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= 020960
         (319 letters)

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

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



>pdb|3RGF|B Chain B, Crystal Structure Of Human Cdk8CYCC
          Length = 285

 Score = 28.5 bits (62), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 12/28 (42%), Positives = 19/28 (67%)

Query: 79  EPIFLRERLLGTATIALKEFLAKYSKNS 106
           E + LR++++ TAT+  K F A+YS  S
Sbjct: 55  EHLKLRQQVIATATVYFKRFYARYSLKS 82


>pdb|4DGV|H Chain H, Structure Of The Hepatitis C Virus Envelope Glycoprotein
          E2 Antigenic Region 412-423 Bound To The Broadly
          Neutralizing Antibody Hcv1, P2(1) Form
 pdb|4DGY|H Chain H, Structure Of The Hepatitis C Virus Envelope Glycoprotein
          E2 Antigenic Region 412-423 Bound To The Broadly
          Neutralizing Antibody Hcv1, C2 Form
          Length = 226

 Score = 28.1 bits (61), Expect = 6.4,   Method: Compositional matrix adjust.
 Identities = 10/15 (66%), Positives = 11/15 (73%)

Query: 25 LQWFAVGWIDPNNKY 39
          L+W AV W D NNKY
Sbjct: 45 LEWLAVIWFDENNKY 59


  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
   0.314    0.133    0.405 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,545,931
Number of Sequences: 62578
Number of extensions: 380726
Number of successful extensions: 431
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 429
Number of HSP's gapped (non-prelim): 2
length of query: 319
length of database: 14,973,337
effective HSP length: 99
effective length of query: 220
effective length of database: 8,778,115
effective search space: 1931185300
effective search space used: 1931185300
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 bits)