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= 029115
         (199 letters)

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

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



>pdb|2VK5|A Chain A, The Structure Of Clostridium Perfringens Nani Sialidase
           And Its Catalytic Intermediates
 pdb|2VK6|A Chain A, The Structure Of Clostridium Perfringens Nani Sialidase
           And Its Catalytic Intermediates
 pdb|2VK7|A Chain A, The Structure Of Clostridium Perfringens Nani Sialidase
           And Its Catalytic Intermediates
 pdb|2VK7|B Chain B, The Structure Of Clostridium Perfringens Nani Sialidase
           And Its Catalytic Intermediates
          Length = 452

 Score = 28.1 bits (61), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 11/27 (40%), Positives = 15/27 (55%)

Query: 87  INLIFSFTNGVEWDGPYRIKFLVPRAW 113
           INL++S  +G  W  P  I F V + W
Sbjct: 189 INLVYSDDDGKTWSEPQNINFQVKKDW 215


>pdb|2BF6|A Chain A, Atomic Resolution Structure Of The Bacterial Sialidase
           Nani From Clostridium Perfringens In Complex With
           Alpha-Sialic Acid (Neu5ac)
          Length = 449

 Score = 28.1 bits (61), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 11/27 (40%), Positives = 15/27 (55%)

Query: 87  INLIFSFTNGVEWDGPYRIKFLVPRAW 113
           INL++S  +G  W  P  I F V + W
Sbjct: 189 INLVYSDDDGKTWSEPQNINFQVKKDW 215


>pdb|2WWC|A Chain A, 3d-Structure Of The Modular Autolysin Lytc From
           Streptococcus Pneumoniae In Complex With Synthetic
           Peptidoglycan Ligand
          Length = 468

 Score = 26.9 bits (58), Expect = 7.7,   Method: Compositional matrix adjust.
 Identities = 9/22 (40%), Positives = 16/22 (72%), Gaps = 1/22 (4%)

Query: 82  VPKHAINLIFSFTNGVEWDGPY 103
           + KH +N + ++TN +EW+ PY
Sbjct: 420 ILKH-VNWVAAYTNALEWENPY 440


>pdb|2WW5|A Chain A, 3d-Structure Of The Modular Autolysin Lytc From
           Streptococcus Pneumoniae At 1.6 A Resolution
 pdb|2WWD|A Chain A, 3d-Structure Of The Modular Autolysin Lytc From
           Streptococcus Pneumoniae In Complex With Pneummococcal
           Peptidoglycan Fragment
          Length = 468

 Score = 26.9 bits (58), Expect = 7.7,   Method: Compositional matrix adjust.
 Identities = 9/22 (40%), Positives = 16/22 (72%), Gaps = 1/22 (4%)

Query: 82  VPKHAINLIFSFTNGVEWDGPY 103
           + KH +N + ++TN +EW+ PY
Sbjct: 420 ILKH-VNWVAAYTNALEWENPY 440


  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
   0.321    0.143    0.468 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,180,175
Number of Sequences: 62578
Number of extensions: 325233
Number of successful extensions: 464
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 456
Number of HSP's gapped (non-prelim): 12
length of query: 199
length of database: 14,973,337
effective HSP length: 94
effective length of query: 105
effective length of database: 9,091,005
effective search space: 954555525
effective search space used: 954555525
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)