SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing GFF3761 FitnessBrowser__psRCH2:GFF3761 to proteins with known functional sites using BLASTp with E ≤ 0.001.

Or try Sites on a Tree, PaperBLAST, Conserved Domains, or compare to all protein structures

Found 20 (the maximum) hits to proteins with known functional sites (download)

3gqtC Crystal structure of glutaryl-coa dehydrogenase from burkholderia pseudomallei with fragment (1,4-dimethyl-1,2,3,4- tetrahydroquinoxalin-6-yl)methylamine (see paper)
82% identity, 99% coverage: 5:392/393 of query aligns to 1:385/385 of 3gqtC

query
sites
3gqtC

A

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active site: L135 (= L139), T136 (= T140), A250 (= A251), E365 (= E372), R377 (= R384)
binding 1-(1,4-dimethyl-1,2,3,4-tetrahydroquinoxalin-6-yl)methanamine: W166 (= W170), K210 (= K211), L213 (= L214), T218 (= T219), Y364 (= Y371)

3eonC 2.55a crystal structure of native glutaryl-coa dehydrogenase from burkholderia pseudomallei in complex with a small molecule (see paper)
82% identity, 98% coverage: 5:391/393 of query aligns to 1:382/382 of 3eonC

query
sites
3eonC

A

A

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A

active site: L135 (= L139), T136 (= T140), A244 (= A251), E363 (= E372), R375 (= R384)
binding (3,5-difluorophenyl)methanol: R94 (= R98), S95 (= S99), I248 (= I255), K322 (= K329), Y362 (= Y371)

3gncA Crystal structure of glutaryl-coa dehydrogenase from burkholderia pseudomallei with fragment 6421 (see paper)
81% identity, 98% coverage: 5:391/393 of query aligns to 2:380/380 of 3gncA

query
sites
3gncA

A

A

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F

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M

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A

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D

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A

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K

-

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E

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D

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C

C

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L

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A

active site: L136 (= L139), T137 (= T140), A242 (= A251), E361 (= E372), R373 (= R384)
binding 1-(1-methylethyl)-1H-benzimidazole-2-sulfonic acid: R95 (= R98), S96 (= S99), I246 (= I255), V357 (= V368), Y360 (= Y371), E361 (= E372)

3d6bC 2.2 a crystal structure of glutaryl-coa dehydrogenase from burkholderia pseudomallei (see paper)
81% identity, 98% coverage: 5:391/393 of query aligns to 1:377/377 of 3d6bC

