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|15645123|ref|NP_207293.1| conserved hypothetical
protein [Helicobacter pylori 26695]
         (133 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|1LO7|A  Chain A, X-Ray Structure Of 4-Hydroxybenzoyl Coa...    42  3e-05
pdb|1LO9|A  Chain A, X-Ray Crystal Structure Of 4-Hydroxyben...    40  1e-04
pdb|1NLD|H  Chain H, Fab Fragment Of A Neutralizing Antibody...    24  5.1

>pdb|1LO7|A Chain A, X-Ray Structure Of 4-Hydroxybenzoyl Coa Thioesterase
          Complexed With 4-Hydroxyphenacyl Coa
 pdb|1LO8|A Chain A, X-Ray Crystal Structure Of 4-Hydroxybenzoyl Coa
          Thioesterase Complexed With 4-Hydroxybenzyl Coa
 pdb|1BVQ|A Chain A, Three-Dimensional Structure Of 4-Hydroxybenzoyl Coa
          Thioesterase From Pseudomonas Sp. Strain Cbs-3
          Length = 141

 Score = 41.6 bits (96), Expect = 3e-05
 Identities = 28/83 (33%), Positives = 41/83 (48%), Gaps = 6/83 (7%)

Query: 1  MRCRVYYEDTDSEGVVYHANYLKYCERARSEFFFKQNVLPEN----EEGVF--VIRSIKA 54
          M+ R+ + D D  G+V++ NY ++ + A   +F K  + P      E G+    I S  A
Sbjct: 7  MQQRIEFGDCDPAGIVWYPNYHRWLDAASRNYFIKCGLPPWRQTVVERGIVGTPIVSCNA 66

Query: 55 DFFTPASLGQVLEIRTQIKELRK 77
           F   AS   VL I T IKE R+
Sbjct: 67 SFVCTASYDDVLTIETCIKEWRR 89



>pdb|1LO9|A Chain A, X-Ray Crystal Structure Of 4-Hydroxybenzoyl Coa
          Thioesterase Mutant D17n Complexed With
          4-Hydroxybenzoyl Coa
          Length = 141

 Score = 39.7 bits (91), Expect = 1e-04
 Identities = 27/83 (32%), Positives = 41/83 (48%), Gaps = 6/83 (7%)

Query: 1  MRCRVYYEDTDSEGVVYHANYLKYCERARSEFFFKQNVLPEN----EEGVF--VIRSIKA 54
          M+ R+ + D +  G+V++ NY ++ + A   +F K  + P      E G+    I S  A
Sbjct: 7  MQQRIEFGDCNPAGIVWYPNYHRWLDAASRNYFIKCGLPPWRQTVVERGIVGTPIVSCNA 66

Query: 55 DFFTPASLGQVLEIRTQIKELRK 77
           F   AS   VL I T IKE R+
Sbjct: 67 SFVCTASYDDVLTIETCIKEWRR 89



>pdb|1NLD|H Chain H, Fab Fragment Of A Neutralizing Antibody Directed Against
           An Epitope Of Gp41 From Hiv-1
          Length = 215

 Score = 24.3 bits (51), Expect = 5.1
 Identities = 9/32 (28%), Positives = 17/32 (53%)

Query: 26  ERARSEFFFKQNVLPENEEGVFVIRSIKADFF 57
           + ++S+ FFK N L  N+  ++       DF+
Sbjct: 72  DNSKSQVFFKMNSLQPNDRAIYYCARRGGDFW 103



  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
   0.326    0.141    0.409 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 701,096
Number of Sequences: 13198
Number of extensions: 24507
Number of successful extensions: 32
Number of sequences better than 10.0: 3
Number of HSP's better than 10.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 29
Number of HSP's gapped (non-prelim): 3
length of query: 133
length of database: 2,899,336
effective HSP length: 78
effective length of query: 55
effective length of database: 1,869,892
effective search space: 102844060
effective search space used: 102844060
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 bits)