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|15644906|ref|NP_207076.1| guanosine pentaphosphate
phosphohydrolase (gppA) [Helicobacter pylori 26695]
         (484 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|1JCF|A  Chain A, Mreb From Thermotoga Maritima, Trigonal...    29  1.3
pdb|1JCE|A  Chain A, Mreb From Thermotoga Maritima                 28  2.3
pdb|1JR3|A  Chain A, Crystal Structure Of The Processivity C...    26  8.7
pdb|1DQL|H  Chain H, Crystal Structure Of An Unliganded (Nat...    26  8.7

>pdb|1JCF|A Chain A, Mreb From Thermotoga Maritima, Trigonal
 pdb|1JCG|A Chain A, Mreb From Thermotoga Maritima, Amppnp
          Length = 344

 Score = 28.9 bits (63), Expect = 1.3
 Identities = 12/28 (42%), Positives = 18/28 (63%)

Query: 125 NLLHKNSGITIDIGGGSTECALIEKGKI 152
           N+   +  + +DIGGG+TE A+I  G I
Sbjct: 142 NVEEPSGNMVVDIGGGTTEVAVISLGSI 169



>pdb|1JCE|A Chain A, Mreb From Thermotoga Maritima
          Length = 344

 Score = 28.1 bits (61), Expect = 2.3
 Identities = 12/28 (42%), Positives = 17/28 (59%)

Query: 125 NLLHKNSGITIDIGGGSTECALIEKGKI 152
           N+   +    +DIGGG+TE A+I  G I
Sbjct: 142 NVEEPSGNXVVDIGGGTTEVAVISLGSI 169



>pdb|1JR3|A Chain A, Crystal Structure Of The Processivity Clamp Loader Gamma
           Complex Of E. Coli Dna Polymerase Iii
 pdb|1JR3|C Chain C, Crystal Structure Of The Processivity Clamp Loader Gamma
           Complex Of E. Coli Dna Polymerase Iii
 pdb|1JR3|B Chain B, Crystal Structure Of The Processivity Clamp Loader Gamma
           Complex Of E. Coli Dna Polymerase Iii
          Length = 373

 Score = 26.2 bits (56), Expect = 8.7
 Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 4/48 (8%)

Query: 119 GGIACANLLHKN----SGITIDIGGGSTECALIEKGKIKDLISLDVGT 162
           G  + A LL K     +GIT    G    C  IE+G+  DLI +D  +
Sbjct: 50  GKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAAS 97



>pdb|1DQL|H Chain H, Crystal Structure Of An Unliganded (Native) Fv From A
           Human Igm Anti-Peptide Antibody
          Length = 123

 Score = 26.2 bits (56), Expect = 8.7
 Identities = 16/46 (34%), Positives = 24/46 (51%), Gaps = 4/46 (8%)

Query: 425 LQWLSFILSLAENLCLTDSHHLKYTLEKNKLVIHSNDTLYLAKEML 470
           L+W++ I S   N   TDS   ++T+ +N     S +TLYL    L
Sbjct: 45  LEWVAVISSDGGNKYYTDSVKGRFTISRN----DSKNTLYLQMNSL 86



  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
   0.323    0.139    0.394 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,505,658
Number of Sequences: 13198
Number of extensions: 99224
Number of successful extensions: 212
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: 210
Number of HSP's gapped (non-prelim): 4
length of query: 484
length of database: 2,899,336
effective HSP length: 92
effective length of query: 392
effective length of database: 1,685,120
effective search space: 660567040
effective search space used: 660567040
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (26.2 bits)