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= 040492
         (77 letters)

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

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



>pdb|2NUD|C Chain C, The Structure Of The Type Iii Effector Avrb Complexed
          With A High-Affinity Rin4 Peptide
 pdb|2NUD|D Chain D, The Structure Of The Type Iii Effector Avrb Complexed
          With A High-Affinity Rin4 Peptide
          Length = 35

 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 20/34 (58%), Positives = 27/34 (79%)

Query: 3  EKGGPLPKFGEWDVNDPASAEGFTVIFNKARNEK 36
          EK   +PKFG+WD N+P+SA+G+T IFNK R E+
Sbjct: 2  EKVTVVPKFGDWDENNPSSADGYTHIFNKVREER 35


>pdb|3ST1|A Chain A, Crystal Structure Of Necrosis And Ethylene Inducing
           Protein 2 From The Causal Agent Of Cocoa's Witches Broom
           Disease
          Length = 214

 Score = 25.8 bits (55), Expect = 5.8,   Method: Compositional matrix adjust.
 Identities = 17/67 (25%), Positives = 25/67 (37%), Gaps = 15/67 (22%)

Query: 1   MAEKGGPLPKFGEWDVNDPASAEGFTVIFNKARNEKKTGGKPDSPVKDDSQFKHGAVLGK 60
           + +KGG LP    W        EG       A NE+   G  + P+ D       +++G 
Sbjct: 162 LTDKGGDLPTLASW--------EGMGADARAAINERSHWGDANPPIAD-------SLIGS 206

Query: 61  PQSKKWF 67
             S  W 
Sbjct: 207 SLSGAWM 213


  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
   0.313    0.131    0.413 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,675,473
Number of Sequences: 62578
Number of extensions: 97225
Number of successful extensions: 135
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: 134
Number of HSP's gapped (non-prelim): 2
length of query: 77
length of database: 14,973,337
effective HSP length: 46
effective length of query: 31
effective length of database: 12,094,749
effective search space: 374937219
effective search space used: 374937219
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 45 (21.9 bits)