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= psy4709
         (86 letters)

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

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



>pdb|2EBK|A Chain A, Solution Structure Of The Rwd Domain Of Human Rwd Domain
           Containing Protein 3
          Length = 128

 Score = 27.7 bits (60), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 1/52 (1%)

Query: 3   SKLPKSTLNFRQFLLRAEVLGLYKTFLRTAKEIPDESSRKEMIDWIRSEFKH 54
           S LP  ++N  Q L RA+ + + +  L  A+ +  E    E++ WI+   +H
Sbjct: 70  SCLPGISINSEQ-LTRAQCVTVKEKLLEQAESLLSEPMVHELVLWIQQNLRH 120


  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
   0.316    0.129    0.349 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,996,726
Number of Sequences: 62578
Number of extensions: 57779
Number of successful extensions: 179
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 178
Number of HSP's gapped (non-prelim): 2
length of query: 86
length of database: 14,973,337
effective HSP length: 54
effective length of query: 32
effective length of database: 11,594,125
effective search space: 371012000
effective search space used: 371012000
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: 45 (21.9 bits)