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|15645952|ref|NP_208131.1| biopolymer transport
protein (exbB) [Helicobacter pylori 26695]
         (166 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|1KFU|L  Chain L, Crystal Structure Of Human M-Calpain Fo...    30  0.19
pdb|1DF0|A  Chain A, Crystal Structure Of M-Calpain                28  0.41

>pdb|1KFU|L Chain L, Crystal Structure Of Human M-Calpain Form Ii
 pdb|1KFX|L Chain L, Crystal Structure Of Human M-Calpain Form I
          Length = 699

 Score = 29.6 bits (65), Expect = 0.19
 Identities = 23/75 (30%), Positives = 35/75 (46%), Gaps = 10/75 (13%)

Query: 1   MSVSHVALILRKLFYHRQGVFMGGFSVGMLK---DYVDIFVFAVLGVASFLALWFAIERV 57
           +S   +  ILR++   RQ +   GFS+   K   D +D      LG+  F  LW  I++ 
Sbjct: 547 ISAFELQTILRRVLAKRQDIKSDGFSIETCKIMVDMLDSDGSGKLGLKEFYILWTKIQK- 605

Query: 58  IFYSKVDLKAYDDID 72
             Y K+    Y +ID
Sbjct: 606 --YQKI----YREID 614



>pdb|1DF0|A Chain A, Crystal Structure Of M-Calpain
          Length = 700

 Score = 28.5 bits (62), Expect = 0.41
 Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 10/75 (13%)

Query: 1   MSVSHVALILRKLFYHRQGVFMGGFSVGMLKDYVDIF---VFAVLGVASFLALWFAIERV 57
           +S   +  ILR++   R+ +   GFS+   K  VD+        LG+  F  LW  I++ 
Sbjct: 548 ISAFELQTILRRVLAKREDIKSDGFSIETCKIMVDMLDEDGSGKLGLKEFYILWTKIQK- 606

Query: 58  IFYSKVDLKAYDDID 72
             Y K+    Y +ID
Sbjct: 607 --YQKI----YREID 615



  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
   0.330    0.145    0.410 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 825,757
Number of Sequences: 13198
Number of extensions: 30828
Number of successful extensions: 85
Number of sequences better than 10.0: 2
Number of HSP's better than 10.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 85
Number of HSP's gapped (non-prelim): 2
length of query: 166
length of database: 2,899,336
effective HSP length: 81
effective length of query: 85
effective length of database: 1,830,298
effective search space: 155575330
effective search space used: 155575330
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: 51 (24.3 bits)