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= psy969
(106 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1JCL|A Chain A, Observation Of Covalent Intermediates In An Enzyme
Mechanism At Atomic Resolution
pdb|1JCL|B Chain B, Observation Of Covalent Intermediates In An Enzyme
Mechanism At Atomic Resolution
pdb|1P1X|A Chain A, Comparison Of Class I Aldolase Binding Site Architecture
Based On The Crystal Structure Of
2-Deoxyribose-5-Phosphate Aldolase Determined At 0.99
Angstrom Resolution
pdb|1P1X|B Chain B, Comparison Of Class I Aldolase Binding Site Architecture
Based On The Crystal Structure Of
2-Deoxyribose-5-Phosphate Aldolase Determined At 0.99
Angstrom Resolution
Length = 260
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 25/41 (60%)
Query: 51 KKIGLKPAGGISTFEDSVRWIYLVLIMLGPDWLNKDLFRIG 91
K +G KPAGG+ T ED+ +++ + + G DW + +R G
Sbjct: 197 KTVGFKPAGGVRTAEDAQKYLAIADELFGADWADARHYRFG 237
>pdb|1KTN|A Chain A, Structural Genomics, Protein Ec1535
pdb|1KTN|B Chain B, Structural Genomics, Protein Ec1535
Length = 250
Score = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 25/41 (60%)
Query: 51 KKIGLKPAGGISTFEDSVRWIYLVLIMLGPDWLNKDLFRIG 91
K +G KPAGG+ T ED+ +++ + + G DW + +R G
Sbjct: 196 KTVGFKPAGGVRTAEDAQKYLAIADELFGADWADARHYRFG 236
>pdb|1JCJ|A Chain A, Observation Of Covalent Intermediates In An Enzyme
Mechanism At Atomic Resolution
pdb|1JCJ|B Chain B, Observation Of Covalent Intermediates In An Enzyme
Mechanism At Atomic Resolution
Length = 260
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 24/41 (58%)
Query: 51 KKIGLKPAGGISTFEDSVRWIYLVLIMLGPDWLNKDLFRIG 91
K +G PAGG+ T ED+ +++ + + G DW + +R G
Sbjct: 197 KTVGFLPAGGVRTAEDAQKYLAIADELFGADWADARHYRFG 237
>pdb|2A4A|A Chain A, Deoxyribose-Phosphate Aldolase From P. Yoelii
pdb|2A4A|B Chain B, Deoxyribose-Phosphate Aldolase From P. Yoelii
Length = 281
Score = 35.0 bits (79), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 24/59 (40%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 41 AIKHFHK---LSGKKIGLKPAGGISTFEDSVRWIYLVLIMLGPDWLNKDLFRIGASSLL 96
AIK + K KIGLK +GGIS + +I L L + D FRIG+SSL+
Sbjct: 211 AIKEYIKNNPEKNNKIGLKVSGGISDLNTASHYILLARRFLSSLACHPDNFRIGSSSLV 269
>pdb|3NQ8|A Chain A, Optimization Of The In Silico Designed Kemp Eliminase Ke70
By Computational Design And Directed Evolution R4 85A
Length = 269
Score = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 23/41 (56%)
Query: 53 IGLKPAGGISTFEDSVRWIYLVLIMLGPDWLNKDLFRIGAS 93
+G P GG+ T ED+ +++ + + G DW + + GAS
Sbjct: 200 VGFIPVGGVRTAEDAQKYLAIADELFGADWADARHYAFGAS 240
>pdb|3NPU|A Chain A, Optimization Of The In Silico Designed Kemp Eliminase Ke70
By Computational Design And Directed Evolution
pdb|3NPU|B Chain B, Optimization Of The In Silico Designed Kemp Eliminase Ke70
By Computational Design And Directed Evolution
pdb|3NPV|B Chain B, Optimization Of The In Silico Designed Kemp Eliminase Ke70
By Computational Design And Directed Evolution
pdb|3NPV|A Chain A, Optimization Of The In Silico Designed Kemp Eliminase Ke70
