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= psy16990
         (250 letters)

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

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



>pdb|2IY9|A Chain A, Crystal Structure Of The A-Subunit Of The Ab5 Toxin From
           E. Coli
          Length = 347

 Score = 31.6 bits (70), Expect = 0.47,   Method: Compositional matrix adjust.
 Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 5/52 (9%)

Query: 178 RKLEKYISNQKLHPGKSKIVGAKGGENGEPLVFASTNEIWTASLHTSPSNTD 229
           R +E  +SN  L PG+ KI+   GG+ G      ++  +WT  L     N D
Sbjct: 128 RAIESIMSNVFLAPGEEKIINISGGQKG-----VASASVWTELLSRMGRNND 174


  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
   0.316    0.135    0.408 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,944,161
Number of Sequences: 62578
Number of extensions: 334209
Number of successful extensions: 645
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 644
Number of HSP's gapped (non-prelim): 5
length of query: 250
length of database: 14,973,337
effective HSP length: 96
effective length of query: 154
effective length of database: 8,965,849
effective search space: 1380740746
effective search space used: 1380740746
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)