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= psy16200
(183 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1H7X|A Chain A, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex Of A Mutant Enzyme (C671a), Nadph And 5-
Fluorouracil
pdb|1H7X|B Chain B, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex Of A Mutant Enzyme (C671a), Nadph And 5-
Fluorouracil
pdb|1H7X|C Chain C, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex Of A Mutant Enzyme (C671a), Nadph And 5-
Fluorouracil
pdb|1H7X|D Chain D, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex Of A Mutant Enzyme (C671a), Nadph And 5-
Fluorouracil
Length = 1025
Score = 210 bits (535), Expect = 3e-55, Method: Compositional matrix adjust.
Identities = 107/176 (60%), Positives = 127/176 (72%), Gaps = 2/176 (1%)
Query: 6 LRKDGYTAIFIGIGKPNANVIPIFQGLTEEMGFYTSKTFLPRVATXXXXXXXXXXXXXXX 65
L+++GY A FIGIG P IFQGLT++ GFYTSK FLP VA
Sbjct: 271 LKEEGYKAAFIGIGLPEPKTDDIFQGLTQDQGFYTSKDFLPLVA--KSSKAGMCACHSPL 328
Query: 66 PILKGTVIVLGAGDTAFDCATSALRCGANKVLVVFRKGCTNIRAVPEEVQLAWEEKCEFL 125
P ++G VIVLGAGDTAFDCATSALRCGA +V +VFRKG NIRAVPEEV+LA EEKCEFL
Sbjct: 329 PSIRGAVIVLGAGDTAFDCATSALRCGARRVFLVFRKGFVNIRAVPEEVELAKEEKCEFL 388
Query: 126 PFMSPVQVDVKDNKIAGMQFNRTEQNEKGEWVEDEEQRIKLKANYIISAFGSTLLD 181
PF+SP +V VK +I +QF RTEQ+E G+W EDE+Q + LKA+ +ISAFGS L D
Sbjct: 389 PFLSPRKVIVKGGRIVAVQFVRTEQDETGKWNEDEDQIVHLKADVVISAFGSVLRD 444
>pdb|1H7W|A Chain A, Dihydropyrimidine Dehydrogenase (Dpd) From Pig
pdb|1H7W|B Chain B, Dihydropyrimidine Dehydrogenase (Dpd) From Pig
pdb|1H7W|C Chain C, Dihydropyrimidine Dehydrogenase (Dpd) From Pig
pdb|1H7W|D Chain D, Dihydropyrimidine Dehydrogenase (Dpd) From Pig
pdb|1GT8|A Chain A, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex With Nadph And Uracil-4-Acetic Acid
pdb|1GT8|B Chain B, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex With Nadph And Uracil-4-Acetic Acid
pdb|1GT8|C Chain C, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex With Nadph And Uracil-4-Acetic Acid
pdb|1GT8|D Chain D, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex With Nadph And Uracil-4-Acetic Acid
pdb|1GTE|A Chain A, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary
Complex With 5-Iodouracil
pdb|1GTE|B Chain B, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary
Complex With 5-Iodouracil
pdb|1GTE|C Chain C, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary
Complex With 5-Iodouracil
pdb|1GTE|D Chain D, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary
Complex With 5-Iodouracil
pdb|1GTH|A Chain A, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex With Nadph And 5-Iodouracil
pdb|1GTH|B Chain B, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex With Nadph And 5-Iodouracil
pdb|1GTH|C Chain C, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex With Nadph And 5-Iodouracil
pdb|1GTH|D Chain D, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex With Nadph And 5-Iodouracil
Length = 1025
Score = 210 bits (535), Expect = 3e-55, Method: Compositional matrix adjust.
Identities = 107/176 (60%), Positives = 127/176 (72%), Gaps = 2/176 (1%)
Query: 6 LRKDGYTAIFIGIGKPNANVIPIFQGLTEEMGFYTSKTFLPRVATXXXXXXXXXXXXXXX 65
L+++GY A FIGIG P IFQGLT++ GFYTSK FLP VA
Sbjct: 271 LKEEGYKAAFIGIGLPEPKTDDIFQGLTQDQGFYTSKDFLPLVA--KSSKAGMCACHSPL 328
Query: 66 PILKGTVIVLGAGDTAFDCATSALRCGANKVLVVFRKGCTNIRAVPEEVQLAWEEKCEFL 125
P ++G VIVLGAGDTAFDCATSALRCGA +V +VFRKG NIRAVPEEV+LA EEKCEFL
Sbjct: 329 PSIRGAVIVLGAGDTAFDCATSALRCGARRVFLVFRKGFVNIRAVPEEVELAKEEKCEFL 388
Query: 126 PFMSPVQVDVKDNKIAGMQFNRTEQNEKGEWVEDEEQRIKLKANYIISAFGSTLLD 181
PF+SP +V VK +I +QF RTEQ+E G+W EDE+Q + LKA+ +ISAFGS L D
Sbjct: 389 PFLSPRKVIVKGGRIVAVQFVRTEQDETGKWNEDEDQIVHLKADVVISAFGSVLRD 444
>pdb|2VDC|G Chain G, The 9.5 A Resolution Structure Of Glutamate Synthase From
Cryo-Electron Microscopy And Its Oligomerization
Behavior In Solution: Functional Implications.