By Computational Design And Directed Evolution
Length = 263
Score = 34.7 bits (78), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 23/41 (56%)
Query: 51 KKIGLKPAGGISTFEDSVRWIYLVLIMLGPDWLNKDLFRIG 91
K +G PAGG+ T ED+ +++ + + G DW + + G
Sbjct: 196 KTVGFIPAGGVRTAEDAQKYLAIADELFGADWADARHYAFG 236
>pdb|3NQV|A Chain A, Optimization Of The In Silico Designed Kemp Eliminase Ke70
By Computational Design And Directed Evolution R5 74A
Length = 272
Score = 33.5 bits (75), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 51 KKIGLKPAGGISTFEDSVRWIYLVLIMLGPDWLNKDLFRIG 91
K +G P GG+ T ED+ +++ + + G DW + + G
Sbjct: 198 KTVGFIPVGGVRTAEDAQKYLAIADELFGADWADSRHYAFG 238
>pdb|3NR0|A Chain A, Optimization Of The In Silico Designed Kemp Eliminase Ke70
By Computational Design And Directed Evolution R6 610A
pdb|3NR0|B Chain B, Optimization Of The In Silico Designed Kemp Eliminase Ke70
By Computational Design And Directed Evolution R6 610A
Length = 271
Score = 33.5 bits (75), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 51 KKIGLKPAGGISTFEDSVRWIYLVLIMLGPDWLNKDLFRIG 91
K +G P GG+ T ED+ +++ + + G DW + + G
Sbjct: 197 KTVGFIPVGGVRTAEDAQKYLAIADELFGADWADARHYAFG 237
>pdb|3Q2D|A Chain A, Optimization Of The In Silico Designed Kemp Eliminase Ke70
By Computational Design And Directed Evolution
pdb|3Q2D|B Chain B, Optimization Of The In Silico Designed Kemp Eliminase Ke70
By Computational Design And Directed Evolution
Length = 272
Score = 33.1 bits (74), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 51 KKIGLKPAGGISTFEDSVRWIYLVLIMLGPDWLNKDLFRIG 91
K +G P GG+ T ED+ +++ + + G DW + + G
Sbjct: 198 KTVGFIPVGGVRTAEDAQKYLAIADELFGADWADARHYAFG 238
>pdb|3NPW|A Chain A, In Silico Designed Of An Improved Kemp Eliminase Ke70
Mutant By Computational Design And Directed Evolution
pdb|3NPW|B Chain B, In Silico Designed Of An Improved Kemp Eliminase Ke70
Mutant By Computational Design And Directed Evolution
Length = 264
Score = 33.1 bits (74), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 23/41 (56%)
Query: 51 KKIGLKPAGGISTFEDSVRWIYLVLIMLGPDWLNKDLFRIG 91
K +G PAGG+ T E++ +++ + + G DW + + G
Sbjct: 197 KTVGFIPAGGVRTAEEAQKYLAIADELFGADWADARHYAFG 237
>pdb|3NQ2|A Chain A, Optimization Of The In Silico Designed Kemp Eliminase Ke70
By Computational Design And Directed Evolution R2 35G
pdb|3NQ2|B Chain B, Optimization Of The In Silico Designed Kemp Eliminase Ke70
By Computational Design And Directed Evolution R2 35G
Length = 264
Score = 33.1 bits (74), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 51 KKIGLKPAGGISTFEDSVRWIYLVLIMLGPDWLNKDLFRIG 91
K +G P GG+ T ED+ +++ + + G DW + + G
Sbjct: 197 KTVGFIPVGGVRTAEDAQKYLAIADELFGADWADARHYAFG 237
>pdb|3NPX|A Chain A, Optimization Of The In Silico Designed Kemp Eliminase Ke70
By Computational Design And Directed Evolution
pdb|3NPX|B Chain B, Optimization Of The In Silico Designed Kemp Eliminase Ke70
By Computational Design And Directed Evolution
Length = 264
Score = 33.1 bits (74), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 23/41 (56%)