query
sites
3d6bC

A

A

S

T

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F

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W

I

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D

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P

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L

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D

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G

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K

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L

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Y

Y

L

L

P

P

K

K

L

L

A

A

S

T

G

G

E

E

Y

W

I

I

G

G

C

C

F

F

G

G

L
|
L

T
|
T

E

E

P

P

N

N

H

H

G

G

S

-

D

-

P

-

G

G

S

S

M

M

V

V

T

T

R

R

A

A

K

R

K

K

V

V

D

P

G

G

Y

Y

R

S

L

L

S

S

G

G

S

S

K

K

M

M

W

W

I

I

T

T

N

N

S

S

P

P

I

I

A

A

D

D

V

V

F

F

V

V

W

W

A

A

K

K

-

L

-

D

-

E

D

D

D

G

A

R

G

D

E

E

I

I

R

R

G

G

F

F

V

I

L

L

E

E

K

K

G

G

W

C

E

K

G

G

L

L

S

S

A

A

P

P

T

A

I

I

H

H

G

G

K

K

V

V

G

G

L

L

R

R

A

A

S

S

I

I

T

T

G

G

E

E

I

I

V

V

M

L

D

D

N

E

V

A

F

F

C

V

P

P

E

E

N

N

A

I

F

L

P

P

D

H

V

V

R

K

G

G

L

L

K

R

G

G

P

P

F

F

T

T

C

C

L

L

N

N

S

S

A
|
A

R

R

Y

Y

G

G

I
|
I

S

A

W

W

G

G

A

A

L

L

G

G

A

A

E

E

F

S

C

C

W

W

H

H

T

I

A

A

R

R

Q

Q

Y

Y

T

V

L

L

D

D

R

R

Q

K

Q

Q

F

-

G

-

R

-

P

P

L

L

A

A

N

N

Q

Q

L

L

I

I

Q

Q

K

K

L

L

A

A

D

D

M

M

Q

Q

T

T

E

E

I

I

T

T

L

L

A

G

L

L

Q

Q

G

G

C

V

L

L

R

R

L

L

G

G

R

R

M

M

K

K

D

D

E

E

G

G

T

T

A

A

V

V

E

E

I

I

T

T

S

S

I

I

M

M

K

K

R

R

N

N

S

S

C

C

G

G

K

K

A

A

L

L

D

D

I

I

A

A

R

R

M

L

A

A

R

R

D

D

M

M

L

L

G

G

G

-

N

-

G

-

I

-

S

-

D

-

E

-

F

F

G

G

V

V

A

A

R

R

H

H

L

L

V

V

N

N

L

L

E

E

V

V

N

N

T

T

Y
|
Y

E
|
E

G

G

T

T

H

H

D

D

V

I

H

H

A

A

L

L

I

I

L

L

G

G

R
|
R

A

A

Q

Q

T

T

G

G

I

I

Q

Q

A

A

active site: L135 (= L139), T136 (= T140), A247 (= A251), E358 (= E372), R370 (= R384)
binding methyl thiophene-2-carboxylate: I251 (= I255), Y357 (= Y371), E358 (= E372)

2r0nA The effect of a glu370asp mutation in glutaryl-coa dehydrogenase on proton transfer to the dienolate intermediate (see paper)
65% identity, 98% coverage: 7:392/393 of query aligns to 2:388/390 of 2r0nA

