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= psy14123
         (102 letters)

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

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



>pdb|4FM9|A Chain A, Human Topoisomerase Ii Alpha Bound To Dna
          Length = 763

 Score = 26.6 bits (57), Expect = 4.1,   Method: Composition-based stats.
 Identities = 9/20 (45%), Positives = 12/20 (60%)

Query: 28  LNEFAHNNWRSFARHEYFDE 47
           L  F H+NW S  RH + +E
Sbjct: 123 LINFIHHNWPSLLRHRFLEE 142


>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 = 25.4 bits (54), Expect = 9.1,   Method: Composition-based stats.
 Identities = 11/44 (25%), Positives = 23/44 (52%), Gaps = 4/44 (9%)

Query: 26  ENLNEFAHNNWRSFARHEYFDEKGMFISIVFSIPLL----LNCM 65
           E L E  + +  ++ +H+Y ++ G F  ++  +P L    L C+
Sbjct: 395 EALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCL 438


  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
   0.333    0.148    0.471 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,582,970
Number of Sequences: 62578
Number of extensions: 81787
Number of successful extensions: 154
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 136
Number of HSP's gapped (non-prelim): 18
length of query: 102
length of database: 14,973,337
effective HSP length: 67
effective length of query: 35
effective length of database: 10,780,611
effective search space: 377321385
effective search space used: 377321385
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 bits)
S2: 45 (21.9 bits)