Query: 51 KKIGLKPAGGISTFEDSVRWIYLVLIMLGPDWLNKDLFRIG 91
K +G PAGG+ T E++ +++ + + G DW + + G
Sbjct: 197 KTVGFIPAGGVRTAEEAQKYLAIADELFGADWADARHYAFG 237
>pdb|3R12|A Chain A, Crystal Structure Of A Deoxyribose-Phosphate Aldolase
(Tm_1559) From Thermotoga Maritima At 1.75 A Resolution
pdb|3R12|B Chain B, Crystal Structure Of A Deoxyribose-Phosphate Aldolase
(Tm_1559) From Thermotoga Maritima At 1.75 A Resolution
pdb|3R13|A Chain A, Crystal Structure Of A Deoxyribose-Phosphate Aldolase
(Tm_1559) From Thermotoga Maritima At 1.83 A Resolution
pdb|3R13|B Chain B, Crystal Structure Of A Deoxyribose-Phosphate Aldolase
(Tm_1559) From Thermotoga Maritima At 1.83 A Resolution
Length = 260
Score = 29.6 bits (65), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 25/47 (53%), Gaps = 12/47 (25%)
Query: 48 LSGKKIGLKPAGGISTFEDSVRWIYLVLIMLGPDWLNKDLFRIGASS 94
+ G + G+K +GGI TFED+V+ I G D RIG SS
Sbjct: 212 IVGDEXGVKASGGIRTFEDAVK-----XIXYGAD-------RIGTSS 246
>pdb|3NGJ|A Chain A, Crystal Structure Of A Putative Deoxyribose-Phosphate
Aldolase From Entamoeba Histolytica
pdb|3NGJ|B Chain B, Crystal Structure Of A Putative Deoxyribose-Phosphate
Aldolase From Entamoeba Histolytica
pdb|3NGJ|C Chain C, Crystal Structure Of A Putative Deoxyribose-Phosphate
Aldolase From Entamoeba Histolytica
pdb|3NGJ|D Chain D, Crystal Structure Of A Putative Deoxyribose-Phosphate
Aldolase From Entamoeba Histolytica
Length = 239
Score = 28.9 bits (63), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 29/61 (47%), Gaps = 15/61 (24%)
Query: 42 IKHFHKLSGKKIGLKPAGGISTFEDSVRWIYLVLIMLGPDWLNKDLFRIGAS---SLLNN 98
+K G K +K AGGI TF+D+++ I N RIGAS ++LN
Sbjct: 190 VKLMKDTVGDKALVKAAGGIRTFDDAMKMI------------NNGASRIGASAGIAILNG 237
Query: 99 I 99
I
Sbjct: 238 I 238
>pdb|1AY0|A Chain A, Identification Of Catalytically Important Residues In
Yeast Transketolase
pdb|1AY0|B Chain B, Identification Of Catalytically Important Residues In
Yeast Transketolase
Length = 680
Score = 26.6 bits (57), Expect = 3.7, Method: Composition-based stats.
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 10/55 (18%)
Query: 50 GKKIGLKPAGGISTFEDSVRWIYLVLIMLGPDWLNKDLFRIG---ASSLLNNILQ 101
G +G+ PA V W + + PDW+N+D F + A +LL ++L
Sbjct: 32 GAPLGMAPAA-------HVLWSQMRMNPTNPDWINRDRFVLSNGHAVALLYSMLH 79
>pdb|1TRK|A Chain A, Refined Structure Of Transketolase From Saccharomyces
Cerevisiae At 2.0 Angstroms Resolution
pdb|1TRK|B Chain B, Refined Structure Of Transketolase From Saccharomyces
Cerevisiae At 2.0 Angstroms Resolution
pdb|1NGS|A Chain A, Complex Of Transketolase With Thiamin Diphosphate, Ca2+
And Acceptor Substrate Erythrose-4-phosphate
pdb|1NGS|B Chain B, Complex Of Transketolase With Thiamin Diphosphate, Ca2+
And Acceptor Substrate Erythrose-4-phosphate
pdb|1GPU|A Chain A, Transketolase Complex With Reaction Intermediate
pdb|1GPU|B Chain B, Transketolase Complex With Reaction Intermediate
Length = 680
Score = 26.6 bits (57), Expect = 3.9, Method: Composition-based stats.
