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= psy939
(67 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3Q9T|A Chain A, Crystal Structure Analysis Of Formate Oxidase
pdb|3Q9T|B Chain B, Crystal Structure Analysis Of Formate Oxidase
pdb|3Q9T|C Chain C, Crystal Structure Analysis Of Formate Oxidase
Length = 577
Score = 40.8 bits (94), Expect = 2e-04, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 27/46 (58%)
Query: 7 GKVMGGTTVLNGLMYCRGDSSDYDEYEKLGATGWGYKNVLPYFLKS 52
GK +GG++ LN + G + +D++E+ G W + ++PY KS
Sbjct: 87 GKTLGGSSSLNYFTWVPGHKATFDQWEEFGGKEWTWDPLVPYLRKS 132
>pdb|1GPE|A Chain A, Glucose Oxidase From Penicillium Amagasakiense
pdb|1GPE|B Chain B, Glucose Oxidase From Penicillium Amagasakiense
Length = 587
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 4 IFDGKVMGGTTVLNGLMYCRGDSSDYDEYEKL-GATGWGYKNVLPYFLKSE 53
I GK +GG+T++NG + R D D +EK+ G GW + N+ Y K+E
Sbjct: 98 IKAGKGLGGSTLINGDSWTRPDKVQIDSWEKVFGMEGWNWDNMFEYMKKAE 148
>pdb|3FIM|B Chain B, Crystal Structure Of Aryl-Alcohol-Oxidase From Pleurotus
Eryingii
Length = 566
Score = 37.0 bits (84), Expect = 0.003, Method: Composition-based stats.
Identities = 14/48 (29%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 7 GKVMGGTTVLNGLMYCRGDSSDYDEYEKL-GATGWGYKNVLPYFLKSE 53
G+++GG++ ++ ++ RG + D+D Y + G GW + N+ + K+E
Sbjct: 81 GRMLGGSSSVHYMVMMRGSTEDFDRYAAVTGDEGWNWDNIQQFVRKNE 128
>pdb|3T37|A Chain A, Crystal Structure Of Pyridoxine 4-Oxidase From Mesorbium
Loti
Length = 526
Score = 36.6 bits (83), Expect = 0.003, Method: Composition-based stats.
Identities = 15/44 (34%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 7 GKVMGGTTVLNGLMYCRGDSSDYDEY-EKLGATGWGYKNVLPYF 49
G+++GG++ L+ + Y RG SD+ + + G WG+ +LP F
Sbjct: 94 GRLIGGSSCLHAMGYMRGHPSDFQAWVDASGDRRWGWDELLPVF 137
>pdb|1CF3|A Chain A, Glucose Oxidase From Apergillus Niger
pdb|1GAL|A Chain A, Crystal Structure Of Glucose Oxidase From Aspergillus
Niger: Refined At 2.3 Angstroms Resolution
pdb|3QVP|A Chain A, Crystal Structure Of Glucose Oxidase For Space Group C2221
At 1.2 A Resolution
pdb|3QVR|A Chain A, Crystal Structure Of Glucose Oxidase For Space Group P3121
At 1.3 A Resolution
Length = 583
Score = 35.8 bits (81), Expect = 0.006, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 4 IFDGKVMGGTTVLNGLMYCRGDSSDYDEYEKL-GATGWGYKNVLPYFLKSEHNLQYNYQS 62
I G +GG+T++NG + R + D +E + G GW + NV Y L++E N +
Sbjct: 94 IRSGNGLGGSTLVNGGTWTRPHKAQVDSWETVFGNEGWNWDNVAAYSLQAERARAPNAKQ 153
Query: 63 YSA 65
+A
Sbjct: 154 IAA 156
>pdb|3NNE|A Chain A, Crystal Structure Of Choline Oxidase S101a Mutant
pdb|3NNE|B Chain B, Crystal Structure Of Choline Oxidase S101a Mutant
pdb|3NNE|C Chain C, Crystal Structure Of Choline Oxidase S101a Mutant
pdb|3NNE|D Chain D, Crystal Structure Of Choline Oxidase S101a Mutant
pdb|3NNE|E Chain E, Crystal Structure Of Choline Oxidase S101a Mutant
pdb|3NNE|F Chain F, Crystal Structure Of Choline Oxidase S101a Mutant
pdb|3NNE|G Chain G, Crystal Structure Of Choline Oxidase S101a Mutant
pdb|3NNE|H Chain H, Crystal Structure Of Choline Oxidase S101a Mutant
Length = 546
Score = 35.4 bits (80), Expect = 0.008, Method: Composition-based stats.
