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= psy13711
         (580 letters)

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

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



>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 = 29.6 bits (65), Expect = 4.3,   Method: Composition-based stats.
 Identities = 16/48 (33%), Positives = 28/48 (58%), Gaps = 4/48 (8%)

Query: 278 MEKRRRARINQSLALLKALILDSAKTENTKHSKLEKADILELTVRHLQ 325
           +EKRRR ++N  +  L +L+     T N    KL+K  +L + V+H++
Sbjct: 16  IEKRRRDKMNSFIDELASLV----PTCNAMSRKLDKLTVLRMAVQHMK 59


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

 Score = 29.3 bits (64), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 16/48 (33%), Positives = 28/48 (58%), Gaps = 4/48 (8%)

Query: 278 MEKRRRARINQSLALLKALILDSAKTENTKHSKLEKADILELTVRHLQ 325
           +EKRRR ++N  +  L +L+     T N    KL+K  +L + V+H++
Sbjct: 20  IEKRRRDKMNSFIDELASLV----PTCNAMSRKLDKLTVLRMAVQHMK 63


  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
   0.314    0.132    0.383 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,533,401
Number of Sequences: 62578
Number of extensions: 387009
Number of successful extensions: 670
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 670
Number of HSP's gapped (non-prelim): 2
length of query: 580
length of database: 14,973,337
effective HSP length: 104
effective length of query: 476
effective length of database: 8,465,225
effective search space: 4029447100
effective search space used: 4029447100
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 54 (25.4 bits)