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|15646156|ref|NP_208340.1| protein-export membrane
protein (secF) [Helicobacter pylori 26695]
         (323 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|1PBV|    Sec7 Domain Of The Exchange Factor Arno               27  4.1
pdb|1E79|G  Chain G, Bovine F1-Atpase Inhibited By Dccd (Dic...    26  5.4

>pdb|1PBV|   Sec7 Domain Of The Exchange Factor Arno
          Length = 195

 Score = 26.6 bits (57), Expect = 4.1
 Identities = 22/69 (31%), Positives = 31/69 (44%), Gaps = 6/69 (8%)

Query: 42  GIDFAGGSLVQVRYTQNAPIKEVRDLFEKEARFKGVQVSEFGSKEE--ILIKFPFVETAE 99
           GI F    LV+    QN P +  R L++ E   K       G +EE  + +   FV+  E
Sbjct: 28  GIQF----LVENELLQNTPEEIARFLYKGEGLNKTAIGDYLGEREELNLAVLHAFVDLHE 83

Query: 100 NEDLNAIVA 108
             DLN + A
Sbjct: 84  FTDLNLVQA 92



>pdb|1E79|G Chain G, Bovine F1-Atpase Inhibited By Dccd
           (Dicyclohexylcarbodiimide)
 pdb|1H8E|G Chain G, (Adp.Alf4)2(Adp.So4) Bovine F1-Atpase (All Three Catalytic
           Sites Occupied)
 pdb|1E1R|G Chain G, Bovine Mitochondrial F1-Atpase Inhibited By Mg2+adp And
           Aluminium Fluoride
 pdb|1E1Q|G Chain G, Bovine Mitochondrial F1-Atpase At 100k
 pdb|1BMF|G Chain G, Bovine Mitochondrial F1-Atpase
 pdb|1H8H|G Chain G, Bovine Mitochondrial F1-Atpase Crystallised In The
           Presence Of 5mm Amppnp
 pdb|1NBM|G Chain G, The Structure Of Bovine F1-Atpase Covalently Inhibited
           With 4-Chloro-7-Nitrobenzofurazan
 pdb|1EFR|G Chain G, Bovine Mitochondrial F1-Atpase Complexed With The Peptide
           Antibiotic Efrapeptin
 pdb|1COW|G Chain G, Bovine Mitochondrial F1-Atpase Complexed With Aurovertin B
 pdb|1QO1|G Chain G, Molecular Architecture Of The Rotary Motor In Atp Synthase
           From Yeast Mitochondria
          Length = 272

 Score = 26.2 bits (56), Expect = 5.4
 Identities = 21/87 (24%), Positives = 43/87 (49%), Gaps = 7/87 (8%)

Query: 171 DVILVASSVIVFKIDMNLEVIA-----ALLTLIGYSINDTIIIFDRIREEMLSQKTKNAT 225
           D I  A S+ ++  D++ +V+      +L  +I YS+ ++       R   +   +KNA+
Sbjct: 182 DTISSAESMSIYD-DIDADVLRNYQEYSLANIIYYSLKESTTSEQSARMTAMDNASKNAS 240

Query: 226 QAIDEAISSTLTRTLLTSLTVFFVVLI 252
           + ID+ ++ T  RT    +T   + +I
Sbjct: 241 EMIDK-LTLTFNRTRQAVITKELIEII 266



  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    0.142    0.385 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,538,921
Number of Sequences: 13198
Number of extensions: 57191
Number of successful extensions: 186
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: 185
Number of HSP's gapped (non-prelim): 3
length of query: 323
length of database: 2,899,336
effective HSP length: 88
effective length of query: 235
effective length of database: 1,737,912
effective search space: 408409320
effective search space used: 408409320
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (25.4 bits)