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= 018257
         (359 letters)

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

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



>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 = 32.0 bits (71), Expect = 0.53,   Method: Compositional matrix adjust.
 Identities = 31/125 (24%), Positives = 49/125 (39%), Gaps = 19/125 (15%)

Query: 171 LSAKTKTYFATAVSMWDAEFYIKVDDDVHVNLATLGMTLAAHRTKP-RVYVGCMKSGPVL 229
           L    +T    AVSM +    ++VDD    N+  LG  L +H   P RV  G M+   ++
Sbjct: 141 LRTDIQTVLCGAVSMGNPHCVVQVDDIQTANVEQLGPLLESHERFPERVNAGFMQ---II 197

Query: 230 ARKGVKYYEPEYWKFGEIGNKYFRHATGQLYALSKD--LATYISINQHLLHKYANEDVSL 287
            ++ +K              + +    G+  A       A  + I Q LL+     D+  
Sbjct: 198 NKEHIKL-------------RVYERGAGETQACGSGACAAVAVGIMQGLLNNNVQVDLPG 244

Query: 288 GSWFI 292
           GS  I
Sbjct: 245 GSLMI 249


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

 Score = 32.0 bits (71), Expect = 0.59,   Method: Compositional matrix adjust.
 Identities = 31/125 (24%), Positives = 49/125 (39%), Gaps = 19/125 (15%)

Query: 171 LSAKTKTYFATAVSMWDAEFYIKVDDDVHVNLATLGMTLAAHRTKP-RVYVGCMKSGPVL 229
           L    +T    AVSM +    ++VDD    N+  LG  L +H   P RV  G M+   ++
Sbjct: 141 LRTDIQTVLCGAVSMGNPHCVVQVDDIQTANVEQLGPLLESHERFPERVNAGFMQ---II 197

Query: 230 ARKGVKYYEPEYWKFGEIGNKYFRHATGQLYALSKD--LATYISINQHLLHKYANEDVSL 287
            ++ +K              + +    G+  A       A  + I Q LL+     D+  
Sbjct: 198 NKEHIKL-------------RVYERGAGETQACGSGACAAVAVGIMQGLLNNNVQVDLPG 244

Query: 288 GSWFI 292
           GS  I
Sbjct: 245 GSLMI 249


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

 Score = 32.0 bits (71), Expect = 0.60,   Method: Compositional matrix adjust.
 Identities = 31/125 (24%), Positives = 49/125 (39%), Gaps = 19/125 (15%)

Query: 171 LSAKTKTYFATAVSMWDAEFYIKVDDDVHVNLATLGMTLAAHRTKP-RVYVGCMKSGPVL 229
           L    +T    AVSM +    ++VDD    N+  LG  L +H   P RV  G M+   ++
Sbjct: 141 LRTDIQTVLCGAVSMGNPHCVVQVDDIQTANVEQLGPLLESHERFPERVNAGFMQ---II 197

Query: 230 ARKGVKYYEPEYWKFGEIGNKYFRHATGQLYALSKD--LATYISINQHLLHKYANEDVSL 287
            ++ +K              + +    G+  A       A  + I Q LL+     D+  
Sbjct: 198 NKEHIKL-------------RVYERGAGETQACGSGACAAVAVGIMQGLLNNNVQVDLPG 244

Query: 288 GSWFI 292
           GS  I
Sbjct: 245 GSLMI 249


>pdb|2Q9J|A Chain A, Crystal Structure Of The C217s Mutant Of Diaminopimelate
           Epimerase
          Length = 274

 Score = 31.2 bits (69), Expect = 0.97,   Method: Compositional matrix adjust.
 Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 1/55 (1%)

Query: 171 LSAKTKTYFATAVSMWDAEFYIKVDDDVHVNLATLGMTLAAHRTKP-RVYVGCMK 224
           L    +T    AVSM +    ++VDD    N+  LG  L +H   P RV  G M+
Sbjct: 141 LRTDIQTVLCGAVSMGNPHCVVQVDDIQTANVEQLGPLLESHERFPERVNAGFMQ 195


>pdb|2GR9|A Chain A, Crystal Structure Of P5cr Complexed With Nadh
 pdb|2GR9|B Chain B, Crystal Structure Of P5cr Complexed With Nadh
 pdb|2GR9|C Chain C, Crystal Structure Of P5cr Complexed With Nadh
 pdb|2GR9|D Chain D, Crystal Structure Of P5cr Complexed With Nadh
 pdb|2GR9|E Chain E, Crystal Structure Of P5cr Complexed With Nadh
 pdb|2GRA|A Chain A, Crystal Structure Of Human Pyrroline-5-carboxylate
           Reductase Complexed With Nadp
 pdb|2GRA|B Chain B, Crystal Structure Of Human Pyrroline-5-carboxylate
           Reductase Complexed With Nadp
 pdb|2GRA|C Chain C, Crystal Structure Of Human Pyrroline-5-carboxylate
           Reductase Complexed With Nadp
 pdb|2GRA|D Chain D, Crystal Structure Of Human Pyrroline-5-carboxylate
           Reductase Complexed With Nadp
 pdb|2GRA|E Chain E, Crystal Structure Of Human Pyrroline-5-carboxylate
           Reductase Complexed With Nadp
          Length = 277

