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= psy7655
(110 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XAF|A Chain A, Crystal Structure Of Lsd1-Corest In Complex With
Para-Bromo- (+)-Cis-2-Phenylcyclopropyl-1-Amine
pdb|2XAG|A Chain A, Crystal Structure Of Lsd1-Corest In Complex With
Para-Bromo- (-)-Trans-2-Phenylcyclopropyl-1-Amine
pdb|2XAH|A Chain A, Crystal Structure Of Lsd1-Corest In Complex With (+)-
Trans-2-Phenylcyclopropyl-1-Amine
pdb|2XAJ|A Chain A, Crystal Structure Of Lsd1-Corest In Complex With
(-)-Trans- 2-Phenylcyclopropyl-1-Amine
pdb|2XAQ|A Chain A, Crystal Structure Of Lsd1-Corest In Complex With A
Tranylcypromine Derivative (Mc2584, 13b)
pdb|2XAS|A Chain A, Crystal Structure Of Lsd1-Corest In Complex With A
Tranylcypromine Derivative (Mc2580, 14e)
Length = 852
Score = 48.1 bits (113), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 34/116 (29%), Positives = 54/116 (46%), Gaps = 14/116 (12%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSI---------R 51
ME+++D + + + G+ +P+P + + W ++ RGSYS
Sbjct: 715 MENISDDVIVGRCLAILKGIFGSS-AVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDY 773
Query: 52 TLTTERLNTSAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRI 107
L + + + GAP P L FAGE T + ATV+GA+ +G REA RI
Sbjct: 774 DLMAQPITPGPSIPGAP----QPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRI 825
>pdb|2V1D|A Chain A, Structural Basis Of Lsd1-Corest Selectivity In Histone H3
Recognition
pdb|2Y48|A Chain A, Crystal Structure Of Lsd1-Corest In Complex With A N-
Terminal Snail Peptide
Length = 730
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 34/116 (29%), Positives = 54/116 (46%), Gaps = 14/116 (12%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSI---------R 51
ME+++D + + + G+ +P+P + + W ++ RGSYS
Sbjct: 593 MENISDDVIVGRCLAILKGIFGSS-AVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDY 651
Query: 52 TLTTERLNTSAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRI 107
L + + + GAP P L FAGE T + ATV+GA+ +G REA RI
Sbjct: 652 DLMAQPITPGPSIPGAP----QPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRI 703
>pdb|2DW4|A Chain A, Crystal Structure Of Human Lsd1 At 2.3 A Resolution
Length = 660
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 34/116 (29%), Positives = 54/116 (46%), Gaps = 14/116 (12%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSI---------R 51
ME+++D + + + G+ +P+P + + W ++ RGSYS
Sbjct: 544 MENISDDVIVGRCLAILKGIFGSS-AVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDY 602
Query: 52 TLTTERLNTSAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRI 107
L + + + GAP P L FAGE T + ATV+GA+ +G REA RI
Sbjct: 603 DLMAQPITPGPSIPGAP----QPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRI 654
>pdb|2IW5|A Chain A, Structural Basis For Corest-dependent Demethylation Of
Nucleosomes By The Human Lsd1 Histone Demethylase
pdb|2UXN|A Chain A, Structural Basis Of Histone Demethylation By Lsd1 Revealed
By Suicide Inactivation
pdb|2UXX|A Chain A, Human Lsd1 Histone Demethylase-Corest In Complex With An
Fad-Tranylcypromine Adduct
Length = 666
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 34/116 (29%), Positives = 54/116 (46%), Gaps = 14/116 (12%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSI---------R 51
ME+++D + + + G+ +P+P + + W ++ RGSYS
Sbjct: 545 MENISDDVIVGRCLAILKGIFGSS-AVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDY 603
Query: 52 TLTTERLNTSAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRI 107
L + + + GAP P L FAGE T + ATV+GA+ +G REA RI
Sbjct: 604 DLMAQPITPGPSIPGAP----QPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRI 655
