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= 040591
         (514 letters)

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

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



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

 Score = 34.3 bits (77), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 35/108 (32%), Positives = 48/108 (44%), Gaps = 11/108 (10%)

Query: 97  SLTETQATEFEPSCNLSSKSTVTNRLVNTQLANTLISSIFATFSSFEASYLQLQTAHVPF 156
           SL + +  E E    L SKS   N++     AN+    IFA  +  EA+    + A    
Sbjct: 362 SLRKREHLEKEVEKKLESKSGNKNKMEAKAQANSQKDEIFALINK-EAN----RDARAIA 416

Query: 157 VEENIKAADRALVSHLQRLS-DFKQFYKDV-----CKNPDFIGAEEDL 198
             +N+K   R L   L+++S D K F K        KN DF  AEE L
Sbjct: 417 YTQNLKGIKRELSDKLEKISKDLKDFSKSFDEFKNGKNKDFSKAEETL 464


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

 Score = 33.5 bits (75), Expect = 0.31,   Method: Compositional matrix adjust.
 Identities = 35/108 (32%), Positives = 48/108 (44%), Gaps = 11/108 (10%)

Query: 97  SLTETQATEFEPSCNLSSKSTVTNRLVNTQLANTLISSIFATFSSFEASYLQLQTAHVPF 156
           SL + +  E E    L SKS   N++     AN+    IFA  +  EA+    + A    
Sbjct: 622 SLRKREHLEKEVEKKLESKSGNKNKMEAKAQANSQKDEIFALINK-EAN----RDARAIA 676

Query: 157 VEENIKAADRALVSHLQRLS-DFKQFYKDV-----CKNPDFIGAEEDL 198
             +N+K   R L   L+++S D K F K        KN DF  AEE L
Sbjct: 677 YTQNLKGIKRELSDKLEKISKDLKDFSKSFDEFKNGKNKDFSKAEETL 724


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

 Score = 33.5 bits (75), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 35/108 (32%), Positives = 48/108 (44%), Gaps = 11/108 (10%)

Query: 97  SLTETQATEFEPSCNLSSKSTVTNRLVNTQLANTLISSIFATFSSFEASYLQLQTAHVPF 156
           SL + +  E E    L SKS   N++     AN+    IFA  +  EA+      A+   
Sbjct: 622 SLRKREHLEKEVEKKLESKSGNKNKMEAKAQANSQKDEIFALINK-EANRDARAIAYT-- 678

Query: 157 VEENIKAADRALVSHLQRLS-DFKQFYKDV-----CKNPDFIGAEEDL 198
             +N+K   R L   L+++S D K F K        KN DF  AEE L
Sbjct: 679 --QNLKGIKRELSDKLEKISKDLKDFSKSFDEFKNGKNKDFSKAEETL 724


  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
   0.321    0.135    0.391 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,614,874
Number of Sequences: 62578
Number of extensions: 449915
Number of successful extensions: 945
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 945
Number of HSP's gapped (non-prelim): 5
length of query: 514
length of database: 14,973,337
effective HSP length: 103
effective length of query: 411
effective length of database: 8,527,803
effective search space: 3504927033
effective search space used: 3504927033
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: 54 (25.4 bits)