query
sites
2r0nA

F

F

N

D

W

W

I

Q

D

D

P

P

L

L

L

V

L

L

D

E

Q

E

Q

Q

L

L

T

T

E

T

E

D

E

E

R

I

M

L

V

I

Q

R

G

D

S

T

A

F

A

R

Q

T

F

Y

A

C

A

Q

D

E

K

R

L

L

A

M

P

P

R

R

V

I

L

L

E

L

A

A

F

N

R

R

H

N

E

E

Q

V

T

F

D

H

P

R

A

E

I

I

F

I

R

S

E

E

M

M

G

G

E

E

T

L

G

G

L

V

L

L

G

G

A

P

T

T

I

I

P

-

E

K

A

G

Y

Y

G

G

G

C

S

A

G

G

L

V

N

S

Y

S

V

V

C

A

Y

Y

G

G

L

L

I

L

A

A

R

R

E

E

V

L

E

E

R

R

I

V

D

D

S

S

G

G

Y

Y

R
|
R

S
|
S

M

A

M

M

S

S

V
|
V

Q

Q

S

S

L

L

V

V

M

M

V

H

P

P

I

I

Y

Y

E

A

F

Y

G

G

N

S

E

E

A

E

T

Q

R

R

Q

Q

K

K

Y

Y

L

L

P

P

K

Q

L

L

A

A

S

K

G

G

E

E

Y

L

I

L

G

G

C

C

F
|
F

G

G

L
|
L

T
|
T

E

E

P

P

N

N

H

S

G
|
G

S
|
S

D

D

P
|
P

G

S

S

S

M

M

V

E

T

T

R

R

A

A

-

H

-

Y

K

N

K

S

V

S

D

N

G

K

G

S

Y

Y

R

T

L

L

S

N

G

G

S

T

K

K

M

T

W
|
W

I
|
I

T
|
T

N

N

S

S

P

P

I

M

A

A

D

D

V

L

F

F

V

V

W

W

A

A

K

R

D

C

D

E

A

D

G

G

E

C

I

I

R

R

G

G

F

F

V

L

L

L

E

E

K

K

G

G

W

M

E

R

G

G

L

L

S

S

A

A

P

P

T

R

I

I

H

Q

G

G

K

K

V

F

G

S

L

L

R

R

A

A

S

S

I

A

T

T

G

G

E

M

I

I

V

I

M

M

D

D

N

G

V

V

F

E

C

V

P

P

E

E

N

N

A

V

F

L

P

P

D

G

V

A

R

S

G

S

L

L

K
x
G

G

G

P

P

F
|
F

T

G

C

C

L
|
L

N
|
N

S

N

A
|
A

R

R

Y

Y

G

G

I

I

S

A

W

W

G

G

A

V

L

L

G

G

A

A

A

S

E

E

F

F

C

C

W

L

H

H

T

T

A

A

R

R

Q

Q

Y

Y

T

A

L

L

D

D

R

R

Q

M

Q

Q

F

F

G

G

R

V

P

P

L

L

A

A

A

R

N

N

Q

Q

L

L

I

I

Q

Q

K

K

L

L

A

A

D

D

M

M

Q

L

T

T

E

E

I

I

T

T

L

L

A

G

L

L

Q

H

G

A

C

C

L

L

R

Q

L

L

G

G

R

R

M

L

K

K

D

D

E

Q

G

D

T

K

A

A

V
x
P

E

E

I

M

T

V

S

S

I

L

M

L

K

K

R

R

N

N

S

N

C

C

G

G

K

K

A

A

L

L

D

D

I

I

A

A

R

R

M

Q

A

A

R

R

D

D

M

M

L

L

G

G

N

N

G

G

I

I

S

S

D

D

E

E

F

Y

G

H

V

V

A

I

R

R

H

H

L

A

V

M

N

N

L

L

E

E

V

A

V

V

N

N

T

T

Y
|
Y

E
|
E

G

G

T
|
T

H

H

D
|
D

V

I

H

H

A

A

L

L

I
|
I

L

L

G

G

R
|
R

A

A

Q

I

T

T

G

G

I

I

Q

Q

A

A

F

F

active site: L133 (= L139), T134 (= T140), A247 (= A251), E368 (= E372), R380 (= R384)
binding flavin-adenine dinucleotide: F131 (= F137), L133 (= L139), T134 (= T140), G139 (= G145), S140 (= S146), W166 (= W170), I167 (= I171), T168 (= T172), Y367 (= Y371), T370 (= T374), D372 (= D376)
binding 3-thiaglutaryl-CoA: R92 (= R98), S93 (= S99), V97 (= V103), P142 (= P148), G238 (≠ K242), F241 (= F245), L244 (= L248), N245 (= N249), P318 (≠ V322), Y367 (= Y371), E368 (= E372), I377 (= I381)

1sirA The crystal structure and mechanism of human glutaryl-coa dehydrogenase (see paper)
65% identity, 98% coverage: 7:392/393 of query aligns to 2:388/390 of 1sirA

