BLASTP 2.2.1 [Apr-13-2001]


Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, 
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.

Query= gi|15645165|ref|NP_207335.1| cag pathogenicity island
protein (cag18) [Helicobacter pylori 26695]
         (237 letters)

Database: /var/www/html/HP/blast_new/blast/db/pdbaa
           13,198 sequences; 2,899,336 total letters

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

pdb|1MHC|A  Chain A, Model Of Mhc Class I H2-M3 With Nonapep...    25  7.9

>pdb|1MHC|A Chain A, Model Of Mhc Class I H2-M3 With Nonapeptide From Rat Nd1
           Refined At 2.3 Angstroms Resolution
 pdb|1MHC|D Chain D, Model Of Mhc Class I H2-M3 With Nonapeptide From Rat Nd1
           Refined At 2.3 Angstroms Resolution
          Length = 282

 Score = 25.0 bits (53), Expect = 7.9
 Identities = 12/31 (38%), Positives = 18/31 (57%)

Query: 140 EGKLKIEQEKQNIRERLETSLKAYQSNIGGT 170
           E KLK++   Q+ R  L T L+ Y  + GG+
Sbjct: 62  ELKLKVKNIAQSARANLRTLLRYYNQSEGGS 92



  Database: /var/www/html/HP/blast_new/blast/db/pdbaa
    Posted date:  Dec 20, 2002 11:08 AM
  Number of letters in database: 2,899,336
  Number of sequences in database:  13,198
  
Lambda     K      H
   0.313    0.130    0.334 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,082,710
Number of Sequences: 13198
Number of extensions: 39382
Number of successful extensions: 76
Number of sequences better than 10.0: 1
Number of HSP's better than 10.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 75
Number of HSP's gapped (non-prelim): 1
length of query: 237
length of database: 2,899,336
effective HSP length: 85
effective length of query: 152
effective length of database: 1,777,506
effective search space: 270180912
effective search space used: 270180912
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (25.0 bits)