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= 040928
         (115 letters)

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

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



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

 Score = 25.4 bits (54), Expect = 7.5,   Method: Composition-based stats.
 Identities = 9/26 (34%), Positives = 15/26 (57%)

Query: 12  GSHWLQMYSTFLRGKTSHEDVKDSTN 37
           G  WL ++ +F+  K    DVK++ N
Sbjct: 209 GGDWLDIFLSFIFNKKQSSDVKEAIN 234


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

 Score = 25.4 bits (54), Expect = 7.5,   Method: Composition-based stats.
 Identities = 9/26 (34%), Positives = 15/26 (57%)

Query: 12  GSHWLQMYSTFLRGKTSHEDVKDSTN 37
           G  WL ++ +F+  K    DVK++ N
Sbjct: 209 GGDWLDIFLSFIFNKKQSSDVKEAIN 234


  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
   0.329    0.141    0.455 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,345,969
Number of Sequences: 62578
Number of extensions: 112818
Number of successful extensions: 220
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: 218
Number of HSP's gapped (non-prelim): 2
length of query: 115
length of database: 14,973,337
effective HSP length: 78
effective length of query: 37
effective length of database: 10,092,253
effective search space: 373413361
effective search space used: 373413361
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 45 (21.9 bits)