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= 015848
         (399 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 = 30.0 bits (66), Expect = 2.6,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 32/54 (59%), Gaps = 2/54 (3%)

Query: 207 VESQRMTHIAVERNRRRQMNDHLNTLRSLMPP--AYVQRGDQASIIGGAIDFVK 258
           +++ R  H  +E+ RR +MN  ++ L SL+P   A  ++ D+ +++  A+  +K
Sbjct: 6   IKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMK 59


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

 Score = 29.6 bits (65), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 15/54 (27%), Positives = 32/54 (59%), Gaps = 2/54 (3%)

Query: 207 VESQRMTHIAVERNRRRQMNDHLNTLRSLMPP--AYVQRGDQASIIGGAIDFVK 258
           +++ R  H  +E+ RR +MN  ++ L SL+P   A  ++ D+ +++  A+  +K
Sbjct: 10  IKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMK 63


>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 = 28.5 bits (62), Expect = 7.0,   Method: Composition-based stats.
 Identities = 13/51 (25%), Positives = 30/51 (58%), Gaps = 2/51 (3%)

Query: 210 QRMTHIAVERNRRRQMNDHLNTLRSLMPPAY--VQRGDQASIIGGAIDFVK 258
           ++  H  +ER RR  +ND +  L +L+P +     R ++ +I+  ++D+++
Sbjct: 27  KKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIR 77


  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
   0.317    0.132    0.380 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,326,966
Number of Sequences: 62578
Number of extensions: 305863
Number of successful extensions: 549
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 547
Number of HSP's gapped (non-prelim): 3
length of query: 399
length of database: 14,973,337
effective HSP length: 101
effective length of query: 298
effective length of database: 8,652,959
effective search space: 2578581782
effective search space used: 2578581782
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)