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= psy9840
         (126 letters)

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

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



>pdb|1KNW|A Chain A, Crystal Structure Of Diaminopimelate Decarboxylase
 pdb|1KO0|A Chain A, Crystal Structure Of A D,L-Lysine Complex Of
           Diaminopimelate Decarboxylase
          Length = 425

 Score = 27.7 bits (60), Expect = 1.5,   Method: Composition-based stats.
 Identities = 16/28 (57%), Positives = 16/28 (57%)

Query: 45  LVIAGIGDLTRPAEKLSISQSSALAATG 72
           LV AG  DL RPA   S    SALAA G
Sbjct: 297 LVDAGFNDLMRPAMYGSYHHISALAADG 324


>pdb|1TUF|A Chain A, Crystal Structure Of Diaminopimelate Decarboxylase From M.
           Jannaschi
 pdb|1TUF|B Chain B, Crystal Structure Of Diaminopimelate Decarboxylase From M.
           Jannaschi
          Length = 434

 Score = 26.9 bits (58), Expect = 2.8,   Method: Composition-based stats.
 Identities = 9/19 (47%), Positives = 14/19 (73%)

Query: 39  PMFKWGLVIAGIGDLTRPA 57
           P+ KW ++ AG+ D+ RPA
Sbjct: 313 PVTKWVMIDAGMNDMMRPA 331


>pdb|1TWI|A Chain A, Crystal Structure Of Diaminopimelate Decarboxylase From M.
           Jannaschii In Co-Complex With L-Lysine
 pdb|1TWI|B Chain B, Crystal Structure Of Diaminopimelate Decarboxylase From M.
           Jannaschii In Co-Complex With L-Lysine
 pdb|1TWI|C Chain C, Crystal Structure Of Diaminopimelate Decarboxylase From M.
           Jannaschii In Co-Complex With L-Lysine
 pdb|1TWI|D Chain D, Crystal Structure Of Diaminopimelate Decarboxylase From M.
           Jannaschii In Co-Complex With L-Lysine
          Length = 434

 Score = 26.9 bits (58), Expect = 2.8,   Method: Composition-based stats.
 Identities = 9/19 (47%), Positives = 14/19 (73%)

Query: 39  PMFKWGLVIAGIGDLTRPA 57
           P+ KW ++ AG+ D+ RPA
Sbjct: 313 PVTKWVMIDAGMNDMMRPA 331


  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
   0.321    0.131    0.403 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,377,586
Number of Sequences: 62578
Number of extensions: 113200
Number of successful extensions: 230
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 227
Number of HSP's gapped (non-prelim): 3
length of query: 126
length of database: 14,973,337
effective HSP length: 87
effective length of query: 39
effective length of database: 9,529,051
effective search space: 371632989
effective search space used: 371632989
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)