query
sites
1sirA

F

F

N

D

W

W

I

Q

D

D

P

P

L

L

L

V

L

L

D

E

Q

E

Q

Q

L

L

T

T

E

T

E

D

E

E

R

I

M

L

V

I

Q

R

G

D

S

T

A

F

A

R

Q

T

F

Y

A

C

A

Q

D

E

K

R

L

L

A

M

P

P

R

R

V

I

L

L

E

L

A

A

F

N

R

R

H

N

E

E

Q

V

T

F

D

H

P

R

A

E

I

I

F

I

R

S

E

E

M

M

G

G

E

E

T

L

G

G

L

V

L

L

G

G

A

P

T

T

I

I

P

-

E

K

A

G

Y

Y

G

G

G

C

S

A

G

G

L

V

N

S

Y

S

V

V

C

A

Y

Y

G

G

L

L

I

L

A

A

R

R

E

E

V

L

E

E

R

R

I

V

D

D

S

S

G

G

Y

Y

R

R

S
|
S

M

A

M

M

S

S

V

V

Q

Q

S

S

L

L

V

V

M

M

V

H

P

P

I

I

Y

Y

E

A

F

Y

G

G

N

S

E

E

A

E

T

Q

R

R

Q

Q

K

K

Y

Y

L

L

P

P

K

Q

L

L

A

A

S

K

G

G

E

E

Y

L

I

L

G

G

C

C

F
|
F

G

G

L
|
L

T
|
T

E

E

P

P

N

N

H

S

G
|
G

S
|
S

D

D

P

P

G

S

S

S

M

M

V

E

T

T

R

R

A

A

-

H

-

Y

K

N

K

S

V

S

D

N

G

K

G

S

Y

Y

R

T

L

L

S

N

G

G

S

T

K

K

M

T

W
|
W

I
|
I

T
|
T

N

N

S

S

P

P

I

M

A

A

D

D

V

L

F

F

V

V

W

W

A

A

K

R

D

C

D

E

A

D

G

G

E

C

I

I

R

R

G

G

F

F

V

L

L

L

E

E

K

K

G

G

W

M

E

R

G

G

L

L

S

S

A

A

P

P

T

R

I

I

H

Q

G

G

K

K

V

F

G

S

L

L

R

R

A

A

S

S

I

A

T

T

G

G

E

M

I

I

V

I

M

M

D

D

N

G

V

V

F

E

C

V

P

P

E

E

N

N

A

V

F

L

P

P

D

G

V

A

R

S

G

S

L

L

K

G

G

G

P

P

F
|
F

T
x
G

C

C

L
|
L

N
|
N

S

N

A
|
A

R
|
R

Y

Y

G

G

I

I

S

A

W

W

G

G

A

V

L

L

G

G

A

A

A

S

E

E

F

F

C

C

W

L

H

H

T

T

A

A

R

R

Q

Q

Y

Y

T

A

L

L

D

D

R

R

Q

M

Q

Q

F

F

G

G

R

V

P

P

L

L

A

A

A

R

N

N

Q

Q

L

L

I

I

Q

Q

K

K

L

L

A

A

D

D

M

M

Q

L

T

T

E

E

I

I

T

T

L

L

A

G

L

L

Q

H

G

A

C

C

L

L

R

Q

L

L

G

G

R

R

M

L

K

K

D

D

E

Q

G

D

T

K

A

A

V
x
P

E

E

I

M

T

V

S

S

I

L

M

L

K

K

R

R

N

N

S

N

C

C

G

G

K

K

A

A

L

L

D

D

I

I

A

A

R

R

M

Q

A

A

R

R

D

D

M

M

L

L

G

G

N

N

G

G

I

I

S

S

D

D

E

E

F

Y

G

H

V

V

A

I

R

R

H

H

L

A

V

M

N

N

L

L

E

E

V

A

V

V

N

N

T

T

Y
|
Y

E
|
E

G

G

T
|
T

H

H

D

D

V

I

H

H

A

A

L

L

I

I

L

L

G

G

R
|
R

A

A

Q

I

T

T

G

G

I

I

Q

Q

A

A

F

F

active site: L133 (= L139), T134 (= T140), A247 (= A251), E368 (= E372), R380 (= R384)
binding flavin-adenine dinucleotide: F131 (= F137), L133 (= L139), T134 (= T140), G139 (= G145), S140 (= S146), W166 (= W170), I167 (= I171), T168 (= T172), Y367 (= Y371), T370 (= T374)
binding s-4-nitrobutyryl-coa: S93 (= S99), S140 (= S146), F241 (= F245), G242 (≠ T246), L244 (= L248), N245 (= N249), R248 (= R252), P318 (≠ V322), Y367 (= Y371), E368 (= E372), R380 (= R384)

2r0mA The effect of a glu370asp mutation in glutaryl-coa dehydrogenase on proton transfer to the dienolate intermediate (see paper)
65% identity, 98% coverage: 7:392/393 of query aligns to 2:388/390 of 2r0mA

