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= 048665
         (336 letters)

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

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



>pdb|2FM8|A Chain A, Crystal Structure Of The Salmonella Secretion Chaperone
           Invb In Complex With Sipa
 pdb|2FM8|B Chain B, Crystal Structure Of The Salmonella Secretion Chaperone
           Invb In Complex With Sipa
          Length = 135

 Score = 30.0 bits (66), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 21/53 (39%), Positives = 28/53 (52%), Gaps = 10/53 (18%)

Query: 80  ADRIGMNILEGVNFASGGS-------GILNTTGLVYNNFMSLGEQINLFATVL 125
           A  I M I+EG +FA GG        G L    LV+ +F+S GE+   F+T L
Sbjct: 70  AYEILMTIMEGCHFARGGQLLLGEQNGELTLKALVHPDFLSDGEK---FSTAL 119


  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    0.136    0.411 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,414,013
Number of Sequences: 62578
Number of extensions: 379171
Number of successful extensions: 623
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 623
Number of HSP's gapped (non-prelim): 2
length of query: 336
length of database: 14,973,337
effective HSP length: 99
effective length of query: 237
effective length of database: 8,778,115
effective search space: 2080413255
effective search space used: 2080413255
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: 52 (24.6 bits)