pdb|2VDC|H Chain H, The 9.5 A Resolution Structure Of Glutamate Synthase From
Cryo-Electron Microscopy And Its Oligomerization
Behavior In Solution: Functional Implications.
pdb|2VDC|I Chain I, The 9.5 A Resolution Structure Of Glutamate Synthase From
Cryo-Electron Microscopy And Its Oligomerization
Behavior In Solution: Functional Implications.
pdb|2VDC|J Chain J, The 9.5 A Resolution Structure Of Glutamate Synthase From
Cryo-Electron Microscopy And Its Oligomerization
Behavior In Solution: Functional Implications.
pdb|2VDC|K Chain K, The 9.5 A Resolution Structure Of Glutamate Synthase From
Cryo-Electron Microscopy And Its Oligomerization
Behavior In Solution: Functional Implications.
pdb|2VDC|L Chain L, The 9.5 A Resolution Structure Of Glutamate Synthase From
Cryo-Electron Microscopy And Its Oligomerization
Behavior In Solution: Functional Implications
Length = 456
Score = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/59 (42%), Positives = 34/59 (57%)
Query: 72 VIVLGAGDTAFDCATSALRCGANKVLVVFRKGCTNIRAVPEEVQLAWEEKCEFLPFMSP 130
V+VLG GDTA DC +A+R GA V ++R+ N+ EV A EE EF+ +P
Sbjct: 267 VVVLGGGDTAMDCVRTAIRQGATSVKCLYRRDRKNMPGSQREVAHAEEEGVEFIWQAAP 325
>pdb|1QO8|A Chain A, The Structure Of The Open Conformation Of A
Flavocytochrome C3 Fumarate Reductase
pdb|1QO8|D Chain D, The Structure Of The Open Conformation Of A
Flavocytochrome C3 Fumarate Reductase
Length = 566
Score = 29.3 bits (64), Expect = 1.2, Method: Composition-based stats.
Identities = 12/27 (44%), Positives = 19/27 (70%)
Query: 72 VIVLGAGDTAFDCATSALRCGANKVLV 98
V+V+GAG F+ + +A + GAN +LV
Sbjct: 124 VLVVGAGSAGFNASLAAKKAGANVILV 150
>pdb|2XXB|A Chain A, Penta-Mutant Of Thermus Thermophilus Lactate
Dehydrogenase, Complex With Amp
pdb|2XXB|B Chain B, Penta-Mutant Of Thermus Thermophilus Lactate
Dehydrogenase, Complex With Amp
pdb|2XXJ|A Chain A, Penta Mutant Of Lactate Dehydrogenase From Thermus
Thermophilus, Ternary Complex
pdb|2XXJ|B Chain B, Penta Mutant Of Lactate Dehydrogenase From Thermus
Thermophilus, Ternary Complex
pdb|2XXJ|C Chain C, Penta Mutant Of Lactate Dehydrogenase From Thermus
Thermophilus, Ternary Complex
pdb|2XXJ|D Chain D, Penta Mutant Of Lactate Dehydrogenase From Thermus
Thermophilus, Ternary Complex
pdb|3ZZN|A Chain A, 5-Mutant (R79w, R151a, E279a, E299a,E313a)
Lactate-Dehydrogenase From Thermus Thermophillus
pdb|3ZZN|B Chain B, 5-Mutant (R79w, R151a, E279a, E299a,E313a)
Lactate-Dehydrogenase From Thermus Thermophillus
pdb|3ZZN|C Chain C, 5-Mutant (R79w, R151a, E279a, E299a,E313a)
Lactate-Dehydrogenase From Thermus Thermophillus
pdb|3ZZN|D Chain D, 5-Mutant (R79w, R151a, E279a, E299a,E313a)
Lactate-Dehydrogenase From Thermus Thermophillus
Length = 310
Score = 28.1 bits (61), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 9 DGYTAIFIGIGKPNANVIPIFQGLTEEMGFYTSKTFLPRVA 49
+G A + GIG A ++ LT+E G YT F P VA
Sbjct: 222 EGKGATYYGIGAGLARLVRAI--LTDEKGVYTVSAFTPEVA 260
>pdb|3URH|A Chain A, Crystal Structure Of A Dihydrolipoamide Dehydrogenase From
Sinorhizobium Meliloti 1021
pdb|3URH|B Chain B, Crystal Structure Of A Dihydrolipoamide Dehydrogenase From
Sinorhizobium Meliloti 1021
Length = 491
Score = 26.6 bits (57), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 72 VIVLGAGDTAFDCATSALRCGANKVLVVFRKG-----CTNIRAVPEEVQLAWEE 120
