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= 043003
         (855 letters)

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

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



>pdb|4FEM|A Chain A, Structure Of Suse With Alpha-Cyclodextrin
          Length = 358

 Score = 31.2 bits (69), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 12/33 (36%), Positives = 18/33 (54%)

Query: 787 NLKAGTALKLNCQQPDDGFKQAASFVMQKGISQ 819
           +LK    ++L C QPD GF  A ++ +Q    Q
Sbjct: 22  DLKNAQTVELTCSQPDYGFPAATTYTVQASFEQ 54


>pdb|1KCX|A Chain A, X-Ray Structure Of Nysgrc Target T-45
 pdb|1KCX|B Chain B, X-Ray Structure Of Nysgrc Target T-45
          Length = 518

 Score = 30.0 bits (66), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 5/69 (7%)

Query: 410 LKVSRYLFKWTKQVTYADYYERALTNGVLGIQRGTEPGVMIYMLPLSPGSSKAKSYHGWG 469
           + V+ YL K ++ +T AD + +     + G   GT   ++ +++P  PGSS   S+  W 
Sbjct: 63  IDVNTYLQKPSQGMTSADDFFQGTKAALAG---GTT-MIIDHVVP-EPGSSLLTSFEKWH 117

Query: 470 DAFDSFWCC 478
           +A D+  CC
Sbjct: 118 EAADTKSCC 126


  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
   0.318    0.134    0.406 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 26,781,204
Number of Sequences: 62578
Number of extensions: 1153007
Number of successful extensions: 2529
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 2524
Number of HSP's gapped (non-prelim): 8
length of query: 855
length of database: 14,973,337
effective HSP length: 107
effective length of query: 748
effective length of database: 8,277,491
effective search space: 6191563268
effective search space used: 6191563268
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)