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= 016036
         (396 letters)

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

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



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

 Score = 32.0 bits (71), Expect = 0.54,   Method: Compositional matrix adjust.
 Identities = 31/125 (24%), Positives = 49/125 (39%), Gaps = 19/125 (15%)

Query: 208 LSAKTKTYFATAVSMWDAEFYIKVDDDVHVNLATLGMTLAAHRTKP-RVYVGCMKSGPVL 266
           L    +T    AVSM +    ++VDD    N+  LG  L +H   P RV  G M+   ++
Sbjct: 141 LRTDIQTVLCGAVSMGNPHCVVQVDDIQTANVEQLGPLLESHERFPERVNAGFMQ---II 197

Query: 267 ARKGVKYYEPEYWKFGEIGNKYFRHATGQLYALSKD--LATYISINQHLLHKYANEDVSL 324
            ++ +K              + +    G+  A       A  + I Q LL+     D+  
Sbjct: 198 NKEHIKL-------------RVYERGAGETQACGSGACAAVAVGIMQGLLNNNVQVDLPG 244

Query: 325 GSWFI 329
           GS  I
Sbjct: 245 GSLMI 249


>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 = 0.55,   Method: Compositional matrix adjust.
 Identities = 31/125 (24%), Positives = 49/125 (39%), Gaps = 19/125 (15%)

Query: 208 LSAKTKTYFATAVSMWDAEFYIKVDDDVHVNLATLGMTLAAHRTKP-RVYVGCMKSGPVL 266
           L    +T    AVSM +    ++VDD    N+  LG  L +H   P RV  G M+   ++
Sbjct: 141 LRTDIQTVLCGAVSMGNPHCVVQVDDIQTANVEQLGPLLESHERFPERVNAGFMQ---II 197

Query: 267 ARKGVKYYEPEYWKFGEIGNKYFRHATGQLYALSKD--LATYISINQHLLHKYANEDVSL 324
            ++ +K              + +    G+  A       A  + I Q LL+     D+  
Sbjct: 198 NKEHIKL-------------RVYERGAGETQACGSGACAAVAVGIMQGLLNNNVQVDLPG 244

Query: 325 GSWFI 329
           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 = 0.59,   Method: Compositional matrix adjust.
 Identities = 31/125 (24%), Positives = 49/125 (39%), Gaps = 19/125 (15%)

Query: 208 LSAKTKTYFATAVSMWDAEFYIKVDDDVHVNLATLGMTLAAHRTKP-RVYVGCMKSGPVL 266
           L    +T    AVSM +    ++VDD    N+  LG  L +H   P RV  G M+   ++
Sbjct: 141 LRTDIQTVLCGAVSMGNPHCVVQVDDIQTANVEQLGPLLESHERFPERVNAGFMQ---II 197

Query: 267 ARKGVKYYEPEYWKFGEIGNKYFRHATGQLYALSKD--LATYISINQHLLHKYANEDVSL 324
            ++ +K              + +    G+  A       A  + I Q LL+     D+  
Sbjct: 198 NKEHIKL-------------RVYERGAGETQACGSGACAAVAVGIMQGLLNNNVQVDLPG 244

Query: 325 GSWFI 329
           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 = 31/125 (24%), Positives = 49/125 (39%), Gaps = 19/125 (15%)

Query: 208 LSAKTKTYFATAVSMWDAEFYIKVDDDVHVNLATLGMTLAAHRTKP-RVYVGCMKSGPVL 266
           L    +T    AVSM +    ++VDD    N+  LG  L +H   P RV  G M+   ++
Sbjct: 141 LRTDIQTVLCGAVSMGNPHCVVQVDDIQTANVEQLGPLLESHERFPERVNAGFMQ---II 197

Query: 267 ARKGVKYYEPEYWKFGEIGNKYFRHATGQLYALSKD--LATYISINQHLLHKYANEDVSL 324
            ++ +K              + +    G+  A       A  + I Q LL+     D+  
Sbjct: 198 NKEHIKL-------------RVYERGAGETQASGSGACAAVAVGIMQGLLNNNVQVDLPG 244

Query: 325 GSWFI 329
           GS  I
Sbjct: 245 GSLMI 249


>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 = 30.4 bits (67), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 20/51 (39%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 175 SATSGGILDKAIDAEEKMHGDFLRLEHIEGYLELSAKTKTYFATAVSMWDA 225
           S T GG LDKA   +E++  D L++  I  YL  S   +TY A   + +DA
Sbjct: 544 STTKGGSLDKAKALKEQLEKDGLKVTVIAEYL-ASGVDQTYSAADATAFDA 593


>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 = 2.2,   Method: Compositional matrix adjust.
 Identities = 20/44 (45%), Positives = 21/44 (47%), Gaps = 1/44 (2%)

Query: 215 YFATAVSMWDAEFYIKVDDDVHVNLATLGMTLAAHRTKP-RVYV 257
           Y  TAVSM +    I VDD     L TLG  L  H   P RV V
Sbjct: 177 YAFTAVSMGNPHAVIFVDDVEQAPLTTLGPVLETHEMFPERVNV 220


>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 = 30.0 bits (66), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 228 YIKVDDDVHVNLATLGMTLAAHRTKPRVYVGCMKSGPVLARKGVKYY 274
           +I V     V ++++   L+A R  PRV + CM + PV+ R+G   Y
Sbjct: 112 HIVVSCAAGVTISSIEKKLSAFRPAPRV-IRCMTNTPVVVREGATVY 157


>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 = 30.0 bits (66), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 228 YIKVDDDVHVNLATLGMTLAAHRTKPRVYVGCMKSGPVLARKGVKYY 274
           +I V     V ++++   L+A R  PRV + CM + PV+ R+G   Y
Sbjct: 92  HIVVSCAAGVTISSIEKKLSAFRPAPRV-IRCMTNTPVVVREGATVY 137


>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 = 29.6 bits (65), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 228 YIKVDDDVHVNLATLGMTLAAHRTKPRVYVGCMKSGPVLARKGVKYY 274
           +I V     V ++++   L+A R  PRV + CM + PV+ R+G   Y
Sbjct: 92  HIVVSCAAGVTISSIEKKLSAFRPAPRV-IRCMTNTPVVVREGATVY 137


  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
   0.320    0.134    0.410 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,990,447
Number of Sequences: 62578
Number of extensions: 481694
Number of successful extensions: 1113
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 1111
Number of HSP's gapped (non-prelim): 10
length of query: 396
length of database: 14,973,337
effective HSP length: 101
effective length of query: 295
effective length of database: 8,652,959
effective search space: 2552622905
effective search space used: 2552622905
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)