>pdb|2X0L|A Chain A, Crystal Structure Of A Neuro-Specific Splicing Variant Of
Human Histone Lysine Demethylase Lsd1
Length = 734
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 34/116 (29%), Positives = 54/116 (46%), Gaps = 14/116 (12%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSI---------R 51
ME+++D + + + G+ +P+P + + W ++ RGSYS
Sbjct: 597 MENISDDVIVGRCLAILKGIFGSS-AVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDY 655
Query: 52 TLTTERLNTSAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRI 107
L + + + GAP P L FAGE T + ATV+GA+ +G REA RI
Sbjct: 656 DLMAQPITPGPSIPGAP----QPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRI 707
>pdb|2EJR|A Chain A, Lsd1-Tranylcypromine Complex
pdb|2Z3Y|A Chain A, Crystal Structure Of Lysine-Specific Demethylase1
pdb|2Z5U|A Chain A, Crystal Structure Of Lysine-Specific Histone Demethylase 1
pdb|3ABT|A Chain A, Crystal Structure Of Lsd1 In Complex With Trans-2-
Pentafluorophenylcyclopropylamine
pdb|3ABU|A Chain A, Crystal Structure Of Lsd1 In Complex With A 2-Pcpa
Derivative, S1201
Length = 662
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 34/116 (29%), Positives = 54/116 (46%), Gaps = 14/116 (12%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSI---------R 51
ME+++D + + + G+ +P+P + + W ++ RGSYS
Sbjct: 544 MENISDDVIVGRCLAILKGIFGSS-AVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDY 602
Query: 52 TLTTERLNTSAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRI 107
L + + + GAP P L FAGE T + ATV+GA+ +G REA RI
Sbjct: 603 DLMAQPITPGPSIPGAP----QPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRI 654
>pdb|2HKO|A Chain A, Crystal Structure Of Lsd1
Length = 664
Score = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 34/116 (29%), Positives = 54/116 (46%), Gaps = 14/116 (12%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSI---------R 51
ME+++D + + + G+ +P+P + + W ++ RGSYS
Sbjct: 544 MENISDDVIVGRCLAILKGIFGSS-AVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDY 602
Query: 52 TLTTERLNTSAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRI 107
L + + + GAP P L FAGE T + ATV+GA+ +G REA RI
Sbjct: 603 DLMAQPITPGPSIPGAP----QPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRI 654
>pdb|2H94|A Chain A, Crystal Structure And Mechanism Of Human Lysine-Specific
Demethylase-1
Length = 664
Score = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 34/116 (29%), Positives = 54/116 (46%), Gaps = 14/116 (12%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSI---------R 51
ME+++D + + + G+ +P+P + + W ++ RGSYS
Sbjct: 544 MENISDDVIVGRCLAILKGIFGSS-AVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDY 602
Query: 52 TLTTERLNTSAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRI 107
L + + + GAP P L FAGE T + ATV+GA+ +G REA RI
Sbjct: 603 DLMAQPITPGPSIPGAP----QPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRI 654
>pdb|3KPF|A Chain A, X-Ray Structure Of The Mutant Lys300met Of Polyamine
Oxidase From Zea Mays
pdb|3KPF|B Chain B, X-Ray Structure Of The Mutant Lys300met Of Polyamine
Oxidase From Zea Mays
pdb|3KU9|A Chain A, X-Ray Structure Of The Mutant Lys300met Of Polyamine
Oxidase From Zea Mays In Complex With Spermine
pdb|3KU9|B Chain B, X-Ray Structure Of The Mutant Lys300met Of Polyamine
Oxidase From Zea Mays In Complex With Spermine
pdb|3L1R|A Chain A, X-Ray Structure Of The Mutant Lys300met Of Polyamine
Oxidase From Zea Mays In Complex With Spermidine
pdb|3L1R|B Chain B, X-Ray Structure Of The Mutant Lys300met Of Polyamine
Oxidase From Zea Mays In Complex With Spermidine
Length = 478
Score = 43.9 bits (102), Expect = 2e-05, Method: Composition-based stats.