+IV+G+G + CA A + G KV VV ++ C N+ +P + L E
Sbjct: 28 LIVIGSGPGGYVCAIKAAQLGX-KVAVVEKRSTYGGTCLNVGCIPSKALLHASE 80
>pdb|2E37|A Chain A, Structure Of Tt0471 Protein From Thermus Thermophilus
pdb|2E37|B Chain B, Structure Of Tt0471 Protein From Thermus Thermophilus
pdb|2E37|C Chain C, Structure Of Tt0471 Protein From Thermus Thermophilus
pdb|2E37|D Chain D, Structure Of Tt0471 Protein From Thermus Thermophilus
pdb|2E37|E Chain E, Structure Of Tt0471 Protein From Thermus Thermophilus
pdb|2E37|F Chain F, Structure Of Tt0471 Protein From Thermus Thermophilus
pdb|2E37|G Chain G, Structure Of Tt0471 Protein From Thermus Thermophilus
pdb|2E37|H Chain H, Structure Of Tt0471 Protein From Thermus Thermophilus
Length = 310
Score = 26.6 bits (57), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 2/40 (5%)
Query: 9 DGYTAIFIGIGKPNANVIPIFQGLTEEMGFYTSKTFLPRV 48
+G A + GIG A ++ LT+E G YT F P V
Sbjct: 222 EGKGATYYGIGAGLARLVRAI--LTDEKGVYTVSAFTPEV 259
>pdb|4A73|A Chain A, Single Point Mutant Of Thermus Thermophilus Lactate
Dehydrogenase
pdb|4A73|B Chain B, Single Point Mutant Of Thermus Thermophilus Lactate
Dehydrogenase
pdb|4A73|C Chain C, Single Point Mutant Of Thermus Thermophilus Lactate
Dehydrogenase
pdb|4A73|D Chain D, Single Point Mutant Of Thermus Thermophilus Lactate
Dehydrogenase
Length = 310
Score = 26.6 bits (57), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 2/40 (5%)
Query: 9 DGYTAIFIGIGKPNANVIPIFQGLTEEMGFYTSKTFLPRV 48
+G A + GIG A ++ LT+E G YT F P V
Sbjct: 222 EGKGATYYGIGAGLARLVRAI--LTDEKGVYTVSAFTPEV 259
>pdb|2V6M|A Chain A, Crystal Structure Of Lactate Dehydrogenase From Thermus
Thermophilus Hb8 (Apo Form)
pdb|2V6M|B Chain B, Crystal Structure Of Lactate Dehydrogenase From Thermus
Thermophilus Hb8 (Apo Form)
pdb|2V6M|C Chain C, Crystal Structure Of Lactate Dehydrogenase From Thermus
Thermophilus Hb8 (Apo Form)
pdb|2V6M|D Chain D, Crystal Structure Of Lactate Dehydrogenase From Thermus
Thermophilus Hb8 (Apo Form)
pdb|2V7P|A Chain A, Crystal Structure Of Lactate Dehydrogenase From Thermus
Thermophilus Hb8 (Holo Form)
pdb|2V7P|B Chain B, Crystal Structure Of Lactate Dehydrogenase From Thermus
Thermophilus Hb8 (Holo Form)
pdb|2V7P|C Chain C, Crystal Structure Of Lactate Dehydrogenase From Thermus
Thermophilus Hb8 (Holo Form)
pdb|2V7P|D Chain D, Crystal Structure Of Lactate Dehydrogenase From Thermus
Thermophilus Hb8 (Holo Form)
Length = 310
Score = 26.6 bits (57), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 2/40 (5%)
Query: 9 DGYTAIFIGIGKPNANVIPIFQGLTEEMGFYTSKTFLPRV 48
+G A + GIG A ++ LT+E G YT F P V
Sbjct: 222 EGKGATYYGIGAGLARLVRAI--LTDEKGVYTVSAFTPEV 259
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 0.137 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,938,507
Number of Sequences: 62578
Number of extensions: 176592
Number of successful extensions: 505
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 497
Number of HSP's gapped (non-prelim): 13
length of query: 183
length of database: 14,973,337
effective HSP length: 93
effective length of query: 90
effective length of database: 9,153,583
effective search space: 823822470
effective search space used: 823822470
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: 48 (23.1 bits)