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= 028150
         (213 letters)

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

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



>pdb|1XEZ|A Chain A, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
           Pro-Toxin With Octylglucoside Bound
          Length = 721

 Score = 33.1 bits (74), Expect = 0.12,   Method: Composition-based stats.
 Identities = 22/72 (30%), Positives = 31/72 (43%), Gaps = 7/72 (9%)

Query: 103 AYLHPWKSSSTAEKYQLGFLLSAFAFNLTNLFVFTPMTIEMMKQRHKVEREENIGDEVGW 162
           AY   W + + A+ Y+       F FN +N       T  +     K ER+E  G E+G 
Sbjct: 245 AYFREWSTDAIAQDYR-------FVFNASNNKAQILKTFPVDNINEKFERKEVSGFELGV 297

Query: 163 TKNREVAKSNPK 174
           T   EV+   PK
Sbjct: 298 TGGVEVSGDGPK 309


>pdb|3O44|A Chain A, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
           Heptameric Pore
 pdb|3O44|B Chain B, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
           Heptameric Pore
 pdb|3O44|C Chain C, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
           Heptameric Pore
 pdb|3O44|D Chain D, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
           Heptameric Pore
 pdb|3O44|E Chain E, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
           Heptameric Pore
 pdb|3O44|F Chain F, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
           Heptameric Pore
 pdb|3O44|G Chain G, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
           Heptameric Pore
 pdb|3O44|H Chain H, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
           Heptameric Pore
 pdb|3O44|I Chain I, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
           Heptameric Pore
 pdb|3O44|J Chain J, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
           Heptameric Pore
 pdb|3O44|K Chain K, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
           Heptameric Pore
 pdb|3O44|L Chain L, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
           Heptameric Pore
 pdb|3O44|M Chain M, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
           Heptameric Pore
 pdb|3O44|N Chain N, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
           Heptameric Pore
          Length = 593

 Score = 31.2 bits (69), Expect = 0.42,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 31/72 (43%), Gaps = 7/72 (9%)

Query: 103 AYLHPWKSSSTAEKYQLGFLLSAFAFNLTNLFVFTPMTIEMMKQRHKVEREENIGDEVGW 162
           AY   W + + A+ Y+       F FN +N       T  +     K ER+E  G E+G 
Sbjct: 117 AYFREWSTDAIAQDYR-------FVFNASNNKAQILKTFPVDNINEKFERKEVSGFELGV 169

Query: 163 TKNREVAKSNPK 174
           T   EV+   PK
Sbjct: 170 TGGVEVSGDGPK 181


>pdb|2LCH|A Chain A, Solution Nmr Structure Of A Protein With A Redesigned
           Hydrophobic Core, Northeast Structural Genomics
           Consortium Target Or38
 pdb|3U3B|A Chain A, Crystal Structure Of Computationally Redesigned Four-Helix
           Bundle
 pdb|3U3B|B Chain B, Crystal Structure Of Computationally Redesigned Four-Helix
           Bundle
          Length = 113

 Score = 27.3 bits (59), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 12/48 (25%), Positives = 25/48 (52%), Gaps = 5/48 (10%)

Query: 154 ENIGDEVGWTKNREVAKSNPKLAAMNKKFGMIHGLSSLANIMSFGSLA 201
           +N+ D++     +EV K+   +   NK + ++H +  +   M F S+A
Sbjct: 20  QNVNDDI-----KEVEKNPEDMEYWNKIYRLVHTMKEITETMGFSSVA 62


  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
   0.325    0.135    0.422 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,758,364
Number of Sequences: 62578
Number of extensions: 198506
Number of successful extensions: 520
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 520
Number of HSP's gapped (non-prelim): 3
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: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 bits)