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= 030500
         (176 letters)

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

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



>pdb|3MNV|A Chain A, Crystal Structure Of The Non-Neutralizing Hiv Antibody
           13h11 Fab Fragment
 pdb|3MNV|C Chain C, Crystal Structure Of The Non-Neutralizing Hiv Antibody
           13h11 Fab Fragment
 pdb|3MNW|A Chain A, Crystal Structure Of The Non-Neutralizing Hiv Antibody
           13h11 Fab Fragment With A Gp41 Mper-Derived Peptide In A
           Helical Conformation
 pdb|3MNZ|A Chain A, Crystal Structure Of The Non-Neutralizing Hiv Antibody
           13h11 Fab Fragment With A Gp41 Mper-Derived Peptide
           Bearing Ala Substitutions In A Helical Conformation
 pdb|3MO1|A Chain A, Crystal Structure Of The Non-Neutralizing Hiv Antibody
           13h11 Fab Fragment
          Length = 224

 Score = 29.6 bits (65), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 3/32 (9%)

Query: 94  AENISD---LTHYAPPWNYNRGRKKPVSREVA 122
           AE+++D   L HY  PW +  G K  + R VA
Sbjct: 88  AEDLADYFCLQHYNTPWTFGGGTKLEIKRTVA 119


>pdb|1NCA|L Chain L, Refined Crystal Structure Of The Influenza Virus N9
           Neuraminidase-Nc41 Fab Complex
 pdb|1NCB|L Chain L, Crystal Structures Of Two Mutant Neuraminidase-Antibody
           Complexes With Amino Acid Substitutions In The Interface
 pdb|1NCC|L Chain L, Crystal Structures Of Two Mutant Neuraminidase-Antibody
           Complexes With Amino Acid Substitutions In The Interface
 pdb|1NCD|L Chain L, Refined Crystal Structure Of The Influenza Virus N9
           Neuraminidase-Nc41 Fab Complex
          Length = 214

 Score = 26.9 bits (58), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 9/21 (42%), Positives = 12/21 (57%)

Query: 102 HYAPPWNYNRGRKKPVSREVA 122
           HY+PPW +  G K  + R  A
Sbjct: 91  HYSPPWTFGGGTKLEIKRADA 111


  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
   0.317    0.131    0.378 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,308,543
Number of Sequences: 62578
Number of extensions: 154810
Number of successful extensions: 378
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 377
Number of HSP's gapped (non-prelim): 5
length of query: 176
length of database: 14,973,337
effective HSP length: 92
effective length of query: 84
effective length of database: 9,216,161
effective search space: 774157524
effective search space used: 774157524
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)