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= 040216
         (265 letters)

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

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



>pdb|2EZD|A Chain A, Solution Structure Of A Complex Of The Second Dna
          Binding Domain Of Human Hmg-I(Y) Bound To Dna Dodecamer
          Containing The Prdii Site Of The Interferon-Beta
          Promoter, Nmr, Minimized Average Structure
 pdb|2EZE|A Chain A, Solution Structure Of A Complex Of The Second Dna
          Binding Domain Of Human Hmg-I(Y) Bound To Dna Dodecamer
          Containing The Prdii Site Of The Interferon-Beta
          Promoter, Nmr, 35 Structures
          Length = 25

 Score = 27.3 bits (59), Expect = 9.8,   Method: Compositional matrix adjust.
 Identities = 12/15 (80%), Positives = 13/15 (86%)

Query: 57 TLRRPRGRPAGSKNK 71
          T +RPRGRP GSKNK
Sbjct: 3  TPKRPRGRPKGSKNK 17


  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    0.131    0.386 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,858,577
Number of Sequences: 62578
Number of extensions: 242005
Number of successful extensions: 811
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 806
Number of HSP's gapped (non-prelim): 7
length of query: 265
length of database: 14,973,337
effective HSP length: 97
effective length of query: 168
effective length of database: 8,903,271
effective search space: 1495749528
effective search space used: 1495749528
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: 50 (23.9 bits)