query
sites
2r0mA

F

F

N

D

W

W

I

Q

D

D

P

P

L

L

L

V

L

L

D

E

Q

E

Q

Q

L

L

T

T

E

T

E

D

E

E

R

I

M

L

V

I

Q

R

G

D

S

T

A

F

A

R

Q

T

F

Y

A

C

A

Q

D

E

K

R

L

L

A

M

P

P

R

R

V

I

L

L

E

L

A

A

F

N

R

R

H

N

E

E

Q

V

T

F

D

H

P

R

A

E

I

I

F

I

R

S

E

E

M

M

G

G

E

E

T

L

G

G

L

V

L

L

G

G

A

P

T

T

I

I

P

-

E

K

A

G

Y

Y

G

G

G

C

S

A

G

G

L

V

N

S

Y

S

V

V

C

A

Y

Y

G

G

L

L

I

L

A

A

R

R

E

E

V

L

E

E

R

R

I

V

D

D

S

S

G

G

Y

Y

R

R

S

S

M

A

M

M

S

S

V

V

Q

Q

S

S

L
|
L

V

V

M

M

V

H

P

P

I

I

Y

Y

E

A

F

Y

G

G

N

S

E

E

A

E

T

Q

R

R

Q

Q

K

K

Y

Y

L

L

P

P

K

Q

L

L

A

A

S

K

G

G

E

E

Y

L

I

L

G

G

C

C

F
|
F

G

G

L
|
L

T
|
T

E

E

P

P

N

N

H

S

G
|
G

S
|
S

D

D

P

P

G

S

S

S

M

M

V

E

T

T

R

R

A

A

-

H

-

Y

K

N

K

S

V

S

D

N

G

K

G

S

Y

Y

R

T

L

L

S

N

G

G

S

T

K

K

M

T

W
|
W

I
|
I

T
|
T

N

N

S

S

P

P

I

M

A

A

D

D

V

L

F

F

V

V

W

W

A

A

K

R

D

C

D

E

A

D

G

G

E

C

I

I

R

R

G

G

F

F

V

L

L

L

E

E

K

K

G

G

W

M

E

R

G

G

L

L

S

S

A

A

P

P

T

R

I

I

H

Q

G

G

K

K

V

F

G

S

L
|
L

R

R

A

A

S

S

I

A

T

T

G

G

E

M

I

I

V

I

M

M

D

D

N

G

V

V

F

E

C

V

P

P

E

E

N

N

A

V

F

L

P

P

D

G

V

A

R

S

G

S

L

L

K

G

G

G

P

P

F

F

T

G

C

C

L

L

N

N

S

N

A
|
A

R

R

Y

Y

G

G

I

I

S

A

W

W

G

G

A

V

L

L

G

G

A

A

A

S

E

E

F

F

C

C

W

L

H

H

T

T

A

A

R

R

Q

Q

Y

Y

T

A

L

L

D

D

R

R

Q

M

Q

Q

F

F

G

G

R

V

P

P

L

L

A

A

A

R

N

N

Q

Q

L

L

I

I

Q

Q

K

K

L

L

A

A

D

D

M

M

Q

L

T

T

E

E

I

I

T

T

L

L

A

G

L

L

Q

H

G

A

C

C

L

L

R

Q

L

L

G

G

R

R

M

L

K

K

D

D

E

Q

G

D

T

K

A

A

V

P

E

E

I

M

T

V

S

S

I

L

M

L

K

K

R

R

N

N

S

N

C

C

G

G

K

K

A

A

L

L

D

D

I

I

A

A

R

R

M

Q

A

A

R

R

D

D

M

M

L

L

G

G

N

N

G

G

I

I

S

S

D

D

E

E

F

Y

G

H

V

V

A

I

R

R

H

H

L

A

V

M

N

N

L

L

E

E

V

A

V

V

N

N

T

T

Y
|
Y

E
x
D

G

G

T
|
T

H

H

D

D

V

I

H

H

A

A

L

L

I

I

L

L

G

G

R
|
R

A

A

Q

I

T

T

G

G

I

I

Q

Q

A

A

F

F

active site: L133 (= L139), T134 (= T140), A247 (= A251), D368 (≠ E372), R380 (= R384)
binding 4-nitrobutanoic acid: L101 (= L107), Y367 (= Y371), D368 (≠ E372)
binding flavin-adenine dinucleotide: F131 (= F137), L133 (= L139), T134 (= T140), G139 (= G145), S140 (= S146), W166 (= W170), I167 (= I171), T168 (= T172), L210 (= L214), Y367 (= Y371), T370 (= T374)

2ebaA Crystal structure of the putative glutaryl-coa dehydrogenase from thermus thermophilus
47% identity, 97% coverage: 10:392/393 of query aligns to 2:380/380 of 2ebaA

