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|15646198|ref|NP_207478.1| flagellar biosynthesis
protein [Helicobacter pylori 26695]
         (105 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|1KF6|D  Chain D, E. Coli Quinol-Fumarate Reductase With ...    23  3.7
pdb|1K8W|A  Chain A, Crystal Structure Of The E. Coli Pseudo...    22  8.3

>pdb|1KF6|D Chain D, E. Coli Quinol-Fumarate Reductase With Bound Inhibitor
          Hqno
 pdb|1KF6|P Chain P, E. Coli Quinol-Fumarate Reductase With Bound Inhibitor
          Hqno
 pdb|1L0V|D Chain D, Quinol-Fumarate Reductase With Menaquinol Molecules
 pdb|1L0V|P Chain P, Quinol-Fumarate Reductase With Menaquinol Molecules
 pdb|1KFY|D Chain D, Quinol-Fumarate Reductase With Quinol Inhibitor 2-[1-(4-
          Chloro-Phenyl)-Ethyl]-4,6-Dinitro-Phenol
 pdb|1KFY|P Chain P, Quinol-Fumarate Reductase With Quinol Inhibitor 2-[1-(4-
          Chloro-Phenyl)-Ethyl]-4,6-Dinitro-Phenol
          Length = 119

 Score = 23.5 bits (49), Expect = 3.7
 Identities = 10/32 (31%), Positives = 18/32 (56%)

Query: 2  RFFIFLILICPLICPLMSADSALPSVNLSLNA 33
          R F+FL+++ PL C L     A+  + + + A
Sbjct: 65 RVFLFLMIVLPLWCGLHRMHHAMHDLKIHVPA 96



>pdb|1K8W|A Chain A, Crystal Structure Of The E. Coli Pseudouridine Synthase
           Trub Bound To A T Stem-Loop Rna
          Length = 327

 Score = 22.3 bits (46), Expect = 8.3
 Identities = 11/25 (44%), Positives = 15/25 (60%)

Query: 9   LICPLICPLMSADSALPSVNLSLNA 33
           L+ PL+ P+ S  S  P VNL L +
Sbjct: 249 LLDPLLMPMDSPASDYPVVNLPLTS 273



  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
   0.332    0.144    0.426 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 486,168
Number of Sequences: 13198
Number of extensions: 13710
Number of successful extensions: 49
Number of sequences better than 10.0: 2
Number of HSP's better than 10.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 47
Number of HSP's gapped (non-prelim): 2
length of query: 105
length of database: 2,899,336
effective HSP length: 81
effective length of query: 24
effective length of database: 1,830,298
effective search space: 43927152
effective search space used: 43927152
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 bits)
S2: 46 (22.3 bits)