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= 021608
         (310 letters)

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

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



>pdb|1KNO|A Chain A, Crystal Structure Of The Complex Of A Catalytic Antibody
           Fab With A Transition State Analog: Structural
           Similarities In Esterase-Like Abzymes
 pdb|1KNO|C Chain C, Crystal Structure Of The Complex Of A Catalytic Antibody
           Fab With A Transition State Analog: Structural
           Similarities In Esterase-Like Abzymes
 pdb|1KNO|E Chain E, Crystal Structure Of The Complex Of A Catalytic Antibody
           Fab With A Transition State Analog: Structural
           Similarities In Esterase-Like Abzymes
          Length = 214

 Score = 29.3 bits (64), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 29/108 (26%), Positives = 47/108 (43%), Gaps = 11/108 (10%)

Query: 101 IGEKVGISTRINRSDSGYTQGLIEKVGFLMGRDV-ASLVLEACISLRIWELVETLIVHGL 159
           +GE+V ++ R ++  SGY   L +K    + R + A+  L++ +  R           G 
Sbjct: 15  LGERVSLTCRASQEISGYLSWLQQKPDGTIKRLIYAASTLDSGVPKRF---------SGS 65

Query: 160 VDHSSYSNLVTRLATEKRSDLLCLCVKYSP-DLGSSELLCILKYFLCP 206
              S YS  ++ L +E  +D  CL    SP   G    L IL+    P
Sbjct: 66  RSGSDYSLTISSLESEDFADYYCLQYASSPYTFGGGTKLEILRADAAP 113


>pdb|2GFB|A Chain A, Crystal Structure Of A Catalytic Fab Having Esterase-Like
           Activity
 pdb|2GFB|C Chain C, Crystal Structure Of A Catalytic Fab Having Esterase-Like
           Activity
 pdb|2GFB|E Chain E, Crystal Structure Of A Catalytic Fab Having Esterase-Like
           Activity
 pdb|2GFB|G Chain G, Crystal Structure Of A Catalytic Fab Having Esterase-Like
           Activity
 pdb|2GFB|I Chain I, Crystal Structure Of A Catalytic Fab Having Esterase-Like
           Activity
 pdb|2GFB|K Chain K, Crystal Structure Of A Catalytic Fab Having Esterase-Like
           Activity
 pdb|2GFB|M Chain M, Crystal Structure Of A Catalytic Fab Having Esterase-Like
           Activity
 pdb|2GFB|O Chain O, Crystal Structure Of A Catalytic Fab Having Esterase-Like
           Activity
          Length = 214

 Score = 28.9 bits (63), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 29/108 (26%), Positives = 47/108 (43%), Gaps = 11/108 (10%)

Query: 101 IGEKVGISTRINRSDSGYTQGLIEKVGFLMGRDV-ASLVLEACISLRIWELVETLIVHGL 159
           +GE+V ++ R ++  SGY   L +K    + R + A+  L++ +  R           G 
Sbjct: 15  LGERVSLTCRASQEISGYLSWLQQKPDGTIKRLIYAASTLDSGVPKRF---------SGS 65

Query: 160 VDHSSYSNLVTRLATEKRSDLLCLCVKYSP-DLGSSELLCILKYFLCP 206
              S YS  ++ L +E  +D  CL    SP   G    L IL+    P
Sbjct: 66  RSGSDYSLTISSLESEDFADYYCLQYASSPYTFGGGTKLEILRGGAAP 113


>pdb|4F3Y|A Chain A, X-Ray Crystal Structure Of Dihydrodipicolinate Reductase
           From Burkholderia Thailandensis
 pdb|4F3Y|B Chain B, X-Ray Crystal Structure Of Dihydrodipicolinate Reductase
           From Burkholderia Thailandensis
          Length = 272

 Score = 28.5 bits (62), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 89  EFIGILNPYLQKIGEKVGISTRINRSDSGYTQGLIEKVGFLMGRDVASLVLEACISLR 146
           + +G        IGE++ I T  + S   Y QG +    FL GRD     ++  + LR
Sbjct: 216 DIVGDHTVLFAGIGERIEI-THKSASRVSYAQGALRAARFLAGRDAGFFDMQDVLGLR 272


>pdb|3BGF|L Chain L, X-Ray Crystal Structure Of The Sars Coronavirus Spike
           Receptor Binding Domain In Complex With F26g19 Fab
 pdb|3BGF|C Chain C, X-Ray Crystal Structure Of The Sars Coronavirus Spike
           Receptor Binding Domain In Complex With F26g19 Fab
          Length = 212

 Score = 27.7 bits (60), Expect = 8.9,   Method: Compositional matrix adjust.
 Identities = 29/108 (26%), Positives = 46/108 (42%), Gaps = 11/108 (10%)

Query: 101 IGEKVGISTRINRSDSGYTQGLIEKVGFLMGRDV-ASLVLEACISLRIWELVETLIVHGL 159
           +GE+V ++ R ++  SGY   L EK    + R + A+  L++ +  R           G 
Sbjct: 15  LGERVSLTCRASQEISGYLSWLQEKPDGTIKRLIYAASTLDSGVPKRF---------SGS 65

Query: 160 VDHSSYSNLVTRLATEKRSDLLCL-CVKYSPDLGSSELLCILKYFLCP 206
              S YS  ++ L +E  +D  CL  V Y    G    L I +    P
Sbjct: 66  RSGSDYSLTISSLESEDFADYYCLQYVSYPWTFGGGTKLEIKRADAAP 113


  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
   0.319    0.137    0.406 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,663,300
Number of Sequences: 62578
Number of extensions: 331395
Number of successful extensions: 649
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 647
Number of HSP's gapped (non-prelim): 4
length of query: 310
length of database: 14,973,337
effective HSP length: 99
effective length of query: 211
effective length of database: 8,778,115
effective search space: 1852182265
effective search space used: 1852182265
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)