcriptional regulation,
          DNA binding, complex (transcription factor MAX/DNA),
          transcription/DNA complex; HET: DNA; 2.80A {Homo
          sapiens} SCOP: a.38.1.1
          Length = 80

 Score = 28.5 bits (64), Expect = 0.054
 Identities = 9/43 (20%), Positives = 19/43 (44%), Gaps = 2/43 (4%)

Query: 19 KRHRERLNAELDTLANLLPFEQNILSKLDRLSILRLSVSYLRT 61
          ++ R+ +     +L + +P  Q    K  R  IL  +  Y++ 
Sbjct: 21 RKRRDHIKDSFHSLRDSVPSLQG--EKASRAQILDKATEYIQY 61


>1a0a_A BHLH, protein (phosphate system positive regulatory protein
          PHO4); transcription factor, basic helix loop helix;
          HET: DNA; 2.80A {Saccharomyces cerevisiae} SCOP:
          a.38.1.1
          Length = 63

 Score = 25.9 bits (57), Expect = 0.43
 Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 3/45 (6%)

Query: 19 KRHRERLNAELDTLANLLPFE---QNILSKLDRLSILRLSVSYLR 60
          +  R RL   L  LA+L+P E   QN+ +   + + +  +  Y+R
Sbjct: 11 QARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIR 55


>1mdy_A Protein (MYOD BHLH domain); protein-DNA complex,
          transcription/DNA complex; HET: DNA; 2.80A {Mus
          musculus} SCOP: a.38.1.1 PDB: 1mdy_B*
          Length = 68

 Score = 24.3 bits (53), Expect = 2.3
 Identities = 13/57 (22%), Positives = 24/57 (42%), Gaps = 3/57 (5%)

Query: 5  KPPPKDGVTKSNPSKRHR-ERLNAELDTLANLLPFEQNILSKLDRLSILRLSVSYLR 60
          K    D    +   +R R  ++N   +TL        N   +L ++ ILR ++ Y+ 
Sbjct: 6  KTTNADRRKAATMRERRRLSKVNEAFETLKRSTSSNPN--QRLPKVEILRNAIRYIE 60


>2hnh_A DNA polymerase III alpha subunit; DNA replication,
           nucleotidyltransferase, beta, PHP, transferase; HET:
           DNA; 2.30A {Escherichia coli} PDB: 2hqa_A*
          Length = 910

 Score = 23.2 bits (51), Expect = 8.0
 Identities = 7/28 (25%), Positives = 9/28 (32%)

Query: 4   LKPPPKDGVTKSNPSKRHRERLNAELDT 31
           L     D   +      + ERL  EL  
Sbjct: 304 LAFLFPDEEERLKRRPEYDERLETELQV 331


  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    0.133    0.362 

Gapped
Lambda     K      H
   0.267   0.0557    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 928,180
Number of extensions: 38089
Number of successful extensions: 72
Number of sequences better than 10.0: 1
Number of HSP's gapped: 70
Number of HSP's successfully gapped: 10
Length of query: 68
Length of database: 6,701,793
Length adjustment: 38
Effective length of query: 30
Effective length of database: 5,640,795
Effective search space: 169223850
Effective search space used: 169223850
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 (21.6 bits)
S2: 51 (23.8 bits)