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= 022288
         (299 letters)

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

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



>pdb|4H10|B Chain B, Intermolecular Recognition Revealed By The Complex
          Structure Of Human Clock-bmal1 Basic Helix-loop-helix
          Domains With E-box Dna
          Length = 71

 Score = 32.3 bits (72), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 19/50 (38%), Positives = 30/50 (60%), Gaps = 3/50 (6%)

Query: 26 EKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLL---KDLTSQVE 72
          EK RRD+ N    ELG+ L  +  K DK+T+L  ++  L   K++T+ +E
Sbjct: 16 EKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITAWLE 65


>pdb|4F3L|A Chain A, Crystal Structure Of The Heterodimeric Clock:bmal1
          Transcriptional Activator Complex
          Length = 361

 Score = 32.3 bits (72), Expect = 0.31,   Method: Compositional matrix adjust.
 Identities = 16/48 (33%), Positives = 28/48 (58%)

Query: 18 RKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLK 65
          +++ +   EK RRD+ N    ELG+ L  +  K DK+T+L  ++  L+
Sbjct: 12 KRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLR 59


  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
   0.308    0.126    0.347 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,848,128
Number of Sequences: 62578
Number of extensions: 217375
Number of successful extensions: 505
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 491
Number of HSP's gapped (non-prelim): 27
length of query: 299
length of database: 14,973,337
effective HSP length: 98
effective length of query: 201
effective length of database: 8,840,693
effective search space: 1776979293
effective search space used: 1776979293
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 51 (24.3 bits)