query
sites
2ebaA

I

L

D

D

P

F

L

Y

L

A

L

L

D

E

Q

D

Q

L

L

L

T

T

E

P

E

E

R

K

M

E

V

V

Q

Q

G

K

S

A

A

A

A

R

Q

R

F

F

A

L

A

E

D

K

K

E

L

A

A

L

P

P

R

H

V

I

L

R

E

D

A

W

F

W

R

E

H

E

E

G

Q

V

T

F

D

P

P

T

A

H

I

L

F

I

R

P

E

R

M

F

G

A

E

E

T

L

G

G

L

F

L

L

G

G

A

P

T

T

I

L

P

P

E

P

A

E

Y

Y

G

G

S

A

G

G

L

V

N

S

Y

S

V

A

C

A

Y

Y

G

G

L

L

I

I

A

C

R

Y

E

E

V

L

E

E

R

R

I

V

D

D

S

S

G

G

Y

L

R

R

S

S

M

F

M

V

S

S

V

V

Q

Q

S

S

L

L

V

V

M

M

V

Y

P

P

I

I

Y

Y

E

A

F

Y

G

G

N

S

E

E

A

E

T

Q

R

K

Q

R

K

E

Y

F

L

L

P

P

K

K

L

L

A

A

S

R

G

G

E

E

Y

M

I

V

G

G

C

C

F

F

G

G

L
|
L

T
|
T

E

E

P

P

N

D

H
x
G

G
|
G

S
|
S

D

D

P

P

-

Y

G

G

S

N

M

M

V

K

T

T

R

R

A

A

K

R

V

-

D

-

G

D

G

T

Y

W

R

V

L

L

S

N

G

G

S

T

K

K

M

M

W
|
W

I

I

T
|
T

N

N

S

G

P

N

I

L

A

A

D

H

V

L

F

A

V

V

V

I

W

W

A

A

K

K

D

D

D

-

A

-

G

-

E

E

I

V

R

L

G

G

F

F

V

L

L

V

E

P

K

T

G

D

W

T

E

P

G

G

L

F

S

Q

A

A

P

R

T

E

I

V

H

K

G

R

K

K

V

M

G

S

L

L

R

R

A

A

S

S

I

V

T

T

G

S

E

E

I

L

V

V

M

L

D

E

N

E

V

V

F

R

C

V

P

P

E

E

E

S

N

L

A

R

F

L

P

P

D

K

V

A

R

L

G

G

L

L

K

K

G

A

P

P

F

L

T

S

C

C

L

L

N

T

S

Q

A
|
A

R

R

Y

F

G

G

I

I

S

A

W

W

G

G

A

A

L

M

G

G

A

A

A

L

E

E

F

A

C

V

W

Y

H

E

T

E

A

A

R

V

Q

A

Y

F

T

A

L

K

D

S

R
|
R

Q

S

Q

T

F

F

G

G

R

E

P

P

L
|
L

A

A

A

K

N
x
K

Q

Q

L

L

I

V

Q

Q

K

A

K

K

L

L

A

A

D

E

M

M

Q

L

T

A

E

W

I

H

T

T

L

E

A

G

L

L

Q

L

G

L

C

A

L

W

R

R

L

L

G

A

R

R

M

L

K

K

D

D

E

E

G

G

T

K

A

L

A

T

V

P

E

A

I

Q

T

V

S

S

I

L

M

A

K

K

R

R

N

Q

S

N

C

V

G

W

K

K

A

A

L

L

D

Q

I

A

A

A

R

R

M

M

A

A

R

R

D
|
D

M
x
I

L

L

G

G

G
|
G

N

S

G

G

I

I

S

T

D

L

E

E

F

Y

G

H

V

A

A

I

R

R

H

H

L

M

V

L

N

N

L

L

E

E

V
x
T

V

V

N

Y

T
|
T

Y
|
Y

E
|
E

G

G

T
|
T

H

H

D

D

V

V

H

H

A

T

L

L

I

V

L

L

G

G

R
|
R

A

E

Q

I

T

T

G

G

I

L

Q

N

A

A

F

F

active site: L131 (= L139), T132 (= T140), A239 (= A251), E360 (= E372), R372 (= R384)
binding flavin-adenine dinucleotide: L131 (= L139), T132 (= T140), G136 (≠ H144), G137 (= G145), S138 (= S146), W161 (= W170), T163 (= T172), R265 (= R277), L272 (= L284), K275 (≠ N287), D333 (= D345), I334 (≠ M346), G337 (= G349), T355 (≠ V367), T358 (= T370), Y359 (= Y371), T362 (= T374)

