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= 011475
         (485 letters)

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

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



>pdb|3LWK|A Chain A, Crystal Structure Of Human Beta-Crystallin A4 (Cryba4)
          Length = 191

 Score = 32.0 bits (71), Expect = 0.83,   Method: Compositional matrix adjust.
 Identities = 16/44 (36%), Positives = 18/44 (40%)

Query: 292 GQFVKISGVVTCGNVPLESSFQKVPRCIYTSTSLYEYRGWGSKA 335
           G F   SG   C   P    FQ V  C + S     +R WGS A
Sbjct: 135 GSFHVHSGAWVCSQFPGYRGFQYVLECDHHSGDYKHFREWGSHA 178


>pdb|3DZU|A Chain A, Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex On
           Dna Bound With Bvt.13, 9-Cis Retinoic Acid And Ncoa2
           Peptide
 pdb|3DZY|A Chain A, Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex On
           Dna Bound With Rosiglitazone, 9-Cis Retinoic Acid And
           Ncoa2 Peptide
 pdb|3E00|A Chain A, Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex On
           Dna Bound With Gw9662, 9-Cis Retinoic Acid And Ncoa2
           Peptide
          Length = 467

 Score = 30.0 bits (66), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 26/86 (30%), Positives = 34/86 (39%), Gaps = 15/86 (17%)

Query: 119 SGPLNKHGEPLKKSS---GPQSGGVTPSGRQNSGPLAPALPTTGLITSGPISSAPLNSSG 175
           S P+N  G P    S   GP S  V            P  PT G  T  P  S+P+N   
Sbjct: 60  SSPINGMGPPFSVISSPMGPHSMSV------------PTTPTLGFSTGSPQLSSPMNPVS 107

Query: 176 APRKVSGPLDSMGSMKIPSSVPHNQA 201
           +   +  PL   G +K+P+    N A
Sbjct: 108 SSEDIKPPLGLNGVLKVPAHPSGNMA 133


>pdb|1OJ7|A Chain A, Structural Genomics, Unknown Function Crystal Structure
          Of E. Coli K-12 Yqhd
 pdb|1OJ7|B Chain B, Structural Genomics, Unknown Function Crystal Structure
          Of E. Coli K-12 Yqhd
 pdb|1OJ7|C Chain C, Structural Genomics, Unknown Function Crystal Structure
          Of E. Coli K-12 Yqhd
 pdb|1OJ7|D Chain D, Structural Genomics, Unknown Function Crystal Structure
          Of E. Coli K-12 Yqhd
          Length = 408

 Score = 28.5 bits (62), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 15/51 (29%), Positives = 26/51 (50%)

Query: 3  SRFPSHQLSNGLYVSGRPEQPKERTPTMSSVAMPYTGGDIKKSGELGKMFD 53
          + F  H  +  L+  G     +E+ P  + V + Y GG +KK+G L ++ D
Sbjct: 23 NNFNLHTPTRILFGKGAIAGLREQIPHDARVLITYGGGSVKKTGVLDQVLD 73


  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    0.135    0.409 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,710,798
Number of Sequences: 62578
Number of extensions: 610746
Number of successful extensions: 1389
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: 1382
Number of HSP's gapped (non-prelim): 9
length of query: 485
length of database: 14,973,337
effective HSP length: 103
effective length of query: 382
effective length of database: 8,527,803
effective search space: 3257620746
effective search space used: 3257620746
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)