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= psy7602
         (95 letters)

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

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



>pdb|1NYT|A Chain A, Shikimate Dehydrogenase Aroe Complexed With Nadp+
 pdb|1NYT|B Chain B, Shikimate Dehydrogenase Aroe Complexed With Nadp+
 pdb|1NYT|C Chain C, Shikimate Dehydrogenase Aroe Complexed With Nadp+
 pdb|1NYT|D Chain D, Shikimate Dehydrogenase Aroe Complexed With Nadp+
          Length = 271

 Score = 27.3 bits (59), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 7/49 (14%)

Query: 1   MPSTLM-TGLECSHRFCTQ------CWCEYLTTKIIQEGMGQTIACAAH 42
           +PS+L+  G+ C   F  +       WCE   +K   +G+G  +A AAH
Sbjct: 199 IPSSLIHPGIYCYDMFYQKGKTPFLAWCEQRGSKRNADGLGMLVAQAAH 247


>pdb|2Q9H|A Chain A, Crystal Structure Of The C73s Mutant Of Diaminopimelate
           Epimerase
          Length = 274

 Score = 26.2 bits (56), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 16/67 (23%), Positives = 28/67 (41%), Gaps = 15/67 (22%)

Query: 9   LECSHRFCTQCWC--------EYLTTKIIQEGMGQTIACAAHGCNILVDDGKPIEFDVYQ 60
           LE   RF  +           E++  ++ + G G+T AC +  C         +   + Q
Sbjct: 179 LESHERFPERVNAGFMQIINKEHIKLRVYERGAGETQACGSGAC-------AAVAVGIMQ 231

Query: 61  GILSNQV 67
           G+L+N V
Sbjct: 232 GLLNNNV 238


>pdb|1BWZ|A Chain A, Diaminopimelate Epimerase From Hemophilus Influenzae
          Length = 274

 Score = 26.2 bits (56), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 16/67 (23%), Positives = 28/67 (41%), Gaps = 15/67 (22%)

Query: 9   LECSHRFCTQCWC--------EYLTTKIIQEGMGQTIACAAHGCNILVDDGKPIEFDVYQ 60
           LE   RF  +           E++  ++ + G G+T AC +  C         +   + Q
Sbjct: 179 LESHERFPERVNAGFMQIINKEHIKLRVYERGAGETQACGSGAC-------AAVAVGIMQ 231

Query: 61  GILSNQV 67
           G+L+N V
Sbjct: 232 GLLNNNV 238


>pdb|1GQZ|A Chain A, Refinement Of Haemophilus Influenzae Diaminopimelate
           Epimerase At 1.7a
 pdb|2GKE|A Chain A, Crystal Structure Of Diaminopimelate Epimerase In Complex
           With An Irreversible Inhibitor Ll-Azidap
 pdb|2GKJ|A Chain A, Crystal Structure Of Diaminopimelate Epimerase In Complex
           With An Irreversible Inhibitor Dl-Azidap
          Length = 274

 Score = 26.2 bits (56), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 16/67 (23%), Positives = 28/67 (41%), Gaps = 15/67 (22%)

Query: 9   LECSHRFCTQCWC--------EYLTTKIIQEGMGQTIACAAHGCNILVDDGKPIEFDVYQ 60
           LE   RF  +           E++  ++ + G G+T AC +  C         +   + Q
Sbjct: 179 LESHERFPERVNAGFMQIINKEHIKLRVYERGAGETQACGSGAC-------AAVAVGIMQ 231

Query: 61  GILSNQV 67
           G+L+N V
Sbjct: 232 GLLNNNV 238


>pdb|4IK0|A Chain A, Crystal Structure Of Diaminopimelate Epimerase Y268a
           Mutant From Escherichia Coli
 pdb|4IK0|B Chain B, Crystal Structure Of Diaminopimelate Epimerase Y268a
           Mutant From Escherichia Coli
          Length = 280

 Score = 25.4 bits (54), Expect = 7.5,   Method: Compositional matrix adjust.
 Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 15/73 (20%)

Query: 3   STLMTGLECSHRFCTQCWC--------EYLTTKIIQEGMGQTIACAAHGCNILVDDGKPI 54
            TL   LE   RF  +           E++  ++ + G G+T AC +  C         +
Sbjct: 173 ETLGPVLESHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGAC-------AAV 225

Query: 55  EFDVYQGILSNQV 67
              + QG+L+ +V
Sbjct: 226 AVGIQQGLLAEEV 238


>pdb|4IJZ|A Chain A, Crystal Structure Of Diaminopimelate Epimerase From
           Escherichia Coli
 pdb|4IJZ|B Chain B, Crystal Structure Of Diaminopimelate Epimerase From
           Escherichia Coli
          Length = 280

 Score = 25.4 bits (54), Expect = 7.6,   Method: Compositional matrix adjust.
 Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 15/73 (20%)

Query: 3   STLMTGLECSHRFCTQCWC--------EYLTTKIIQEGMGQTIACAAHGCNILVDDGKPI 54
            TL   LE   RF  +           E++  ++ + G G+T AC +  C         +
Sbjct: 173 ETLGPVLESHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGAC-------AAV 225

Query: 55  EFDVYQGILSNQV 67
              + QG+L+ +V
Sbjct: 226 AVGIQQGLLAEEV 238


  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
   0.326    0.140    0.485 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,026,521
Number of Sequences: 62578
Number of extensions: 111577
Number of successful extensions: 272
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 262
Number of HSP's gapped (non-prelim): 15
length of query: 95
length of database: 14,973,337
effective HSP length: 62
effective length of query: 33
effective length of database: 11,093,501
effective search space: 366085533
effective search space used: 366085533
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 45 (21.9 bits)