3sf6A Crystal structure of glutaryl-coa dehydrogenase from mycobacterium smegmatis (see paper)
46% identity, 97% coverage: 11:392/393 of query aligns to 6:386/387 of 3sf6A

query
sites
3sf6A

D

D

P

L

L

I

L

G

L

I

D

N

Q

A

Q

V

L

L

T

S

E

A

E

E

R

R

M

E

V

I

Q

R

G

D

S

T

A

V

A

R

Q

S

F

V

A

V

A

Q

D

R

K

R

L

I

A

K

P

P

R

H

V

I

L

A

E

S

A

W

F

Y

R

E

H

D

E

G

Q

E

T

L

D

-

P

P

A

A

-

R

-

E

I

L

F

A

R

V

E

E

M

L

G

G

E

E

T

L

G

G

L

L

G

G

A

M

T

H

I

L

P

-

E

K

A

G

Y

Y

G

G

G

C

S

A

G

G

L

M

N

S

Y

A

V

V

C

A

Y

Y

G

G

L

L

I

A

A

C

R

L

E

E

V

L

E

E

R

A

I

G

D

D

S

S

G

G

Y

I

R

R

S

S

M

L

M

V

S

S

V

V

Q

Q

S

G

S

S

L

L

V

A

M

M

V

Y

P

A

I

I

Y

H

E

A

F

F

G

G

N

S

E

D

A

E

T

Q

R

K

Q

D

K

Q

Y

W

L

L

P

P

K

D

L

M

A

A

S

S

G

G

E

H

Y

R

I

I

G

G

C

C

F
|
F

G

G

L
|
L

T
|
T

E

E

P

P

N

D

H

H

G
|
G

S
|
S

D

D

P

P

G

A

S

G

M

M

V

R

T

T

R

R

A

A

K

T

K

R

V

S

D

G

G

D

Y

W

R

I

L

L

S

T

G

G

S

T

K

K

M

M

W
|
W

I
|
I

T
|
T

N

N

S

G

P

S

I

V

A

A

D

D

V

V

F

A

V

V

W

W

A

A

K

R

D

T

D

D

A

E

G

G

E

-

I

I

R

R

G

G

F

F

V

V

L

V

E

P

K

T

G

D

W

T

E

P

G

G

L

F

S

T

A

A

P

N

T

T

I

I

H

K

G

S

K

K

V

M

G

S

L

L

R

R

A

A

S

S

I

V

T

T

G

S

E

E

I

L

V

V

M

L

D

D

N

G

V

V

F

R

C

L

P

P

E

D

E

S

N

A

A

R

F

L

P

P

D

G

V

A

R

T

G

S

L

L

K

G

G

A

P

P

F

L

T

R

C

C

L

L

N

N

S

E

A
|
A

R

R

Y

F

G

G

I

I

S

V

W

F

G

G

A

A

L

L

G

G

A

A

E

R

F

D

C

C

W

L

H

E

T

T

A

A

R

L

Q

A

Y

Y

T

A

L

C

D

S

R

R

Q

E

Q

Q

F

F

G

D

R

R

P

P

L

I

A

G

N

F

Q

Q

L

L

I

T

Q

Q

K

Q

K

K

L

L

A

A

D

D

M

M

Q

T

T

L

E

E

I

Y

T

G

L

K

A

G

L

F

Q

L

G

L

C

A

L

L

R

H

L

L

G

G

R

R

M

Q

K

K

D

D

E

A

G

G

T

E

A

L

A

A

V

P

E

E

I

Q

T

V

S

S

I

L

M

G

K

K

R

L

N

N

S

N

C

V

G

R

K

E

A

A

L

I

D

E

I

I

A

A

R

R

M

T

A

A

R

R

D

T

M

V

L

L

G

G

G

A

N

S

G

G

I

I

S

T

D

G

E

E

F

Y

G

P

V

V

A

M

R

R

H

H

L

A

V

N

N

N

L

L

E

E

V
x
S

V

V

N

L

T
|
T

Y
|
Y

E
|
E

G

G

T
|
T

H

S

D
x
E

V
x
M

H

H

A

T

L

L

I

I

L

I

G

G

R
x
Q

A

A

Q

L

T

T

G

G

I

V

Q

G

A

A

F

F

active site: L134 (= L139), T135 (= T140), A245 (= A251), E366 (= E372), Q378 (≠ R384)
binding dihydroflavine-adenine dinucleotide: F132 (= F137), L134 (= L139), T135 (= T140), G140 (= G145), S141 (= S146), W165 (= W170), I166 (= I171), T167 (= T172), S361 (≠ V367), T364 (= T370), Y365 (= Y371), T368 (= T374), E370 (≠ D376), M371 (≠ V377)

