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= 003387
         (824 letters)

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

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



>pdb|4G6V|B Chain B, Cdia-CtCDII TOXIN AND IMMUNITY COMPLEX FROM BURKHOLDERIA
           PSEUDOMALLEI
 pdb|4G6V|D Chain D, Cdia-CtCDII TOXIN AND IMMUNITY COMPLEX FROM BURKHOLDERIA
           PSEUDOMALLEI
 pdb|4G6V|F Chain F, Cdia-CtCDII TOXIN AND IMMUNITY COMPLEX FROM BURKHOLDERIA
           PSEUDOMALLEI
 pdb|4G6V|H Chain H, Cdia-CtCDII TOXIN AND IMMUNITY COMPLEX FROM BURKHOLDERIA
           PSEUDOMALLEI
          Length = 111

 Score = 31.6 bits (70), Expect = 2.1,   Method: Composition-based stats.
 Identities = 16/57 (28%), Positives = 33/57 (57%), Gaps = 1/57 (1%)

Query: 242 LSEIMDKNYEMKKIILHEYLMTKRYLIV-IDDVWSIDMWDVIQEILPDNQNGSRVLI 297
           +S + D ++ +K+I     L+ + + +V ++D  S D+  ++ +IL D  NG  +LI
Sbjct: 37  ISPVRDADFSLKEIAAEHGLVAESFFLVSLNDKNSADLIPIVSKILVDGFNGGAILI 93


>pdb|3PLT|A Chain A, Crystal Structure Of Lsp1 From Saccharomyces Cerevisiae
 pdb|3PLT|B Chain B, Crystal Structure Of Lsp1 From Saccharomyces Cerevisiae
 pdb|3PLT|C Chain C, Crystal Structure Of Lsp1 From Saccharomyces Cerevisiae
          Length = 234

 Score = 30.8 bits (68), Expect = 3.0,   Method: Composition-based stats.
 Identities = 17/70 (24%), Positives = 34/70 (48%)

Query: 66  HDPDLATVMDEINWFTYESEKVIDTFINSITQQKTQSSCSKDIFDALQGLQSRITDIKQR 125
           +D D++ V D++    YE  ++ D FI+   Q +      ++I  ++Q  + R   I   
Sbjct: 60  NDDDVSDVTDKLGVLIYELGELQDQFIDKYDQYRVTLKSIRNIEASVQPSRDRKEKITDE 119

Query: 126 MQQLKHMDSK 135
           +  LK+ D +
Sbjct: 120 IAHLKYKDPQ 129


>pdb|4AJ5|1 Chain 1, Crystal Structure Of The Ska Core Complex
 pdb|4AJ5|2 Chain 2, Crystal Structure Of The Ska Core Complex
 pdb|4AJ5|3 Chain 3, Crystal Structure Of The Ska Core Complex
 pdb|4AJ5|4 Chain 4, Crystal Structure Of The Ska Core Complex
 pdb|4AJ5|U Chain U, Crystal Structure Of The Ska Core Complex
 pdb|4AJ5|V Chain V, Crystal Structure Of The Ska Core Complex
 pdb|4AJ5|W Chain W, Crystal Structure Of The Ska Core Complex
 pdb|4AJ5|X Chain X, Crystal Structure Of The Ska Core Complex
 pdb|4AJ5|Y Chain Y, Crystal Structure Of The Ska Core Complex
 pdb|4AJ5|Z Chain Z, Crystal Structure Of The Ska Core Complex
          Length = 101

 Score = 30.0 bits (66), Expect = 6.1,   Method: Compositional matrix adjust.
 Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 7/48 (14%)

Query: 9  SERLRRVLAGEEVTLPDAAKQPIQNLHAEVEIVTSWLSEFEDDISLLL 56
          + RL+R L GEE    D   + + +LH+EV+ +       +DDI++LL
Sbjct: 22 TARLQRALDGEESDFEDYPMRILYDLHSEVQTL-------KDDINILL 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
   0.321    0.138    0.426 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,875,369
Number of Sequences: 62578
Number of extensions: 896099
Number of successful extensions: 1802
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1801
Number of HSP's gapped (non-prelim): 4
length of query: 824
length of database: 14,973,337
effective HSP length: 107
effective length of query: 717
effective length of database: 8,277,491
effective search space: 5934961047
effective search space used: 5934961047
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: 56 (26.2 bits)