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= psy11108
         (106 letters)

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

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



>pdb|1XKW|A Chain A, Pyochelin Outer Membrane Receptor Fpta From Pseudomonas
           Aeruginosa
          Length = 665

 Score = 29.3 bits (64), Expect = 0.65,   Method: Compositional matrix adjust.
 Identities = 12/17 (70%), Positives = 14/17 (82%)

Query: 82  AENYQLQADRRTWKSKP 98
           AE YQ QADR+TW S+P
Sbjct: 443 AEVYQPQADRQTWNSEP 459


>pdb|3I42|A Chain A, Structure Of Response Regulator Receiver Domain
          (Chey-Like) From Methylobacillus Flagellatus
          Length = 127

 Score = 27.7 bits (60), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 11/19 (57%), Positives = 14/19 (73%)

Query: 45 VNCQDYAGLQLIKSLRALP 63
          +N  D +GL L+K LRALP
Sbjct: 55 LNLPDTSGLALVKQLRALP 73


>pdb|3GYZ|A Chain A, Crystal Structure Of Ipgc From Shigella Flexneri
 pdb|3GYZ|B Chain B, Crystal Structure Of Ipgc From Shigella Flexneri
 pdb|3GZ1|A Chain A, Crystal Structure Of Ipgc In Complex With The Chaperone
          Binding Region Of Ipab
 pdb|3GZ1|B Chain B, Crystal Structure Of Ipgc In Complex With The Chaperone
          Binding Region Of Ipab
 pdb|3GZ2|A Chain A, Crystal Structure Of Ipgc In Complex With An Ipab
          Peptide
 pdb|3GZ2|B Chain B, Crystal Structure Of Ipgc In Complex With An Ipab
          Peptide
          Length = 151

 Score = 26.6 bits (57), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 12/32 (37%), Positives = 20/32 (62%), Gaps = 4/32 (12%)

Query: 56 IKSLRALPDDIMK----HAYIAQHQGRFQTAE 83
          +K + A+PDD+M     +AY   ++GR + AE
Sbjct: 25 LKDINAIPDDMMDDIYSYAYDFYNKGRIEEAE 56


>pdb|3KS2|A Chain A, Crystal Structure Of Type-Iii Secretion Chaperone Ipgc
          From Shigella Flexneri (Residues 10-155)
 pdb|3KS2|B Chain B, Crystal Structure Of Type-Iii Secretion Chaperone Ipgc
          From Shigella Flexneri (Residues 10-155)
 pdb|3KS2|C Chain C, Crystal Structure Of Type-Iii Secretion Chaperone Ipgc
          From Shigella Flexneri (Residues 10-155)
 pdb|3KS2|D Chain D, Crystal Structure Of Type-Iii Secretion Chaperone Ipgc
          From Shigella Flexneri (Residues 10-155)
 pdb|3KS2|E Chain E, Crystal Structure Of Type-Iii Secretion Chaperone Ipgc
          From Shigella Flexneri (Residues 10-155)
 pdb|3KS2|F Chain F, Crystal Structure Of Type-Iii Secretion Chaperone Ipgc
          From Shigella Flexneri (Residues 10-155)
 pdb|3KS2|G Chain G, Crystal Structure Of Type-Iii Secretion Chaperone Ipgc
          From Shigella Flexneri (Residues 10-155)
 pdb|3KS2|H Chain H, Crystal Structure Of Type-Iii Secretion Chaperone Ipgc
          From Shigella Flexneri (Residues 10-155)
 pdb|3KS2|I Chain I, Crystal Structure Of Type-Iii Secretion Chaperone Ipgc
          From Shigella Flexneri (Residues 10-155)
 pdb|3KS2|J Chain J, Crystal Structure Of Type-Iii Secretion Chaperone Ipgc
          From Shigella Flexneri (Residues 10-155)
 pdb|3KS2|K Chain K, Crystal Structure Of Type-Iii Secretion Chaperone Ipgc
          From Shigella Flexneri (Residues 10-155)
 pdb|3KS2|L Chain L, Crystal Structure Of Type-Iii Secretion Chaperone Ipgc
          From Shigella Flexneri (Residues 10-155)
 pdb|3KS2|M Chain M, Crystal Structure Of Type-Iii Secretion Chaperone Ipgc
          From Shigella Flexneri (Residues 10-155)
 pdb|3KS2|N Chain N, Crystal Structure Of Type-Iii Secretion Chaperone Ipgc
          From Shigella Flexneri (Residues 10-155)
 pdb|3KS2|O Chain O, Crystal Structure Of Type-Iii Secretion Chaperone Ipgc
          From Shigella Flexneri (Residues 10-155)
 pdb|3KS2|P Chain P, Crystal Structure Of Type-Iii Secretion Chaperone Ipgc
          From Shigella Flexneri (Residues 10-155)
 pdb|3KS2|Q Chain Q, Crystal Structure Of Type-Iii Secretion Chaperone Ipgc
          From Shigella Flexneri (Residues 10-155)
 pdb|3KS2|R Chain R, Crystal Structure Of Type-Iii Secretion Chaperone Ipgc
          From Shigella Flexneri (Residues 10-155)
          Length = 151

 Score = 26.6 bits (57), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 12/32 (37%), Positives = 20/32 (62%), Gaps = 4/32 (12%)

Query: 56 IKSLRALPDDIMK----HAYIAQHQGRFQTAE 83
          +K + A+PDD+M     +AY   ++GR + AE
Sbjct: 21 LKDINAIPDDMMDDIYSYAYDFYNKGRIEEAE 52


  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
   0.322    0.131    0.404 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,969,419
Number of Sequences: 62578
Number of extensions: 94227
Number of successful extensions: 201
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 197
Number of HSP's gapped (non-prelim): 4
length of query: 106
length of database: 14,973,337
effective HSP length: 71
effective length of query: 35
effective length of database: 10,530,299
effective search space: 368560465
effective search space used: 368560465
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)