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= psy16002
         (229 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 = 26.9 bits (58), Expect = 8.7,   Method: Compositional matrix adjust.
 Identities = 16/49 (32%), Positives = 29/49 (59%), Gaps = 6/49 (12%)

Query: 169 NALMNSFEKGKKKSQSRLKR----LENEI--VIMSERHATQVQHLKQRI 211
           NA +N F+ GK K  S++ +    LEN +  VI++++   +V +L Q +
Sbjct: 748 NAALNEFKNGKNKDFSKVTQAKSDLENSVKDVIINQKVTDKVDNLNQAV 796


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

 Score = 26.9 bits (58), Expect = 8.7,   Method: Compositional matrix adjust.
 Identities = 16/49 (32%), Positives = 29/49 (59%), Gaps = 6/49 (12%)

Query: 169 NALMNSFEKGKKKSQSRLKR----LENEI--VIMSERHATQVQHLKQRI 211
           NA +N F+ GK K  S++ +    LEN +  VI++++   +V +L Q +
Sbjct: 748 NAALNEFKNGKNKDFSKVTQAKSDLENSVKDVIINQKVTDKVDNLNQAV 796


>pdb|4DVZ|A Chain A, Crystal Structure Of The Helicobacter Pylori Caga
           Oncoprotein
          Length = 569

 Score = 26.9 bits (58), Expect = 9.7,   Method: Compositional matrix adjust.
 Identities = 16/49 (32%), Positives = 29/49 (59%), Gaps = 6/49 (12%)

Query: 169 NALMNSFEKGKKKSQSRLKR----LENEI--VIMSERHATQVQHLKQRI 211
           NA +N F+ GK K  S++ +    LEN +  VI++++   +V +L Q +
Sbjct: 488 NAALNEFKNGKNKDFSKVTQAKSDLENSVKDVIINQKVTDKVDNLNQAV 536


  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
   0.310    0.124    0.317 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,549,867
Number of Sequences: 62578
Number of extensions: 192665
Number of successful extensions: 548
Number of sequences better than 100.0: 40
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 36
Number of HSP's that attempted gapping in prelim test: 533
Number of HSP's gapped (non-prelim): 43
length of query: 229
length of database: 14,973,337
effective HSP length: 95
effective length of query: 134
effective length of database: 9,028,427
effective search space: 1209809218
effective search space used: 1209809218
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 50 (23.9 bits)