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= 011986
         (473 letters)

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

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



>pdb|3ZS6|A Chain A, The Structural Characterization Of Burkholderia
           Pseudomallei Oppa
          Length = 506

 Score = 29.6 bits (65), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 16/32 (50%), Positives = 19/32 (59%), Gaps = 3/32 (9%)

Query: 82  CSSKPNTVAYCNSKND-VTSVSNSK--DGVRA 110
           C S  NTV YCN K D + + +N K  DG RA
Sbjct: 422 CGSSQNTVGYCNPKVDSLVAEANQKLDDGARA 453


>pdb|1NH1|A Chain A, Crystal Structure Of The Type Iii Effector Avrb From
           Pseudomonas Syringae
          Length = 330

 Score = 28.9 bits (63), Expect = 6.7,   Method: Compositional matrix adjust.
 Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 6/54 (11%)

Query: 74  KWIDSDTACSSKPNTVAYCNSK-NDVTSVSN--SKDGVRARSFKSLFGKRSVWR 124
           +W D D++ S+ P   AYC S  N + S  +  S+ G+   SF+ L+G+ + WR
Sbjct: 49  RWPD-DSSKSNTPENRAYCQSMYNSIRSAGDEISRGGIT--SFEELWGRATEWR 99


>pdb|2NUD|A Chain A, The Structure Of The Type Iii Effector Avrb Complexed With
           A High-Affinity Rin4 Peptide
 pdb|2NUD|B Chain B, The Structure Of The Type Iii Effector Avrb Complexed With
           A High-Affinity Rin4 Peptide
 pdb|2NUN|A Chain A, The Structure Of The Type Iii Effector Avrb Complexed With
           Adp
          Length = 323

 Score = 28.9 bits (63), Expect = 6.7,   Method: Compositional matrix adjust.
 Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 6/54 (11%)

Query: 74  KWIDSDTACSSKPNTVAYCNSK-NDVTSVSN--SKDGVRARSFKSLFGKRSVWR 124
           +W D D++ S+ P   AYC S  N + S  +  S+ G+   SF+ L+G+ + WR
Sbjct: 51  RWPD-DSSKSNTPENRAYCQSMYNSIRSAGDEISRGGIT--SFEELWGRATEWR 101


  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
   0.321    0.133    0.418 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,358,993
Number of Sequences: 62578
Number of extensions: 523116
Number of successful extensions: 953
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 952
Number of HSP's gapped (non-prelim): 6
length of query: 473
length of database: 14,973,337
effective HSP length: 102
effective length of query: 371
effective length of database: 8,590,381
effective search space: 3187031351
effective search space used: 3187031351
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)