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 10/55 (18%)
Query: 50 GKKIGLKPAGGISTFEDSVRWIYLVLIMLGPDWLNKDLFRIG---ASSLLNNILQ 101
G +G+ PA V W + + PDW+N+D F + A +LL ++L
Sbjct: 32 GAPLGMAPAA-------HVLWSQMRMNPTNPDWINRDRFVLSNGHAVALLYSMLH 79
>pdb|1TKA|A Chain A, Specificity Of Coenzyme Binding In Thiamin Diphosphate
Dependent Enzymes: Crystal Structures Of Yeast
Transketolase In Complex With Analogs Of Thiamin
Diphosphate
pdb|1TKA|B Chain B, Specificity Of Coenzyme Binding In Thiamin Diphosphate
Dependent Enzymes: Crystal Structures Of Yeast
Transketolase In Complex With Analogs Of Thiamin
Diphosphate
pdb|1TKB|A Chain A, Specificity Of Coenzyme Binding In Thiamin Diphosphate
Dependent Enzymes: Crystal Structures Of Yeast
Transketolase In Complex With Analogs Of Thiamin
Diphosphate
pdb|1TKB|B Chain B, Specificity Of Coenzyme Binding In Thiamin Diphosphate
Dependent Enzymes: Crystal Structures Of Yeast
Transketolase In Complex With Analogs Of Thiamin
Diphosphate
pdb|1TKC|A Chain A, Specificity Of Coenzyme Binding In Thiamin Diphosphate
Dependent Enzymes: Crystal Structures Of Yeast
Transketolase In Complex With Analogs Of Thiamin
Diphosphate
pdb|1TKC|B Chain B, Specificity Of Coenzyme Binding In Thiamin Diphosphate
Dependent Enzymes: Crystal Structures Of Yeast
Transketolase In Complex With Analogs Of Thiamin
Diphosphate
Length = 678
Score = 26.6 bits (57), Expect = 3.9, Method: Composition-based stats.
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 10/55 (18%)
Query: 50 GKKIGLKPAGGISTFEDSVRWIYLVLIMLGPDWLNKDLFRIG---ASSLLNNILQ 101
G +G+ PA V W + + PDW+N+D F + A +LL ++L
Sbjct: 30 GAPLGMAPAA-------HVLWSQMRMNPTNPDWINRDRFVLSNGHAVALLYSMLH 77
>pdb|1VCV|A Chain A, Structure Of 2-Deoxyribose-5-Phosphate Aldolase From
Pyrobaculum Aerophilum
pdb|1VCV|B Chain B, Structure Of 2-Deoxyribose-5-Phosphate Aldolase From
Pyrobaculum Aerophilum
Length = 226
Score = 26.6 bits (57), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 39 CSAIKHFHKLSGKKIGLKPAGGISTFEDS 67
+AI + K G ++G+K AGGI T E +
Sbjct: 171 AAAIARYIKEKGYRLGVKMAGGIRTREQA 199
>pdb|3RL5|A Chain A, Rat Metallophosphodiesterase Mpped2 H67r Mutant
Length = 296
Score = 25.8 bits (55), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 5/37 (13%)
Query: 74 VLIMLGP-----DWLNKDLFRIGASSLLNNILQELEA 105
+L+ GP DW+ K+L R+G LLN + + +
Sbjct: 211 ILMTHGPPLGFRDWVPKELQRVGCVELLNTVQRRVRP 247
>pdb|3RL4|A Chain A, Rat Metallophosphodiesterase Mpped2 G252h Mutant
Length = 296
Score = 25.8 bits (55), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 5/37 (13%)
Query: 74 VLIMLGP-----DWLNKDLFRIGASSLLNNILQELEA 105
+L+ GP DW+ K+L R+G LLN + + +
Sbjct: 211 ILMTHGPPLGFRDWVPKELQRVGCVELLNTVQRRVRP 247
>pdb|3RL3|A Chain A, Rat Metallophosphodiesterase Mpped2
Length = 296
Score = 25.8 bits (55), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 5/37 (13%)
Query: 74 VLIMLGP-----DWLNKDLFRIGASSLLNNILQELEA 105
+L+ GP DW+ K+L R+G LLN + + +
Sbjct: 211 ILMTHGPPLGFRDWVPKELQRVGCVELLNTVQRRVRP 247
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
0.323 0.141 0.443
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,382,086
Number of Sequences: 62578
Number of extensions: 125990
Number of successful extensions: 241
Number of sequences better than 100.0: 49
Number of HSP's better than 100.0 without gapping: 41
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 200
Number of HSP's gapped (non-prelim): 49
length of query: 106
length of database: 14,973,337
effective HSP length: 71
effective length of query: 35
effective length of database: 10,530,299
effective search space: 368560465
effective search space used: 368560465
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)