Identities = 30/108 (27%), Positives = 52/108 (48%), Gaps = 9/108 (8%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSIRTLTTERLNT 60
+E +D+Q + E+M+ R K +P+ IL W S++ ++G++S + R
Sbjct: 357 IEQQSDEQTKAEIMQVLRKMFPGK-DVPDATDILVPRWWSDRFYKGTFSNWPVGVNRYEY 415
Query: 61 SAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRIL 108
+L APV + F GE TSE V+GA +G A+ ++
Sbjct: 416 D--QLRAPVGR------VYFTGEHTSEHYNGYVHGAYLSGIDSAEILI 455
>pdb|1B37|A Chain A, A 30 Angstrom U-Shaped Catalytic Tunnel In The Crystal
Structure Of Polyamine Oxidase
pdb|1B37|B Chain B, A 30 Angstrom U-Shaped Catalytic Tunnel In The Crystal
Structure Of Polyamine Oxidase
pdb|1B37|C Chain C, A 30 Angstrom U-Shaped Catalytic Tunnel In The Crystal
Structure Of Polyamine Oxidase
pdb|1B5Q|A Chain A, A 30 Angstrom U-Shaped Catalytic Tunnel In The Crystal
Structure Of Polyamine Oxidase
pdb|1B5Q|B Chain B, A 30 Angstrom U-Shaped Catalytic Tunnel In The Crystal
Structure Of Polyamine Oxidase
pdb|1B5Q|C Chain C, A 30 Angstrom U-Shaped Catalytic Tunnel In The Crystal
Structure Of Polyamine Oxidase
pdb|1H81|A Chain A, Structure Of Polyamine Oxidase In The Reduced State
pdb|1H81|B Chain B, Structure Of Polyamine Oxidase In The Reduced State
pdb|1H81|C Chain C, Structure Of Polyamine Oxidase In The Reduced State
pdb|1H82|A Chain A, Structure Of Polyamine Oxidase In Complex With Guazatine
pdb|1H82|B Chain B, Structure Of Polyamine Oxidase In Complex With Guazatine
pdb|1H82|C Chain C, Structure Of Polyamine Oxidase In Complex With Guazatine
pdb|1H83|A Chain A, Structure Of Polyamine Oxidase In Complex With 1,8-
Diaminooctane
pdb|1H83|B Chain B, Structure Of Polyamine Oxidase In Complex With 1,8-
Diaminooctane
pdb|1H83|C Chain C, Structure Of Polyamine Oxidase In Complex With 1,8-
Diaminooctane
pdb|1H84|A Chain A, Covalent Adduct Between Polyamine Oxidase And N1ethyln11
((Cycloheptyl)methyl)4,8diazaundecane At Ph 4.6
pdb|1H84|B Chain B, Covalent Adduct Between Polyamine Oxidase And N1ethyln11
((Cycloheptyl)methyl)4,8diazaundecane At Ph 4.6
pdb|1H84|C Chain C, Covalent Adduct Between Polyamine Oxidase And N1ethyln11
((Cycloheptyl)methyl)4,8diazaundecane At Ph 4.6
pdb|1H86|A Chain A, Covalent Adduct Between Polyamine Oxidase And N1ethyln11
((Cycloheptyl)methyl)4,8diazaundecane At Ph 7.0
pdb|1H86|B Chain B, Covalent Adduct Between Polyamine Oxidase And N1ethyln11
((Cycloheptyl)methyl)4,8diazaundecane At Ph 7.0
pdb|1H86|C Chain C, Covalent Adduct Between Polyamine Oxidase And N1ethyln11
((Cycloheptyl)methyl)4,8diazaundecane At Ph 7.0
Length = 472
Score = 43.9 bits (102), Expect = 3e-05, Method: Composition-based stats.
