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= psy8266
         (68 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 = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/47 (38%), Positives = 34/47 (72%)

Query: 15 SNPSKRHRERLNAELDTLANLLPFEQNILSKLDRLSILRLSVSYLRT 61
          S   KR R+++N+ +D LA+L+P    +  KLD+L++LR++V +++T
Sbjct: 18 SQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKT 64


>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 = 41.2 bits (95), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/47 (38%), Positives = 34/47 (72%)

Query: 15 SNPSKRHRERLNAELDTLANLLPFEQNILSKLDRLSILRLSVSYLRT 61
          S   KR R+++N+ +D LA+L+P    +  KLD+L++LR++V +++T
Sbjct: 14 SQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKT 60


  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
   0.316    0.133    0.362 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,756,852
Number of Sequences: 62578
Number of extensions: 44515
Number of successful extensions: 119
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 110
Number of HSP's gapped (non-prelim): 11
length of query: 68
length of database: 14,973,337
effective HSP length: 38
effective length of query: 30
effective length of database: 12,595,373
effective search space: 377861190
effective search space used: 377861190
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)