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= 016918
         (380 letters)

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

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



>pdb|4GAG|H Chain H, Structure Of The Broadly Neutralizing Antibody Ap33 In
           Complex With Its Hcv Epitope (E2 Residues 412-423)
 pdb|4GAJ|H Chain H, Structure Of The Broadly Neutralizing Antibody Ap33 In
           Complex With Its Hcv Epitope (E2 Residues 411-424)
 pdb|4GAY|H Chain H, Structure Of The Broadly Neutralizing Antibody Ap33
 pdb|4GAY|A Chain A, Structure Of The Broadly Neutralizing Antibody Ap33
          Length = 218

 Score = 30.0 bits (66), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 15/54 (27%), Positives = 22/54 (40%)

Query: 189 SICKSKWDKCPSFPAGEYEYIDVIVKGETLLVDIDFRSEFEIARSTGAYKAILQ 242
           SI    W+    FP  + EY+  I    +   ++  RS   I R T   +  LQ
Sbjct: 28  SITSGYWNWIRKFPGNKLEYMGYISYSGSTYYNLSLRSRISITRDTSKNQYYLQ 81


>pdb|4G6A|C Chain C, Structure Of The Hepatitis C Virus Envelope Glycoprotein
           E2 Antigenic Region 412-423 Bound To The Broadly
           Neutralizing Antibody Ap33
 pdb|4G6A|H Chain H, Structure Of The Hepatitis C Virus Envelope Glycoprotein
           E2 Antigenic Region 412-423 Bound To The Broadly
           Neutralizing Antibody Ap33
          Length = 224

 Score = 30.0 bits (66), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 15/54 (27%), Positives = 22/54 (40%)

Query: 189 SICKSKWDKCPSFPAGEYEYIDVIVKGETLLVDIDFRSEFEIARSTGAYKAILQ 242
           SI    W+    FP  + EY+  I    +   ++  RS   I R T   +  LQ
Sbjct: 29  SITSGYWNWIRKFPGNKLEYMGYISYSGSTYYNLSLRSRISITRDTSKNQYYLQ 82


  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
   0.315    0.132    0.382 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,052,313
Number of Sequences: 62578
Number of extensions: 377308
Number of successful extensions: 775
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 773
Number of HSP's gapped (non-prelim): 3
length of query: 380
length of database: 14,973,337
effective HSP length: 101
effective length of query: 279
effective length of database: 8,652,959
effective search space: 2414175561
effective search space used: 2414175561
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)