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|15645042|ref|NP_207212.1| IS200 insertion sequence
from SARA17 [Helicobacter pylori 26695]
         (138 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|1D8W|D  Chain D, L-Rhamnose Isomerase >gi|10835502|pdb|1...    25  3.2
pdb|1DE5|A  Chain A, L-Rhamnose Isomerase >gi|10120982|pdb|1...    25  3.2

>pdb|1D8W|D Chain D, L-Rhamnose Isomerase
 pdb|1D8W|A Chain A, L-Rhamnose Isomerase
 pdb|1D8W|B Chain B, L-Rhamnose Isomerase
 pdb|1D8W|C Chain C, L-Rhamnose Isomerase
          Length = 426

 Score = 25.0 bits (53), Expect = 3.2
 Identities = 12/32 (37%), Positives = 19/32 (58%), Gaps = 2/32 (6%)

Query: 87  VSSRLTRQHHFKSVEASLWGKHLWSPSYFAGS 118
           +S +L   HH  +VE+ L+G  + + SY  GS
Sbjct: 219 ISEKLNPAHHIDAVESKLFG--IGAESYTVGS 248



>pdb|1DE5|A Chain A, L-Rhamnose Isomerase
 pdb|1DE6|A Chain A, L-Rhamnose Isomerase
 pdb|1DE6|B Chain B, L-Rhamnose Isomerase
 pdb|1DE6|C Chain C, L-Rhamnose Isomerase
 pdb|1DE6|D Chain D, L-Rhamnose Isomerase
 pdb|1DE5|B Chain B, L-Rhamnose Isomerase
 pdb|1DE5|C Chain C, L-Rhamnose Isomerase
 pdb|1DE5|D Chain D, L-Rhamnose Isomerase
          Length = 426

 Score = 25.0 bits (53), Expect = 3.2
 Identities = 12/32 (37%), Positives = 19/32 (58%), Gaps = 2/32 (6%)

Query: 87  VSSRLTRQHHFKSVEASLWGKHLWSPSYFAGS 118
           +S +L   HH  +VE+ L+G  + + SY  GS
Sbjct: 219 ISEKLNPAHHIDAVESKLFG--IGAESYTVGS 248



  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
   0.324    0.137    0.427 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 794,405
Number of Sequences: 13198
Number of extensions: 26851
Number of successful extensions: 35
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: 35
Number of HSP's gapped (non-prelim): 2
length of query: 138
length of database: 2,899,336
effective HSP length: 79
effective length of query: 59
effective length of database: 1,856,694
effective search space: 109544946
effective search space used: 109544946
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)