Identities = 30/108 (27%), Positives = 52/108 (48%), Gaps = 9/108 (8%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSIRTLTTERLNT 60
+E +D+Q + E+M+ R K +P+ IL W S++ ++G++S + R
Sbjct: 357 IEQQSDEQTKAEIMQVLRKMFPGK-DVPDATDILVPRWWSDRFYKGTFSNWPVGVNRYEY 415
Query: 61 SAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRIL 108
+L APV + F GE TSE V+GA +G A+ ++
Sbjct: 416 D--QLRAPVGR------VYFTGEHTSEHYNGYVHGAYLSGIDSAEILI 455
>pdb|4GUR|A Chain A, Crystal Structure Of Lsd2-npac With H3 In Space Group P21
pdb|4GUS|A Chain A, Crystal Structure Of Lsd2-npac With H3 In Space Group
P3221
pdb|4GUT|A Chain A, Crystal Structure Of Lsd2-npac
pdb|4GUU|A Chain A, Crystal Structure Of Lsd2-npac With Tranylcypromine
pdb|4GU0|A Chain A, Crystal Structure Of Lsd2 With H3
pdb|4GU0|B Chain B, Crystal Structure Of Lsd2 With H3
pdb|4GU0|C Chain C, Crystal Structure Of Lsd2 With H3
pdb|4GU0|D Chain D, Crystal Structure Of Lsd2 With H3
pdb|4HSU|A Chain A, Crystal Structure Of Lsd2-npac With H3(1-26)in Space Group
P21
Length = 776
Score = 42.4 bits (98), Expect = 6e-05, Method: Composition-based stats.
Identities = 31/109 (28%), Positives = 49/109 (44%), Gaps = 12/109 (11%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSIRTL--TTERL 58
+ +L DKQV + M R + +P+P + T W ++ + +YS + E
Sbjct: 675 VRTLDDKQVLQQCMATLRELFKEQ-EVPDPTKYFVTRWSTDPWIQMAYSFVKTGGSGEAY 733
Query: 59 NTSAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRI 107
+ A ++ V FAGEAT+ TV GA +G REA +I
Sbjct: 734 DIIAEDIQGTV---------FFAGEATNRHFPQTVTGAYLSGVREASKI 773
>pdb|4GU1|A Chain A, Crystal Structure Of Lsd2
pdb|4GU1|B Chain B, Crystal Structure Of Lsd2
Length = 784
Score = 42.4 bits (98), Expect = 7e-05, Method: Composition-based stats.
Identities = 31/109 (28%), Positives = 49/109 (44%), Gaps = 12/109 (11%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSIRTL--TTERL 58
+ +L DKQV + M R + +P+P + T W ++ + +YS + E
Sbjct: 683 VRTLDDKQVLQQCMATLRELFKEQ-EVPDPTKYFVTRWSTDPWIQMAYSFVKTGGSGEAY 741
Query: 59 NTSAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRI 107
+ A ++ V FAGEAT+ TV GA +G REA +I
Sbjct: 742 DIIAEDIQGTV---------FFAGEATNRHFPQTVTGAYLSGVREASKI 781
>pdb|4FWE|A Chain A, Native Structure Of Lsd2 /aof1/kdm1b In Spacegroup Of
C2221 At 2.13a
pdb|4FWF|A Chain A, Complex Structure Of Lsd2/aof1/kdm1b With H3k4 Mimic
pdb|4FWJ|A Chain A, Native Structure Of Lsd2/aof1/kdm1b In Spacegroup Of I222
At 2.9a
pdb|4FWJ|B Chain B, Native Structure Of Lsd2/aof1/kdm1b In Spacegroup Of I222
At 2.9a
Length = 796
Score = 42.4 bits (98), Expect = 7e-05, Method: Composition-based stats.
