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= psy3641
         (202 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 = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/52 (38%), Positives = 34/52 (65%), Gaps = 2/52 (3%)

Query: 53  SHRIIEKRRRDRMNNCLADLSRLIPADYLKKGRGRIEKTEIIEMAIKHMKYL 104
           +H  IEKRRRD+MN+ + +L+ L+P         +++K  ++ MA++HMK L
Sbjct: 16  AHSQIEKRRRDKMNSFIDELASLVPT--CNAMSRKLDKLTVLRMAVQHMKTL 65


>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 = 40.4 bits (93), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 20/53 (37%), Positives = 37/53 (69%), Gaps = 4/53 (7%)

Query: 53  SHRIIEKRRRDRMNNCLADLSRLIP-ADYLKKGRGRIEKTEIIEMAIKHMKYL 104
           +H  IEKRRRD+MN+ + +L+ L+P  + + +   +++K  ++ MA++HMK L
Sbjct: 12  AHSQIEKRRRDKMNSFIDELASLVPTCNAMSR---KLDKLTVLRMAVQHMKTL 61


>pdb|1AN4|A Chain A, Structure And Function Of The BHLHZ DOMAIN OF USF
 pdb|1AN4|B Chain B, Structure And Function Of The BHLHZ DOMAIN OF USF
          Length = 65

 Score = 33.1 bits (74), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 16/51 (31%), Positives = 30/51 (58%)

Query: 54  HRIIEKRRRDRMNNCLADLSRLIPADYLKKGRGRIEKTEIIEMAIKHMKYL 104
           H  +E+RRRD++NN +  LS++IP   ++  +    K  I+  A  +++ L
Sbjct: 9   HNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQEL 59


>pdb|1A0A|A Chain A, Phosphate System Positive Regulatory Protein Pho4DNA
           Complex
 pdb|1A0A|B Chain B, Phosphate System Positive Regulatory Protein Pho4DNA
           Complex
          Length = 63

 Score = 32.0 bits (71), Expect = 0.25,   Method: Compositional matrix adjust.
 Identities = 16/53 (30%), Positives = 32/53 (60%), Gaps = 1/53 (1%)

Query: 53  SHRIIEKRRRDRMNNCLADLSRLIPADYLKKGRGRI-EKTEIIEMAIKHMKYL 104
           SH+  E+ RR+R+   L +L+ LIPA++ ++       K   +E A +++++L
Sbjct: 5   SHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHL 57


  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
   0.310    0.128    0.365 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,264,102
Number of Sequences: 62578
Number of extensions: 250387
Number of successful extensions: 331
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 322
Number of HSP's gapped (non-prelim): 8
length of query: 202
length of database: 14,973,337
effective HSP length: 94
effective length of query: 108
effective length of database: 9,091,005
effective search space: 981828540
effective search space used: 981828540
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 49 (23.5 bits)