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= 020210
         (329 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 = 33.1 bits (74), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 17/58 (29%), Positives = 33/58 (56%), Gaps = 2/58 (3%)

Query: 125 EIENQRMTHIAVERNRRKQMNEYLAILRSLMPP--SYVQRGDQASVIGGSINFVKELE 180
            I+N R  H  +E+ RR +MN ++  L SL+P   +  ++ D+ +V+  ++  +K L 
Sbjct: 9   RIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 66


>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 = 32.3 bits (72), Expect = 0.36,   Method: Composition-based stats.
 Identities = 17/56 (30%), Positives = 33/56 (58%), Gaps = 2/56 (3%)

Query: 126 IENQRMTHIAVERNRRKQMNEYLAILRSLMPP--SYVQRGDQASVIGGSINFVKEL 179
           I+N R  H  +E+ RR +MN ++  L SL+P   +  ++ D+ +V+  ++  +K L
Sbjct: 6   IKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTL 61


>pdb|4ATI|A Chain A, Mitf:m-Box Complex
 pdb|4ATI|B Chain B, Mitf:m-Box Complex
 pdb|4ATK|A Chain A, Mitf:e-Box Complex
 pdb|4ATK|B Chain B, Mitf:e-Box Complex
          Length = 118

 Score = 28.9 bits (63), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 13/51 (25%), Positives = 32/51 (62%), Gaps = 2/51 (3%)

Query: 133 HIAVERNRRKQMNEYLAILRSLMPPSY--VQRGDQASVIGGSINFVKELEQ 181
           H  +ER RR  +N+ +  L +L+P S     R ++ +++  S++++++L++
Sbjct: 31  HNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQR 81


  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
   0.313    0.127    0.357 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,537,350
Number of Sequences: 62578
Number of extensions: 314578
Number of successful extensions: 478
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 474
Number of HSP's gapped (non-prelim): 7
length of query: 329
length of database: 14,973,337
effective HSP length: 99
effective length of query: 230
effective length of database: 8,778,115
effective search space: 2018966450
effective search space used: 2018966450
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 52 (24.6 bits)