Identities = 31/109 (28%), Positives = 49/109 (44%), Gaps = 12/109 (11%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSIRTL--TTERL 58
+ +L DKQV + M R + +P+P + T W ++ + +YS + E
Sbjct: 695 VRTLDDKQVLQQCMATLRELFKEQ-EVPDPTKYFVTRWSTDPWIQMAYSFVKTGGSGEAY 753
Query: 59 NTSAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRI 107
+ A ++ V FAGEAT+ TV GA +G REA +I
Sbjct: 754 DIIAEDIQGTV---------FFAGEATNRHFPQTVTGAYLSGVREASKI 793
>pdb|1Z6L|A Chain A, Crystal Structure Of Fms1 In Complex With Its Substrate
pdb|1Z6L|B Chain B, Crystal Structure Of Fms1 In Complex With Its Substrate
pdb|3BI2|A Chain A, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BI2|B Chain B, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BI4|A Chain A, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BI4|B Chain B, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BI5|A Chain A, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BI5|B Chain B, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BNM|B Chain B, Crystal Structure Of Polyamine Oxidase Fms1 From
Saccharomyces Cerevisiae In Complex With Bis-(3r,3'r)-
Methylated Spermine
pdb|3BNM|A Chain A, Crystal Structure Of Polyamine Oxidase Fms1 From
Saccharomyces Cerevisiae In Complex With Bis-(3r,3'r)-
Methylated Spermine
pdb|3BNU|B Chain B, Crystal Structure Of Polyamine Oxidase Fms1 From
Saccharomyces Cerevisiae In Complex With Bis-(3s,3's)-
Methylated Spermine
pdb|3BNU|A Chain A, Crystal Structure Of Polyamine Oxidase Fms1 From
Saccharomyces Cerevisiae In Complex With Bis-(3s,3's)-
Methylated Spermine
pdb|3CN8|B Chain B, Crystal Structure Of Fms1 In Complex With Spermidine
pdb|3CN8|A Chain A, Crystal Structure Of Fms1 In Complex With Spermidine
pdb|3CND|B Chain B, Crystal Structure Of Fms1 In Complex With N1-Acspermine
pdb|3CND|A Chain A, Crystal Structure Of Fms1 In Complex With N1-Acspermine
pdb|3CNP|B Chain B, Crystal Structure Of Fms1 In Complex With
S-n1-acmespermidine
pdb|3CNP|A Chain A, Crystal Structure Of Fms1 In Complex With
S-n1-acmespermidine
pdb|3CNS|A Chain A, Crystal Structure Of Fms1 In Complex With
S-Bz-Mespermidine
pdb|3CNS|B Chain B, Crystal Structure Of Fms1 In Complex With
S-Bz-Mespermidine
pdb|3CNT|B Chain B, Crystal Structure Of Fms1 In Complex With
R-Bz-Mespermidine
pdb|3CNT|A Chain A, Crystal Structure Of Fms1 In Complex With
R-Bz-Mespermidine
Length = 516
Score = 35.0 bits (79), Expect = 0.012, Method: Composition-based stats.
Identities = 26/80 (32%), Positives = 38/80 (47%), Gaps = 6/80 (7%)
Query: 28 PEPARILTTSWGSNKHFRGSYSIRTLTTERLNTSAAELGAPVSNGMGKPVLLFAGEATSE 87
P I+ ++W + + RG+YS + ++ A +SNG + FAGE T
Sbjct: 430 PVLRNIIVSNWTRDPYSRGAYSACFPGDDPVDMVVA-----MSNGQDSRIR-FAGEHTIM 483
Query: 88 DQYATVNGAIETGWREADRI 107
D GA E+G REA RI
Sbjct: 484 DGAGCAYGAWESGRREATRI 503
>pdb|1YY5|A Chain A, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
pdb|1YY5|B Chain B, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
pdb|1XPQ|A Chain A, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
pdb|1XPQ|B Chain B, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
pdb|1XPQ|C Chain C, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
pdb|1XPQ|D Chain D, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
Length = 513
Score = 35.0 bits (79), Expect = 0.012, Method: Composition-based stats.
Identities = 26/80 (32%), Positives = 38/80 (47%), Gaps = 6/80 (7%)
Query: 28 PEPARILTTSWGSNKHFRGSYSIRTLTTERLNTSAAELGAPVSNGMGKPVLLFAGEATSE 87
P I+ ++W + + RG+YS + ++ A +SNG + FAGE T
Sbjct: 430 PVLRNIIVSNWTRDPYSRGAYSACFPGDDPVDMVVA-----MSNGQDSRIR-FAGEHTIM 483
Query: 88 DQYATVNGAIETGWREADRI 107
D GA E+G REA RI
Sbjct: 484 DGAGCAYGAWESGRREATRI 503
>pdb|4GDP|A Chain A, Yeast Polyamine Oxidase Fms1, N195a Mutant
pdb|4GDP|B Chain B, Yeast Polyamine Oxidase Fms1, N195a Mutant
pdb|4GDP|C Chain C, Yeast Polyamine Oxidase Fms1, N195a Mutant
pdb|4GDP|D Chain D, Yeast Polyamine Oxidase Fms1, N195a Mutant
Length = 516
Score = 35.0 bits (79), Expect = 0.012, Method: Composition-based stats.
