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= 048596
         (96 letters)

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

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



>pdb|4G0H|A Chain A, Crystal Structure Of The N-Terminal Domain Of Helicobacter
           Pylori Caga Protein
          Length = 916

 Score = 27.7 bits (60), Expect = 1.8,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 5   QRSEVSFRRQGSSGLVWQDAFISGDLNQMRREQMKKATNSRELRHSQSD 53
           +R E   +  G +G  W D F+S   N+ +   +K+A N   + H Q D
Sbjct: 197 ERQEAE-KNGGPTGGDWLDIFLSFIFNKKQSSDVKEAINQEPVPHVQPD 244


>pdb|4DVY|P Chain P, Crystal Structure Of The Helicobacter Pylori Caga
           Oncoprotein
          Length = 876

 Score = 27.7 bits (60), Expect = 1.9,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 5   QRSEVSFRRQGSSGLVWQDAFISGDLNQMRREQMKKATNSRELRHSQSD 53
           +R E   +  G +G  W D F+S   N+ +   +K+A N   + H Q D
Sbjct: 197 ERQEAE-KNGGPTGGDWLDIFLSFIFNKKQSSDVKEAINQEPVPHVQPD 244


  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
   0.319    0.131    0.407 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,615,167
Number of Sequences: 62578
Number of extensions: 79365
Number of successful extensions: 255
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 253
Number of HSP's gapped (non-prelim): 2
length of query: 96
length of database: 14,973,337
effective HSP length: 62
effective length of query: 34
effective length of database: 11,093,501
effective search space: 377179034
effective search space used: 377179034
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)