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= 030269
         (180 letters)

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

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



>pdb|3GYT|A Chain A, Nuclear Receptor Daf-12 From Parasitic Nematode
           Strongyloides Stercoralis In Complex With Its
           Physiological Ligand Dafachronic Acid Delta 4
          Length = 244

 Score = 26.6 bits (57), Expect = 7.8,   Method: Compositional matrix adjust.
 Identities = 22/82 (26%), Positives = 34/82 (41%), Gaps = 9/82 (10%)

Query: 13  ASIKIQQKQQPTRNWMMMQGLRRRNGKASKRVGVTNCSGNSG---------IEIGDFIGG 63
           AS   +++  PT    +M    RR  K +KR+G  N    +G         IE+    G 
Sbjct: 33  ASTLAKKEHNPTDILNVMDITMRRLVKMAKRLGAFNEISEAGKFSLLKGGMIEMLTIRGV 92

Query: 64  DLLKPDLGRWLSDVEKHKAIAI 85
            +   D G W + V+ H  I+ 
Sbjct: 93  TVFNADKGVWQTPVDGHSQISF 114


  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
   0.319    0.136    0.425 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,876,978
Number of Sequences: 62578
Number of extensions: 161416
Number of successful extensions: 260
Number of sequences better than 100.0: 1
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 260
Number of HSP's gapped (non-prelim): 1
length of query: 180
length of database: 14,973,337
effective HSP length: 93
effective length of query: 87
effective length of database: 9,153,583
effective search space: 796361721
effective search space used: 796361721
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)