Identities = 26/80 (32%), Positives = 38/80 (47%), Gaps = 6/80 (7%)
Query: 28 PEPARILTTSWGSNKHFRGSYSIRTLTTERLNTSAAELGAPVSNGMGKPVLLFAGEATSE 87
P I+ ++W + + RG+YS + ++ A +SNG + FAGE T
Sbjct: 430 PVLRNIIVSNWTRDPYSRGAYSACFPGDDPVDMVVA-----MSNGQDSRIR-FAGEHTIM 483
Query: 88 DQYATVNGAIETGWREADRI 107
D GA E+G REA RI
Sbjct: 484 DGAGCAYGAWESGRREATRI 503
>pdb|4ECH|A Chain A, Yeast Polyamine Oxidase Fms1, H67q Mutant
pdb|4ECH|B Chain B, Yeast Polyamine Oxidase Fms1, H67q Mutant
Length = 516
Score = 35.0 bits (79), Expect = 0.012, Method: Composition-based stats.
Identities = 26/80 (32%), Positives = 38/80 (47%), Gaps = 6/80 (7%)
Query: 28 PEPARILTTSWGSNKHFRGSYSIRTLTTERLNTSAAELGAPVSNGMGKPVLLFAGEATSE 87
P I+ ++W + + RG+YS + ++ A +SNG + FAGE T
Sbjct: 430 PVLRNIIVSNWTRDPYSRGAYSACFPGDDPVDMVVA-----MSNGQDSRIR-FAGEHTIM 483
Query: 88 DQYATVNGAIETGWREADRI 107
D GA E+G REA RI
Sbjct: 484 DGAGCAYGAWESGRREATRI 503
>pdb|1RSG|A Chain A, Crystal Structure Of The Polyamine Oxidase Fms1 From Yeast
pdb|1RSG|B Chain B, Crystal Structure Of The Polyamine Oxidase Fms1 From Yeast
Length = 516
Score = 35.0 bits (79), Expect = 0.012, Method: Composition-based stats.
Identities = 26/80 (32%), Positives = 37/80 (46%), Gaps = 6/80 (7%)
Query: 28 PEPARILTTSWGSNKHFRGSYSIRTLTTERLNTSAAELGAPVSNGMGKPVLLFAGEATSE 87
P I+ ++W + + RG+YS + ++ A SNG + FAGE T
Sbjct: 430 PVLRNIIVSNWTRDPYSRGAYSACFPGDDPVDXVVAX-----SNGQDSRIR-FAGEHTIX 483
Query: 88 DQYATVNGAIETGWREADRI 107
D GA E+G REA RI
Sbjct: 484 DGAGCAYGAWESGRREATRI 503
>pdb|2YG7|A Chain A, Structure-Based Redesign Of Cofactor Binding In Putrescine
Oxidase: A394c-A396t-Q431g Triple Mutant
pdb|2YG7|B Chain B, Structure-Based Redesign Of Cofactor Binding In Putrescine
Oxidase: A394c-A396t-Q431g Triple Mutant
Length = 453
Score = 30.0 bits (66), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 27/108 (25%), Positives = 47/108 (43%), Gaps = 9/108 (8%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSIRTLTTERLNT 60
M L+ ++ + ++ + +LG K EP + WGS + RG Y+ + L+
Sbjct: 350 MFELSAEERKATILASLARYLGPK--AEEPVVYYESDWGSEEWTRGCYTA-SFDLGGLHR 406
Query: 61 SAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRIL 108
A+ PV P+ + +E Y V+GA+ G R A I+
Sbjct: 407 YGADSRTPVG-----PIHFSCSDIAAE-GYGHVDGAVRMGQRTAADII 448
>pdb|2YG3|A Chain A, Structure-Based Redesign Of Cofactor Binding In Putrescine
Oxidase: Wild Type Enzyme
pdb|2YG3|B Chain B, Structure-Based Redesign Of Cofactor Binding In Putrescine
Oxidase: Wild Type Enzyme
pdb|2YG4|A Chain A, Structure-Based Redesign Of Cofactor Binding In Putrescine
Oxidase: Wild Type Bound To Putrescine
pdb|2YG4|B Chain B, Structure-Based Redesign Of Cofactor Binding In Putrescine
Oxidase: Wild Type Bound To Putrescine
Length = 453
Score = 29.6 bits (65), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 27/108 (25%), Positives = 48/108 (44%), Gaps = 9/108 (8%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSIRTLTTERLNT 60
