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= 028225
         (212 letters)

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

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



>pdb|3ESU|F Chain F, Crystal Structure Of Anthrax-Neutralizing Single-Chain
           Antibody 14b7
          Length = 250

 Score = 28.1 bits (61), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 20/47 (42%), Positives = 28/47 (59%), Gaps = 4/47 (8%)

Query: 71  ASLSDNLNTPSPSAQIEILN-INWFQKQPHGNDEVSLTLNITADLQS 116
           ASL D + T S  A  +I N +NW+Q++P G   V L +  T+ LQS
Sbjct: 16  ASLGDRV-TISCRASQDIRNYLNWYQQKPDGT--VKLLIYYTSRLQS 59


>pdb|3U0W|L Chain L, Ad Related Murine Antibody Fragment
          Length = 214

 Score = 26.9 bits (58), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 21/47 (44%), Positives = 27/47 (57%), Gaps = 4/47 (8%)

Query: 71  ASLSDNLNTPSPSAQIEILN-INWFQKQPHGNDEVSLTLNITADLQS 116
           ASL D + T S SA   I N +NWFQ++P G   V L +  T+ L S
Sbjct: 13  ASLGDRV-TISCSASQGISNYLNWFQQKPDGT--VKLLIYYTSSLHS 56


  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
   0.323    0.134    0.412 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,497,710
Number of Sequences: 62578
Number of extensions: 185222
Number of successful extensions: 351
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 351
Number of HSP's gapped (non-prelim): 11
length of query: 212
length of database: 14,973,337
effective HSP length: 95
effective length of query: 117
effective length of database: 9,028,427
effective search space: 1056325959
effective search space used: 1056325959
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)