BLASTP 2.2.26 [Sep-21-2011]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.


Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= psy3614
         (209 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

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



>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
           Transcriptional Activator Complex
          Length = 387

 Score = 37.4 bits (85), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 22/65 (33%), Positives = 38/65 (58%), Gaps = 8/65 (12%)

Query: 39  LERKRRARINRCLDELKDLMVTALQAEGENVSKLEKADILELTVQHLQKMRRQQRLASNP 98
           +E++RR ++N  +DEL  L+ T          KL+K  +L + VQH++ +R     A+NP
Sbjct: 20  IEKRRRDKMNSFIDELASLVPTC----NAMSRKLDKLTVLRMAVQHMKTLRG----ATNP 71

Query: 99  VTDAD 103
            T+A+
Sbjct: 72  YTEAN 76


>pdb|1HLO|A Chain A, The Crystal Structure Of An Intact Human Max-Dna Complex:
           New Insights Into Mechanisms Of Transcriptional Control
 pdb|1HLO|B Chain B, The Crystal Structure Of An Intact Human Max-Dna Complex:
           New Insights Into Mechanisms Of Transcriptional Control
          Length = 80

 Score = 31.6 bits (70), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 6/73 (8%)

Query: 32  RKVMKPMLERKRRARINRCLDELKDLMVTALQAEGENVSKLEKADILELTVQHLQKMRRQ 91
           ++     LERKRR  I      L+D  V +LQ E     K  +A IL+   +++Q MRR+
Sbjct: 12  KRAHHNALERKRRDHIKDSFHSLRD-SVPSLQGE-----KASRAQILDKATEYIQYMRRK 65

Query: 92  QRLASNPVTDADR 104
                  + D  R
Sbjct: 66  NHTHQQDIDDLKR 78


>pdb|1NKP|B Chain B, Crystal Structure Of Myc-Max Recognizing Dna
 pdb|1NKP|E Chain E, Crystal Structure Of Myc-Max Recognizing Dna
          Length = 83

 Score = 31.2 bits (69), Expect = 0.38,   Method: Compositional matrix adjust.
 Identities = 25/88 (28%), Positives = 37/88 (42%), Gaps = 6/88 (6%)

Query: 32  RKVMKPMLERKRRARINRCLDELKDLMVTALQAEGENVSKLEKADILELTVQHLQKMRRQ 91
           ++     LERKRR  I      L+D  V +LQ E     K  +A IL+   +++Q MRR+
Sbjct: 2   KRAHHNALERKRRDHIKDSFHSLRD-SVPSLQGE-----KASRAQILDKATEYIQYMRRK 55

Query: 92  QRLASNPVTDADRFRAGFTTCANEVSKC 119
                  + D  R  A        +  C
Sbjct: 56  NHTHQQDIDDLKRQNALLEQQVRALGGC 83


>pdb|1NLW|B Chain B, Crystal Structure Of Mad-Max Recognizing Dna
 pdb|1NLW|E Chain E, Crystal Structure Of Mad-Max Recognizing Dna
          Length = 76

 Score = 31.2 bits (69), Expect = 0.47,   Method: Compositional matrix adjust.
 Identities = 23/66 (34%), Positives = 32/66 (48%), Gaps = 6/66 (9%)

Query: 39  LERKRRARINRCLDELKDLMVTALQAEGENVSKLEKADILELTVQHLQKMRRQQRLASNP 98
           LERKRR  I      L+D  V +LQ E     K  +A IL+   +++Q MRR+       
Sbjct: 8   LERKRRDHIKDSFHSLRD-SVPSLQGE-----KASRAQILDKATEYIQYMRRKNHTHQQD 61

Query: 99  VTDADR 104
           + D  R
Sbjct: 62  IDDLKR 67


>pdb|4H10|A Chain A, Intermolecular Recognition Revealed By The Complex
          Structure Of Human Clock-bmal1 Basic Helix-loop-helix
          Domains With E-box Dna
          Length = 73

 Score = 30.4 bits (67), Expect = 0.71,   Method: Compositional matrix adjust.
 Identities = 17/51 (33%), Positives = 30/51 (58%), Gaps = 4/51 (7%)

Query: 39 LERKRRARINRCLDELKDLMVTALQAEGENVSKLEKADILELTVQHLQKMR 89
          +E++RR ++N  +DEL  L+ T          KL+K  +L + VQH++ +R
Sbjct: 16 IEKRRRDKMNSFIDELASLVPTC----NAMSRKLDKLTVLRMAVQHMKTLR 62


