BLASTP 2.2.26 [Sep-21-2011]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
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.


Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= 040761
         (215 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|2HI2|A Chain A, Crystal Structure Of Native Neisseria Gonorrhoeae Type Iv
           Pilin At 2.3 Angstroms Resolution
 pdb|2HIL|A Chain A, Structure Of The Neisseria Gonorrhoeae Type Iv Pilus
           Filament From X- Ray Crystallography And Electron
           Cryomicroscopy
 pdb|2HIL|B Chain B, Structure Of The Neisseria Gonorrhoeae Type Iv Pilus
           Filament From X- Ray Crystallography And Electron
           Cryomicroscopy
 pdb|2HIL|C Chain C, Structure Of The Neisseria Gonorrhoeae Type Iv Pilus
           Filament From X- Ray Crystallography And Electron
           Cryomicroscopy
 pdb|2HIL|D Chain D, Structure Of The Neisseria Gonorrhoeae Type Iv Pilus
           Filament From X- Ray Crystallography And Electron
           Cryomicroscopy
 pdb|2HIL|E Chain E, Structure Of The Neisseria Gonorrhoeae Type Iv Pilus
           Filament From X- Ray Crystallography And Electron
           Cryomicroscopy
 pdb|2HIL|F Chain F, Structure Of The Neisseria Gonorrhoeae Type Iv Pilus
           Filament From X- Ray Crystallography And Electron
           Cryomicroscopy
 pdb|2HIL|G Chain G, Structure Of The Neisseria Gonorrhoeae Type Iv Pilus
           Filament From X- Ray Crystallography And Electron
           Cryomicroscopy
 pdb|2HIL|H Chain H, Structure Of The Neisseria Gonorrhoeae Type Iv Pilus
           Filament From X- Ray Crystallography And Electron
           Cryomicroscopy
 pdb|2HIL|I Chain I, Structure Of The Neisseria Gonorrhoeae Type Iv Pilus
           Filament From X- Ray Crystallography And Electron
           Cryomicroscopy
 pdb|2HIL|J Chain J, Structure Of The Neisseria Gonorrhoeae Type Iv Pilus
           Filament From X- Ray Crystallography And Electron
           Cryomicroscopy
 pdb|2HIL|K Chain K, Structure Of The Neisseria Gonorrhoeae Type Iv Pilus
           Filament From X- Ray Crystallography And Electron
           Cryomicroscopy
 pdb|2HIL|L Chain L, Structure Of The Neisseria Gonorrhoeae Type Iv Pilus
           Filament From X- Ray Crystallography And Electron
           Cryomicroscopy
 pdb|2HIL|M Chain M, Structure Of The Neisseria Gonorrhoeae Type Iv Pilus
           Filament From X- Ray Crystallography And Electron
           Cryomicroscopy
 pdb|2HIL|N Chain N, Structure Of The Neisseria Gonorrhoeae Type Iv Pilus
           Filament From X- Ray Crystallography And Electron
           Cryomicroscopy
 pdb|2HIL|O Chain O, Structure Of The Neisseria Gonorrhoeae Type Iv Pilus
           Filament From X- Ray Crystallography And Electron
           Cryomicroscopy
 pdb|2HIL|P Chain P, Structure Of The Neisseria Gonorrhoeae Type Iv Pilus
           Filament From X- Ray Crystallography And Electron
           Cryomicroscopy
 pdb|2HIL|Q Chain Q, Structure Of The Neisseria Gonorrhoeae Type Iv Pilus
           Filament From X- Ray Crystallography And Electron
           Cryomicroscopy
 pdb|2HIL|R Chain R, Structure Of The Neisseria Gonorrhoeae Type Iv Pilus
           Filament From X- Ray Crystallography And Electron
           Cryomicroscopy
          Length = 158

 Score = 29.3 bits (64), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 12/38 (31%), Positives = 19/38 (50%)

Query: 126 NHHQWQGNCTITGVPSFPSSYPGNYANPISPQSSLESA 163
           NH +W  N T  GV S P+   G Y   +  ++ + +A
Sbjct: 53  NHGKWPENNTSAGVASSPTDIKGKYVKEVEVKNGVVTA 90


>pdb|1AY2|A Chain A, Structure Of The Fiber-Forming Protein Pilin At 2.6
           Angstroms Resolution
          Length = 158

 Score = 28.9 bits (63), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 13/38 (34%), Positives = 19/38 (50%)

Query: 126 NHHQWQGNCTITGVPSFPSSYPGNYANPISPQSSLESA 163
           NH +W  N T  GV S PS   G Y   +  ++ + +A
Sbjct: 53  NHGKWPENNTSAGVASPPSDIKGKYVKEVEVKNGVVTA 90


>pdb|2PIL|A Chain A, Crystallographic Structure Of Phosphorylated Pilin From
           Neisseria: Phosphoserine Sites Modify Type Iv Pilus
           Surface Chemistry
          Length = 158

 Score = 27.3 bits (59), Expect = 6.1,   Method: Compositional matrix adjust.
 Identities = 12/38 (31%), Positives = 18/38 (47%)

Query: 126 NHHQWQGNCTITGVPSFPSSYPGNYANPISPQSSLESA 163
           NH +W  N T  GV   PS   G Y   +  ++ + +A
Sbjct: 53  NHGKWPENNTSAGVAXPPSDIKGKYVKEVEVKNGVVTA 90


  Database: pdbaa
    Posted date:  Mar 3, 2013 10:34 PM
  Number of letters in database: 14,973,337
  Number of sequences in database:  62,578
  
Lambda     K      H
   0.322    0.133    0.420 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,596,712
Number of Sequences: 62578
Number of extensions: 190997
Number of successful extensions: 315
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 312
Number of HSP's gapped (non-prelim): 4
length of query: 215
length of database: 14,973,337
effective HSP length: 95
effective length of query: 120
effective length of database: 9,028,427
effective search space: 1083411240
effective search space used: 1083411240
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 bits)