 Score = 30.4 bits (67), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 191 YIKVDDDVHVNLATLGMTLAAHRTKPRVYVGCMKSGPVLARKGVKYY 237
           +I V     V ++++   L+A R  PRV + CM + PV+ R+G   Y
Sbjct: 92  HIVVSCAAGVTISSIEKKLSAFRPAPRV-IRCMTNTPVVVREGATVY 137


>pdb|2IZZ|A Chain A, Crystal Structure Of Human Pyrroline-5-Carboxylate
           Reductase
 pdb|2IZZ|B Chain B, Crystal Structure Of Human Pyrroline-5-Carboxylate
           Reductase
 pdb|2IZZ|C Chain C, Crystal Structure Of Human Pyrroline-5-Carboxylate
           Reductase
 pdb|2IZZ|D Chain D, Crystal Structure Of Human Pyrroline-5-Carboxylate
           Reductase
 pdb|2IZZ|E Chain E, Crystal Structure Of Human Pyrroline-5-Carboxylate
           Reductase
          Length = 322

 Score = 30.4 bits (67), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 191 YIKVDDDVHVNLATLGMTLAAHRTKPRVYVGCMKSGPVLARKGVKYY 237
           +I V     V ++++   L+A R  PRV + CM + PV+ R+G   Y
Sbjct: 112 HIVVSCAAGVTISSIEKKLSAFRPAPRV-IRCMTNTPVVVREGATVY 157


>pdb|3EJ6|A Chain A, Neurospora Crassa Catalase-3 Crystal Structure
 pdb|3EJ6|B Chain B, Neurospora Crassa Catalase-3 Crystal Structure
 pdb|3EJ6|C Chain C, Neurospora Crassa Catalase-3 Crystal Structure
 pdb|3EJ6|D Chain D, Neurospora Crassa Catalase-3 Crystal Structure
          Length = 688

 Score = 30.0 bits (66), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 20/51 (39%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 138 SATSGGILDKAIDAEEKMHGDFLRLEHIEGYLELSAKTKTYFATAVSMWDA 188
           S T GG LDKA   +E++  D L++  I  YL  S   +TY A   + +DA
Sbjct: 544 STTKGGSLDKAKALKEQLEKDGLKVTVIAEYL-ASGVDQTYSAADATAFDA 593


>pdb|2GER|A Chain A, Crystal Structure And Oxidative Mechanism Of Human
           Pyrroline-5- Carboxylate Reductase
 pdb|2GER|B Chain B, Crystal Structure And Oxidative Mechanism Of Human
           Pyrroline-5- Carboxylate Reductase
 pdb|2GER|C Chain C, Crystal Structure And Oxidative Mechanism Of Human
           Pyrroline-5- Carboxylate Reductase
 pdb|2GER|D Chain D, Crystal Structure And Oxidative Mechanism Of Human
           Pyrroline-5- Carboxylate Reductase
 pdb|2GER|E Chain E, Crystal Structure And Oxidative Mechanism Of Human
           Pyrroline-5- Carboxylate Reductase
          Length = 321

 Score = 30.0 bits (66), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 191 YIKVDDDVHVNLATLGMTLAAHRTKPRVYVGCMKSGPVLARKGVKYY 237
           +I V     V ++++   L+A R  PRV + CM + PV+ R+G   Y
Sbjct: 92  HIVVSCAAGVTISSIEKKLSAFRPAPRV-IRCMTNTPVVVREGATVY 137


>pdb|2OTN|A Chain A, Crystal Structure Of The Catalytically Active Form Of
           Diaminopimelate Epimerase From Bacillus Anthracis
 pdb|2OTN|B Chain B, Crystal Structure Of The Catalytically Active Form Of
           Diaminopimelate Epimerase From Bacillus Anthracis
          Length = 308

 Score = 30.0 bits (66), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 20/44 (45%), Positives = 21/44 (47%), Gaps = 1/44 (2%)

Query: 178 YFATAVSMWDAEFYIKVDDDVHVNLATLGMTLAAHRTKP-RVYV 220
           Y  TAVSM +    I VDD     L TLG  L  H   P RV V
Sbjct: 177 YAFTAVSMGNPHAVIFVDDVEQAPLTTLGPVLETHEMFPERVNV 220


>pdb|1G6U|A Chain A, Crystal Structure Of A Domain Swapped Dimer
 pdb|1G6U|B Chain B, Crystal Structure Of A Domain Swapped Dimer
          Length = 48

 Score = 29.3 bits (64), Expect = 3.4,   Method: Composition-based stats.
 Identities = 16/42 (38%), Positives = 29/42 (69%), Gaps = 1/42 (2%)

Query: 23 ELKAVKHESNNNTEKLAMVEQAIQSQDKRLDGLKTKITAVRA 64
          EL+A+K E  +  E+LA +E  +Q+ +K+L  LK+K+ A++ 
Sbjct: 8  ELQALKKEGFS-PEELAALESELQALEKKLAALKSKLQALKG 48


  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    0.133    0.404 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,834,565
Number of Sequences: 62578
Number of extensions: 435826
Number of successful extensions: 1071
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1070
Number of HSP's gapped (non-prelim): 10
length of query: 359
length of database: 14,973,337
effective HSP length: 100
effective length of query: 259
effective length of database: 8,715,537
effective search space: 2257324083
effective search space used: 2257324083
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: 52 (24.6 bits)