>pdb|1AN2|A Chain A, Recognition By Max Of Its Cognate Dna Through A Dimeric
           BHLHZ DOMAIN
          Length = 86

 Score = 30.4 bits (67), Expect = 0.75,   Method: Compositional matrix adjust.
 Identities = 23/66 (34%), Positives = 32/66 (48%), Gaps = 6/66 (9%)

Query: 39  LERKRRARINRCLDELKDLMVTALQAEGENVSKLEKADILELTVQHLQKMRRQQRLASNP 98
           LERKRR  I      L+D  V +LQ E     K  +A IL+   +++Q MRR+       
Sbjct: 10  LERKRRDHIKDSFHSLRD-SVPSLQGE-----KASRAQILDKATEYIQYMRRKNHTHQQD 63

Query: 99  VTDADR 104
           + D  R
Sbjct: 64  IDDLKR 69


>pdb|1R05|A Chain A, Solution Structure Of Max B-Hlh-Lz
 pdb|1R05|B Chain B, Solution Structure Of Max B-Hlh-Lz
          Length = 87

 Score = 29.6 bits (65), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 23/66 (34%), Positives = 32/66 (48%), Gaps = 6/66 (9%)

Query: 39  LERKRRARINRCLDELKDLMVTALQAEGENVSKLEKADILELTVQHLQKMRRQQRLASNP 98
           LERKRR  I      L+D  V +LQ E     K  +A IL+   +++Q MRR+       
Sbjct: 11  LERKRRDHIKDSFHSLRD-SVPSLQGE-----KASRAQILDKATEYIQYMRRKVHTLQQD 64

Query: 99  VTDADR 104
           + D  R
Sbjct: 65  IDDLKR 70


>pdb|2GX5|A Chain A, N-terminal Gaf Domain Of Transcriptional Pleiotropic
           Repressor Cody
 pdb|2GX5|B Chain B, N-terminal Gaf Domain Of Transcriptional Pleiotropic
           Repressor Cody
 pdb|2GX5|C Chain C, N-terminal Gaf Domain Of Transcriptional Pleiotropic
           Repressor Cody
 pdb|2GX5|D Chain D, N-terminal Gaf Domain Of Transcriptional Pleiotropic
           Repressor Cody
          Length = 170

 Score = 28.1 bits (61), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 8/51 (15%)

Query: 98  PVTDADRFRAGFTTCANEVSKCLASTPGIDLRLGTKLMSHLGQRLNEMDKI 148
           PV + D F+AG TT        +    G   RLGT ++S L  + N+ D I
Sbjct: 109 PVENRDLFQAGLTT--------IVPIIGGGERLGTLILSRLQDQFNDDDLI 151


>pdb|2B18|A Chain A, N-Terminal Gaf Domain Of Transcriptional Pleiotropic
           Repressor Cody
          Length = 164

 Score = 27.7 bits (60), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 8/51 (15%)

Query: 98  PVTDADRFRAGFTTCANEVSKCLASTPGIDLRLGTKLMSHLGQRLNEMDKI 148
           PV + D F+AG TT        +    G   RLGT ++S L  + N+ D I
Sbjct: 108 PVENRDLFQAGLTT--------IVPIIGGGERLGTLILSRLQDQFNDDDLI 150


>pdb|2HGV|A Chain A, N-Terminal Gaf Domain Of Transcriptional Pleiotropic
           Repressor Cody
          Length = 164

 Score = 27.7 bits (60), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 8/51 (15%)

Query: 98  PVTDADRFRAGFTTCANEVSKCLASTPGIDLRLGTKLMSHLGQRLNEMDKI 148
           PV + D F+AG TT        +    G   RLGT ++S L  + N+ D I
Sbjct: 108 PVENRDLFQAGLTT--------IVPIIGGGERLGTLILSRLQDQFNDDDLI 150


  Database: pdbaa
    Posted date:  Mar 3, 2013 10:34 PM
  Number of letters in database: 14,973,337
  Number of sequences in database:  62,578
  
Lambda     K      H
   0.317    0.129    0.377 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,627,930
Number of Sequences: 62578
Number of extensions: 196577
Number of successful extensions: 521
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 518
Number of HSP's gapped (non-prelim): 13
length of query: 209
length of database: 14,973,337
effective HSP length: 94
effective length of query: 115
effective length of database: 9,091,005
effective search space: 1045465575
effective search space used: 1045465575
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)