M L+ ++ + ++ + +LG K EP + WGS + RG+Y+ + L+
Sbjct: 350 MFELSAEERKATILASLARYLGPK--AEEPVVYYESDWGSEEWTRGAYAA-SFDLGGLHR 406
Query: 61 SAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRIL 108
A+ PV P+ + +E Y V+GA+ G R A I+
Sbjct: 407 YGADSRTPVG-----PIHFSCSDIAAE-GYQHVDGAVRMGQRTAADII 448
>pdb|2YG5|A Chain A, Structure-Based Redesign Of Cofactor Binding In Putrescine
Oxidase: A394c Mutant
Length = 453
Score = 29.6 bits (65), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 27/108 (25%), Positives = 47/108 (43%), Gaps = 9/108 (8%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSIRTLTTERLNT 60
M L+ ++ + ++ + +LG K EP + WGS + RG Y+ + L+
Sbjct: 350 MFELSAEERKATILASLARYLGPK--AEEPVVYYESDWGSEEWTRGCYAA-SFDLGGLHR 406
Query: 61 SAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRIL 108
A+ PV P+ + +E Y V+GA+ G R A I+
Sbjct: 407 YGADSRTPVG-----PIHFSCSDIAAE-GYQHVDGAVRMGQRTAADII 448
>pdb|2YG6|A Chain A, Structure-Based Redesign Of Cofactor Binding In Putrescine
Oxidase: P15i-A394c Double Mutant
pdb|2YG6|B Chain B, Structure-Based Redesign Of Cofactor Binding In Putrescine
Oxidase: P15i-A394c Double Mutant
Length = 453
Score = 29.6 bits (65), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 27/108 (25%), Positives = 47/108 (43%), Gaps = 9/108 (8%)
Query: 1 MESLTDKQVQIEVMKAFRFFLGAKYTIPEPARILTTSWGSNKHFRGSYSIRTLTTERLNT 60
M L+ ++ + ++ + +LG K EP + WGS + RG Y+ + L+
Sbjct: 350 MFELSAEERKATILASLARYLGPK--AEEPVVYYESDWGSEEWTRGCYAA-SFDLGGLHR 406
Query: 61 SAAELGAPVSNGMGKPVLLFAGEATSEDQYATVNGAIETGWREADRIL 108
A+ PV P+ + +E Y V+GA+ G R A I+
Sbjct: 407 YGADSRTPVG-----PIHFSCSDIAAE-GYQHVDGAVRMGQRTAADII 448
>pdb|3ATQ|A Chain A, Geranylgeranyl Reductase (Ggr) From Sulfolobus
Acidocaldarius
pdb|3ATR|A Chain A, Geranylgeranyl Reductase (Ggr) From Sulfolobus
Acidocaldarius Co- Crystallized With Its Ligand
Length = 453
Score = 25.4 bits (54), Expect = 9.3, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 9/60 (15%)
Query: 58 LNTSAAELGAPVSNGMGKPVLLFAGEATSED---------QYATVNGAIETGWREADRIL 108
L+ S A+ V +G+G+P LLF +A +E Y ++ + RE D +L
Sbjct: 386 LHLSVADKAMRVISGLGRPSLLFKLKAVAESMKKIKELYLNYPRSPSSLGSWRREVDNVL 445
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
0.315 0.130 0.375
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,096,711
Number of Sequences: 62578
Number of extensions: 113060
Number of successful extensions: 289
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 254
Number of HSP's gapped (non-prelim): 29
length of query: 110
length of database: 14,973,337
effective HSP length: 74
effective length of query: 36
effective length of database: 10,342,565
effective search space: 372332340
effective search space used: 372332340
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)