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= 028154
         (213 letters)

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

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



>pdb|3EUP|A Chain A, The Crystal Structure Of The Transcriptional Regulator,
           Tetr Family From Cytophaga Hutchinsonii
 pdb|3EUP|B Chain B, The Crystal Structure Of The Transcriptional Regulator,
           Tetr Family From Cytophaga Hutchinsonii
          Length = 204

 Score = 28.9 bits (63), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 13/25 (52%), Positives = 16/25 (64%)

Query: 90  YNWGLVRGVTSALVCLPNELKEMLI 114
           YNWG V+ V +A V   N  KEML+
Sbjct: 65  YNWGHVKSVLTAKVQACNTYKEMLL 89


  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
   0.315    0.133    0.380 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,405,835
Number of Sequences: 62578
Number of extensions: 194684
Number of successful extensions: 594
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 591
Number of HSP's gapped (non-prelim): 12
length of query: 213
length of database: 14,973,337
effective HSP length: 95
effective length of query: 118
effective length of database: 9,028,427
effective search space: 1065354386
effective search space used: 1065354386
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: 49 (23.5 bits)