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= 042279
         (92 letters)

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

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



>pdb|1MF2|H Chain H, Anti Hiv1 Protease Fab Complex
 pdb|1MF2|N Chain N, Anti Hiv1 Protease Fab Complex
 pdb|2HRP|H Chain H, Antigen-Antibody Complex
 pdb|2HRP|N Chain N, Antigen-Antibody Complex
          Length = 226

 Score = 25.4 bits (54), Expect = 7.4,   Method: Compositional matrix adjust.
 Identities = 10/45 (22%), Positives = 21/45 (46%)

Query: 27 VPKGHFAVYVGETERSRFVVPVSYPKHPSFQKLLSPAEEEFGFHH 71
          +  G   +Y  +T + RF +    PK+  F ++ S   E+   ++
Sbjct: 51 ISSGSSTIYYADTVKGRFTISRDNPKNTLFLQMTSLRSEDTALYY 95


>pdb|2GFB|B Chain B, Crystal Structure Of A Catalytic Fab Having
          Esterase-Like Activity
 pdb|2GFB|D Chain D, Crystal Structure Of A Catalytic Fab Having
          Esterase-Like Activity
 pdb|2GFB|F Chain F, Crystal Structure Of A Catalytic Fab Having
          Esterase-Like Activity
 pdb|2GFB|H Chain H, Crystal Structure Of A Catalytic Fab Having
          Esterase-Like Activity
 pdb|2GFB|J Chain J, Crystal Structure Of A Catalytic Fab Having
          Esterase-Like Activity
 pdb|2GFB|L Chain L, Crystal Structure Of A Catalytic Fab Having
          Esterase-Like Activity
 pdb|2GFB|N Chain N, Crystal Structure Of A Catalytic Fab Having
          Esterase-Like Activity
 pdb|2GFB|P Chain P, Crystal Structure Of A Catalytic Fab Having
          Esterase-Like Activity
          Length = 219

 Score = 25.4 bits (54), Expect = 9.5,   Method: Compositional matrix adjust.
 Identities = 10/45 (22%), Positives = 21/45 (46%)

Query: 27 VPKGHFAVYVGETERSRFVVPVSYPKHPSFQKLLSPAEEEFGFHH 71
          +  G   +Y  +T + RF +    PK+  F ++ S   E+   ++
Sbjct: 51 ISSGSSTIYYADTVKGRFTISRDNPKNTLFLQMTSLRSEDTAMYY 95


>pdb|1KNO|B Chain B, Crystal Structure Of The Complex Of A Catalytic Antibody
          Fab With A Transition State Analog: Structural
          Similarities In Esterase-Like Abzymes
 pdb|1KNO|D Chain D, Crystal Structure Of The Complex Of A Catalytic Antibody
          Fab With A Transition State Analog: Structural
          Similarities In Esterase-Like Abzymes
 pdb|1KNO|F Chain F, Crystal Structure Of The Complex Of A Catalytic Antibody
          Fab With A Transition State Analog: Structural
          Similarities In Esterase-Like Abzymes
          Length = 220

 Score = 25.0 bits (53), Expect = 9.6,   Method: Compositional matrix adjust.
 Identities = 10/45 (22%), Positives = 21/45 (46%)

Query: 27 VPKGHFAVYVGETERSRFVVPVSYPKHPSFQKLLSPAEEEFGFHH 71
          +  G   +Y  +T + RF +    PK+  F ++ S   E+   ++
Sbjct: 51 ISSGSSTIYYADTVKGRFTISRDNPKNTLFLQMTSLRSEDTAMYY 95


  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
   0.325    0.139    0.421 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,781,307
Number of Sequences: 62578
Number of extensions: 99576
Number of successful extensions: 246
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 242
Number of HSP's gapped (non-prelim): 4
length of query: 92
length of database: 14,973,337
effective HSP length: 59
effective length of query: 33
effective length of database: 11,281,235
effective search space: 372280755
effective search space used: 372280755
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)