Identities = 19/50 (38%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 7 GKVMGGTTVLNGLMYCRGDSSDYDEYE-KLGATGWGYKNVLPYFLKSEHN 55
KVMGG + N + D DE+E K GATGW + P + + E N
Sbjct: 90 AKVMGGCSSHNACIAFWAPREDLDEWEAKYGATGWNAEAAWPLYKRLETN 139
>pdb|3LJP|A Chain A, Crystal Structure Of Choline Oxidase V464a Mutant
pdb|3LJP|B Chain B, Crystal Structure Of Choline Oxidase V464a Mutant
Length = 546
Score = 35.0 bits (79), Expect = 0.009, Method: Composition-based stats.
Identities = 19/50 (38%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 7 GKVMGGTTVLNGLMYCRGDSSDYDEYE-KLGATGWGYKNVLPYFLKSEHN 55
KVMGG + N + D DE+E K GATGW + P + + E N
Sbjct: 90 AKVMGGCSSHNSCIAFWAPREDLDEWEAKYGATGWNAEAAWPLYKRLETN 139
>pdb|2JBV|A Chain A, Crystal Structure Of Choline Oxidase Reveals Insights Into
The Catalytic Mechanism
pdb|2JBV|B Chain B, Crystal Structure Of Choline Oxidase Reveals Insights Into
The Catalytic Mechanism
Length = 546
Score = 35.0 bits (79), Expect = 0.009, Method: Composition-based stats.
Identities = 19/50 (38%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 7 GKVMGGTTVLNGLMYCRGDSSDYDEYE-KLGATGWGYKNVLPYFLKSEHN 55
KVMGG + N + D DE+E K GATGW + P + + E N
Sbjct: 90 AKVMGGCSSHNSCIAFWAPREDLDEWEAKYGATGWNAEAAWPLYKRLETN 139
>pdb|1WCQ|A Chain A, Mutagenesis Of The Nucleophilic Tyrosine In A Bacterial
Sialidase To Phenylalanine.
pdb|1WCQ|B Chain B, Mutagenesis Of The Nucleophilic Tyrosine In A Bacterial
Sialidase To Phenylalanine.
pdb|1WCQ|C Chain C, Mutagenesis Of The Nucleophilic Tyrosine In A Bacterial
Sialidase To Phenylalanine
Length = 601
Score = 28.5 bits (62), Expect = 0.94, Method: Composition-based stats.
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 6/37 (16%)
Query: 10 MGGTTVLNGLMYCRGDSS------DYDEYEKLGATGW 40
+GGT ++GL Y R +S DY+ Y L T W
Sbjct: 512 LGGTHTISGLQYTRRQNSANEQVADYEIYTSLNGTTW 548
>pdb|2BER|A Chain A, Y370g Active Site Mutant Of The Sialidase From
Micromonospora Viridifaciens In Complex With Beta-Neu5ac
(Sialic Acid)
Length = 601
Score = 28.5 bits (62), Expect = 0.95, Method: Composition-based stats.
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 6/37 (16%)
Query: 10 MGGTTVLNGLMYCRGDSS------DYDEYEKLGATGW 40
+GGT ++GL Y R +S DY+ Y L T W
Sbjct: 512 LGGTHTISGLQYTRRQNSANEQVADYEIYTSLNGTTW 548
>pdb|1EUT|A Chain A, Sialidase, Large 68kd Form, Complexed With Galactose
pdb|1EUU|A Chain A, Sialidase Or Neuraminidase, Large 68kd Form
Length = 605
Score = 28.5 bits (62), Expect = 0.95, Method: Composition-based stats.
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 6/37 (16%)
Query: 10 MGGTTVLNGLMYCRGDSS------DYDEYEKLGATGW 40
+GGT ++GL Y R +S DY+ Y L T W
Sbjct: 516 LGGTHTISGLQYTRRQNSANEQVADYEIYTSLNGTTW 552
>pdb|1JU2|A Chain A, Crystal Structure Of The Hydroxynitrile Lyase From Almond
pdb|1JU2|B Chain B, Crystal Structure Of The Hydroxynitrile Lyase From Almond
Length = 536
Score = 28.5 bits (62), Expect = 0.98, Method: Composition-based stats.
Identities = 10/23 (43%), Positives = 18/23 (78%)
Query: 7 GKVMGGTTVLNGLMYCRGDSSDY 29
G+V+GGT+++N +Y R ++S Y
Sbjct: 100 GRVLGGTSIINAGVYARANTSIY 122
>pdb|2BZD|A Chain A, Galactose Recognition By The Carbohydrate-Binding Module
Of A Bacterial Sialidase.
pdb|2BZD|B Chain B, Galactose Recognition By The Carbohydrate-Binding Module
Of A Bacterial Sialidase.
pdb|2BZD|C Chain C, Galactose Recognition By The Carbohydrate-Binding Module
Of A Bacterial Sialidase
Length = 601
Score = 28.5 bits (62), Expect = 1.0, Method: Composition-based stats.
