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= 023496
         (281 letters)

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

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



>pdb|2VWE|C Chain C, Crystal Structure Of Vascular Endothelial Growth Factor-B
           In Complex With A Neutralizing Antibody Fab Fragment
 pdb|2VWE|J Chain J, Crystal Structure Of Vascular Endothelial Growth Factor-B
           In Complex With A Neutralizing Antibody Fab Fragment
          Length = 214

 Score = 29.3 bits (64), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 34/78 (43%), Gaps = 8/78 (10%)

Query: 48  LINLVQSRPQGVPLISVSNHMSTLDDPVMWGFRGFPT-MDAELARWVLAAEDICFKNSIL 106
            +N  Q +P G   + +  + STL   V   F G  +  D  L    L  EDI       
Sbjct: 32  FLNWYQQKPDGTVKLLIY-YTSTLHSGVPSRFSGSGSGTDYSLTISNLEQEDIA------ 84

Query: 107 SYFFRVGKCIPITRGGGI 124
           +YF + GK +P T GGG 
Sbjct: 85  TYFCQQGKTLPPTFGGGT 102


>pdb|1BZ7|A Chain A, Fab Fragment From Murine Ascites
          Length = 206

 Score = 29.3 bits (64), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 35/123 (28%), Positives = 50/123 (40%), Gaps = 21/123 (17%)

Query: 48  LINLVQSRPQGVPLISVSNHMSTLDDPVMWGFRGFPT-MDAELARWVLAAEDICFKNSIL 106
            +N  Q +P G  L  +  + S L   V   F G+ +  D  L    L  EDI       
Sbjct: 32  FLNWYQQKPDG-SLKLLIYYTSRLQSGVPSRFSGWGSGTDYSLTISNLEEEDIA------ 84

Query: 107 SYFFRVGKCIPITRGGGIYQEHMNEALERLSDGAWLHTFPEGKVSQEDAPIRQLKWGTAS 166
           ++F + GK +P T GGG   E     ++R      +  FP            QLK GTAS
Sbjct: 85  TFFCQQGKTLPYTFGGGTKLE-----IKRTVAAPSVFIFPPSD--------EQLKSGTAS 131

Query: 167 LIV 169
           ++ 
Sbjct: 132 VVC 134


  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    0.138    0.427 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,158,444
Number of Sequences: 62578
Number of extensions: 333095
Number of successful extensions: 610
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 610
Number of HSP's gapped (non-prelim): 2
length of query: 281
length of database: 14,973,337
effective HSP length: 98
effective length of query: 183
effective length of database: 8,840,693
effective search space: 1617846819
effective search space used: 1617846819
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: 51 (24.3 bits)