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|15645997|ref|NP_208178.1| DNA polymerase III epsilon
subunit (dnaQ) [Helicobacter pylori 26695]
         (350 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|1J53|A  Chain A, Structure Of The N-Terminal Exonuclease...    43  5e-05
pdb|2SLI|    Leech Intramolecular Trans-Sialidase Complexed ...    30  0.54
pdb|1GJX|A  Chain A, Solution Structure Of The Lipoyl Domain...    26  7.7
pdb|1A99|A  Chain A, Putrescine Receptor (Potf) From E. Coli...    26  7.7

>pdb|1J53|A Chain A, Structure Of The N-Terminal Exonuclease Domain Of The
           Epsilon Subunit Of E.Coli Dna Polymerase Iii At Ph 8.5
 pdb|1J54|A Chain A, Structure Of The N-Terminal Exonuclease Domain Of The
           Epsilon Subunit Of E.Coli Dna Polymerase Iii At Ph 5.8
          Length = 186

 Score = 43.1 bits (100), Expect = 5e-05
 Identities = 34/101 (33%), Positives = 48/101 (46%), Gaps = 7/101 (6%)

Query: 112 IDLETTGSCPIK-----HEILEIGAVQVKGGEII-NRFETLVKVKSVPDYIA-ELTGITY 164
           +D ETTG   I      H+I+EIGAV+V    +  N F   +K   + D  A  + GI  
Sbjct: 11  LDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIAD 70

Query: 165 EDTLNAPSAHEALQELRLFLGNSVFVAHNANFDYNFLGRYF 205
           E  L+ P+  E   E   ++  +  V HNA FD  F+   F
Sbjct: 71  EFLLDKPTFAEVADEFMDYIRGAELVIHNAAFDIGFMDYEF 111



>pdb|2SLI|   Leech Intramolecular Trans-Sialidase Complexed With
           2,7-Anhydro-Neu5ac, The Reaction Product
 pdb|3SLI|   Leech Intramolecular Trans-Sialidase Complexed With
           2,7-Anhydro-Neu5ac Prepared By Soaking With
           3'-Sialyllactose
 pdb|4SLI|   Leech Intramolecular Trans-Sialidase Complexed With
           2-Propenyl-Neu5ac, An Inactive Substrate Analogue
 pdb|1SLI|   Leech Intramolecular Trans-Sialidase Complexed With Dana
 pdb|1SLL|   Sialidase L From Leech Macrobdella Decora
          Length = 679

 Score = 29.6 bits (65), Expect = 0.54
 Identities = 22/85 (25%), Positives = 35/85 (40%), Gaps = 6/85 (7%)

Query: 154 DYIAELTGITYEDTLNAPSAHEALQELRLFLGNSVFVAHNANFDYNFLGRYFVEKLHCPL 213
           DY     G+ Y D  N P+      E  L+  ++        +DYNF G   +E      
Sbjct: 351 DYTIREKGVIYNDATNQPTEFRVDGEYNLYQHDTNLTC--KQYDYNFSGNNLIESKTDVD 408

Query: 214 LNLKLCTLDLSKRAI----LSMRYS 234
           +N+ +   +   +A     L+MRYS
Sbjct: 409 VNMNIFYKNSVFKAFPTNYLAMRYS 433



>pdb|1GJX|A Chain A, Solution Structure Of The Lipoyl Domain Of The Chimeric
           Dihydrolipoyl Dehydrogenase P64k From Neisseria
           Meningitidis
          Length = 81

 Score = 25.8 bits (55), Expect = 7.7
 Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 3/45 (6%)

Query: 124 HEILEIGAVQVKGGEIINRFETLVKV---KSVPDYIAELTGITYE 165
           HE ++I AV+V  G+ I   +TL+ +   K+  D  AE+ G+  E
Sbjct: 13  HENVDIIAVEVNVGDTIAVDDTLITLETDKATMDVPAEVAGVVKE 57



>pdb|1A99|A Chain A, Putrescine Receptor (Potf) From E. Coli
 pdb|1A99|B Chain B, Putrescine Receptor (Potf) From E. Coli
 pdb|1A99|C Chain C, Putrescine Receptor (Potf) From E. Coli
 pdb|1A99|D Chain D, Putrescine Receptor (Potf) From E. Coli
          Length = 344

 Score = 25.8 bits (55), Expect = 7.7
 Identities = 9/19 (47%), Positives = 15/19 (78%)

Query: 76  NLEYLKACGLNFIETSENL 94
           NLE LK+CG++F++  E +
Sbjct: 142 NLEKLKSCGVSFLDAPEEV 160



  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    0.140    0.413 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,895,225
Number of Sequences: 13198
Number of extensions: 75692
Number of successful extensions: 162
Number of sequences better than 10.0: 4
Number of HSP's better than 10.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 159
Number of HSP's gapped (non-prelim): 4
length of query: 350
length of database: 2,899,336
effective HSP length: 89
effective length of query: 261
effective length of database: 1,724,714
effective search space: 450150354
effective search space used: 450150354
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: 55 (25.8 bits)