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= 015962
(397 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 = 32.3 bits (72), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 31/125 (24%), Positives = 49/125 (39%), Gaps = 19/125 (15%)
Query: 209 LSAKTKTYFATAVSMWDAEFYIKVDDDVHVNLATLGMTLAAHRTKP-RVYVGCMKSGPVL 267
L +T AVSM + ++VDD N+ LG L +H P RV G M+ ++
Sbjct: 141 LRTDIQTVLCGAVSMGNPHCVVQVDDIQTANVEQLGPLLESHERFPERVNAGFMQ---II 197
Query: 268 ARKGVKYYEPEYWKFGEIGNKYFRHATGQLYALSKD--LATYISINQHLLHKYANEDVSL 325
++ +K + + G+ A A + I Q LL+ D+
Sbjct: 198 NKEHIKL-------------RVYERGAGETQACGSGACAAVAVGIMQGLLNNNVQVDLPG 244
Query: 326 GSWFI 330
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 = 0.56, Method: Compositional matrix adjust.
Identities = 31/125 (24%), Positives = 49/125 (39%), Gaps = 19/125 (15%)
Query: 209 LSAKTKTYFATAVSMWDAEFYIKVDDDVHVNLATLGMTLAAHRTKP-RVYVGCMKSGPVL 267
L +T AVSM + ++VDD N+ LG L +H P RV G M+ ++
Sbjct: 141 LRTDIQTVLCGAVSMGNPHCVVQVDDIQTANVEQLGPLLESHERFPERVNAGFMQ---II 197
Query: 268 ARKGVKYYEPEYWKFGEIGNKYFRHATGQLYALSKD--LATYISINQHLLHKYANEDVSL 325
++ +K + + G+ A A + I Q LL+ D+
Sbjct: 198 NKEHIKL-------------RVYERGAGETQACGSGACAAVAVGIMQGLLNNNVQVDLPG 244
Query: 326 GSWFI 330
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: 209 LSAKTKTYFATAVSMWDAEFYIKVDDDVHVNLATLGMTLAAHRTKP-RVYVGCMKSGPVL 267
L +T AVSM + ++VDD N+ LG L +H P RV G M+ ++
Sbjct: 141 LRTDIQTVLCGAVSMGNPHCVVQVDDIQTANVEQLGPLLESHERFPERVNAGFMQ---II 197
Query: 268 ARKGVKYYEPEYWKFGEIGNKYFRHATGQLYALSKD--LATYISINQHLLHKYANEDVSL 325
++ +K + + G+ A A + I Q LL+ D+
Sbjct: 198 NKEHIKL-------------RVYERGAGETQACGSGACAAVAVGIMQGLLNNNVQVDLPG 244
Query: 326 GSWFI 330
GS I
Sbjct: 245 GSLMI 249
>pdb|2Q9J|A Chain A, Crystal Structure Of The C217s Mutant Of Diaminopimelate
Epimerase
Length = 274
Score = 31.6 bits (70), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 31/125 (24%), Positives = 49/125 (39%), Gaps = 19/125 (15%)
Query: 209 LSAKTKTYFATAVSMWDAEFYIKVDDDVHVNLATLGMTLAAHRTKP-RVYVGCMKSGPVL 267
L +T AVSM + ++VDD N+ LG L +H P RV G M+ ++
Sbjct: 141 LRTDIQTVLCGAVSMGNPHCVVQVDDIQTANVEQLGPLLESHERFPERVNAGFMQ---II 197
Query: 268 ARKGVKYYEPEYWKFGEIGNKYFRHATGQLYALSKD--LATYISINQHLLHKYANEDVSL 325
++ +K + + G+ A A + I Q LL+ D+
Sbjct: 198 NKEHIKL-------------RVYERGAGETQASGSGACAAVAVGIMQGLLNNNVQVDLPG 244
Query: 326 GSWFI 330
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: 176 SATSGGILDKAIDAEEKMHGDFLRLEHIEGYLELSAKTKTYFATAVSMWDA 226
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 = 2.3, Method: Compositional matrix adjust.
Identities = 20/44 (45%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 216 YFATAVSMWDAEFYIKVDDDVHVNLATLGMTLAAHRTKP-RVYV 258
Y TAVSM + I VDD L TLG L H P RV V
Sbjct: 177 YAFTAVSMGNPHAVIFVDDVEQAPLTTLGPVLETHEMFPERVNV 220
>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: 229 YIKVDDDVHVNLATLGMTLAAHRTKPRVYVGCMKSGPVLARKGVKYY 275
+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 = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 229 YIKVDDDVHVNLATLGMTLAAHRTKPRVYVGCMKSGPVLARKGVKYY 275
+I V V ++++ L+A R PRV + CM + PV+ R+G Y
Sbjct: 112 HIVVSCAAGVTISSIEKKLSAFRPAPRV-IRCMTNTPVVVREGATVY 157
>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 = 2.6, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 229 YIKVDDDVHVNLATLGMTLAAHRTKPRVYVGCMKSGPVLARKGVKYY 275
+I V V ++++ L+A R PRV + CM + PV+ R+G Y
Sbjct: 92 HIVVSCAAGVTISSIEKKLSAFRPAPRV-IRCMTNTPVVVREGATVY 137
>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 = 29.6 bits (65), Expect = 3.2, Method: Composition-based stats.
Identities = 16/42 (38%), Positives = 29/42 (69%), Gaps = 1/42 (2%)
Query: 61 ELKAVKHESNNNTEKLAMVEQAIQSQDKRLDGLKTKITAVRA 102
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
0.320 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: 12,019,784
Number of Sequences: 62578
Number of extensions: 483153
Number of successful extensions: 1124
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: 1123
Number of HSP's gapped (non-prelim): 10
length of query: 397
length of database: 14,973,337
effective HSP length: 101
effective length of query: 296
effective length of database: 8,652,959
effective search space: 2561275864
effective search space used: 2561275864
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)