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= 007385
         (605 letters)

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

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



>pdb|1DAB|A Chain A, The Structure Of Bordetella Pertussis Virulence Factor
           P.69 Pertactin
          Length = 539

 Score = 29.6 bits (65), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 23/57 (40%), Positives = 28/57 (49%), Gaps = 4/57 (7%)

Query: 131 GMFISLYSVALEKSQMVLRDRVKKAVPATWEPAAL----ASFIETYGTHIIVGVRMG 183
           G   SL    L  S++VLRD    AVPA+  PAA+    AS +   G HI  G   G
Sbjct: 152 GALQSLQPEDLPPSRVVLRDTNVTAVPASGAPAAVSVLGASELTLDGGHITGGRAAG 208


  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
   0.318    0.136    0.403 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,755,950
Number of Sequences: 62578
Number of extensions: 826402
Number of successful extensions: 1627
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1625
Number of HSP's gapped (non-prelim): 3
length of query: 605
length of database: 14,973,337
effective HSP length: 104
effective length of query: 501
effective length of database: 8,465,225
effective search space: 4241077725
effective search space used: 4241077725
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)