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 6/37 (16%)
Query: 10 MGGTTVLNGLMYCRGDSS------DYDEYEKLGATGW 40
+GGT ++GL Y R +S DY+ Y L T W
Sbjct: 512 LGGTHTISGLQYTRRQNSANEQVADYEIYTSLNGTTW 548
>pdb|1W8N|A Chain A, Contribution Of The Active Site Aspartic Acid To Catalysis
In The Bacterial Neuraminidase From Micromonospora
Viridifaciens.
pdb|1W8O|A Chain A, Contribution Of The Active Site Aspartic Acid To Catalysis
In The Bacterial Neuraminidase From Micromonospora
Viridifaciens
Length = 601
Score = 28.5 bits (62), Expect = 1.0, Method: Composition-based stats.
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 6/37 (16%)
Query: 10 MGGTTVLNGLMYCRGDSS------DYDEYEKLGATGW 40
+GGT ++GL Y R +S DY+ Y L T W
Sbjct: 512 LGGTHTISGLQYTRRQNSANEQVADYEIYTSLNGTTW 548
>pdb|3GDN|A Chain A, Almond Hydroxynitrile Lyase In Complex With Benzaldehyde
pdb|3GDN|B Chain B, Almond Hydroxynitrile Lyase In Complex With Benzaldehyde
pdb|3GDP|A Chain A, Hydroxynitrile Lyase From Almond, Monoclinic Crystal Form
pdb|3GDP|B Chain B, Hydroxynitrile Lyase From Almond, Monoclinic Crystal Form
Length = 521
Score = 28.5 bits (62), Expect = 1.1, Method: Composition-based stats.
Identities = 10/23 (43%), Positives = 18/23 (78%)
Query: 7 GKVMGGTTVLNGLMYCRGDSSDY 29
G+V+GGT+++N +Y R ++S Y
Sbjct: 100 GRVLGGTSIINAGVYARANTSIY 122
>pdb|2VSF|A Chain A, Structure Of Xpd From Thermoplasma Acidophilum
Length = 602
Score = 26.6 bits (57), Expect = 4.1, Method: Composition-based stats.
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 3/40 (7%)
Query: 15 VLNGLMYCRGDS---SDYDEYEKLGATGWGYKNVLPYFLK 51
+L GL + R D+ S +D YE+ GW Y V P +K
Sbjct: 503 ILAGLPFPRPDAINRSLFDYYERKYGKGWEYSVVYPTAIK 542
>pdb|1KDG|A Chain A, Crystal Structure Of The Flavin Domain Of Cellobiose
Dehydrogenase
pdb|1KDG|B Chain B, Crystal Structure Of The Flavin Domain Of Cellobiose
Dehydrogenase
Length = 546
Score = 26.2 bits (56), Expect = 4.3, Method: Composition-based stats.
Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 7/49 (14%)
Query: 2 VKIFDGKVMGGTTVLNGLMYCRGDSSDYDEYEKLGATGW--GYKNVLPY 48
+ +F G ++GG T +NG +Y + D+ + GW + N PY
Sbjct: 85 ITVFAGCLVGGGTSVNGALYWYPNDGDFSS-----SVGWPSSWTNHAPY 128
>pdb|4A15|A Chain A, Crystal Structure Of An Xpd Dna Complex
Length = 620
Score = 26.2 bits (56), Expect = 4.6, Method: Composition-based stats.
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 3/40 (7%)
Query: 15 VLNGLMYCRGDS---SDYDEYEKLGATGWGYKNVLPYFLK 51
+L GL + R D+ S +D YE+ GW Y V P +K
Sbjct: 521 ILAGLPFPRPDAINRSLFDYYERKYGKGWEYSVVYPTAIK 560
>pdb|1NAA|A Chain A, Cellobiose Dehydrogenase Flavoprotein Fragment In Complex
With Cellobionolactam
pdb|1NAA|B Chain B, Cellobiose Dehydrogenase Flavoprotein Fragment In Complex
With Cellobionolactam
Length = 541
Score = 26.2 bits (56), Expect = 4.8, Method: Composition-based stats.
Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 7/49 (14%)
Query: 2 VKIFDGKVMGGTTVLNGLMYCRGDSSDYDEYEKLGATGW--GYKNVLPY 48
+ +F G ++GG T +NG +Y + D+ + GW + N PY
Sbjct: 80 ITVFAGCLVGGGTSVNGALYWYPNDGDFSS-----SVGWPSSWTNHAPY 123
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
0.316 0.136 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,274,708
Number of Sequences: 62578
Number of extensions: 79375
Number of successful extensions: 315
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 299
Number of HSP's gapped (non-prelim): 25
length of query: 67
length of database: 14,973,337
effective HSP length: 38
effective length of query: 29
effective length of database: 12,595,373
effective search space: 365265817
effective search space used: 365265817
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)