3swoA Crystal structure of a glutaryl-coa dehydrogenase from mycobacterium smegmatis in complex with fadh2 (see paper)
43% identity, 99% coverage: 4:392/393 of query aligns to 1:387/388 of 3swoA

query
sites
3swoA

K

K

A

S

S

T

F

Y

N

A

W

P

I

L

D

E

P

L

L

F

L

D

L

T

D

D

Q

R

Q

L

L

L

T

D

E

Q

E

D

E

E

R

R

M

D

V

I

Q

A

G

A

S

T

A

V

A

R

Q

Q

F

F

A

V

A

D

D

T

K

R

L

L

A

K

P

P

R

N

V

V

L

E

E

G

A

W

F

F

R

E

H

S

E

A

Q

T

T

L

D

P

P

S

A

E

I

L

F

A

R

K

E

E

M

F

G

G

E

N

T

L

G

G

L

V

L

L

G

G

A

M

T

H

I

L

P

-

E

Q

A

G

Y

Y

G

G

G

C

S

A

G

G

L

T

N

N

Y

A

V

V

C

S

Y

Y

G

G

L

L

I

A

A

C

R

M

E

E

V

L

E

E

R

A

I

G

D

D

S

S

G

G

Y

F

R

R

S

S

M

F

M

V

S

S

V

V

Q

Q

S

G

S

S

L

L

V

S

M

M

V

F

P

S

I

I

Y

Y

E

R

F

Y

G

G

N

S

E

E

A

E

T

Q

R

K

Q

N

K

E

Y

W

L

L

P

P

K

R

L

L

A

A

S

A

G

G

E

D

Y

A

I

I

G

G

C

C

F
|
F

G

G

L
|
L

T
|
T

E

E

P

P

N

D

H

F

G
|
G

S
|
S

D

N

P

P

G

A

S

G

M

M

V

R

T

T

R

R

A

A

K

R

V

D

D

G

G

S

G

D

Y

W

R

I

L

L

S

N

G

G

S

T

K

K

M

M

W
|
W

I
|
I

T
|
T

N

N

S

G

P

N

I

L

A

A

D

D

V

V

F

A

V

T

V

V

W

W

A

A

K

Q

D

T

D

D

A

D

G

G

E

-

I

I

R

R

G

G

F

F

V

L

L

V

E

P

K

T

G

D

W

T

E

P

G

G

L

F

S

T

A

A

P

N

T

E

I

I

H

H

G

R

K

K

V

L

G

S

L

L

R

R

A

A

S

S

I

V

T

T

G

S

E

E

I

L

V

V

M

L

D

D

N

N

V

V

F

R

C

L

P

P

E

A

E

S

N

A

A

Q

F

L

P

P

D

L

V

A

R

E

G

G

L

L

K

S

G

A

P

P

F

L

T

S

C

C

L

L

N

N

S

E

A
|
A

R

R

Y

F

G

G

I

I

S

V

W

F

G

G

A

A

L

L

G

G

A

A

E

R

F

D

C

S

W

L

H

E

T

T

A

T

R

I

Q

A

Y

Y

T

T

L

Q

D

S

R
|
R

Q

E

Q
x
V

F
|
F

G

D

R

K

P

P

L
|
L

A

S

A

N

N
x
Y

Q

Q

L

L

I

T

Q

Q

K

E

K

K

L

L

A

A

D

N

M

M

Q

T

T

V

E

E

I

L

T

G

L

K

A

G

L

M

Q

L

G

L

C

A

L

I

R

H

L

L

G

G

R

R

M

I

K

K

D

D

E

A

G

E

T

G

A

V

A

R

V

P

E

E

I

Q

T

I

S

S

I

L

M

G

K

K

R

L

N

N

S

N

C

V

G

R

K

E

A

A

L

I

D

A

I

I

A

A

R

R

M

E

A

C

R

R

D
x
T

M
x
L

L

L

G

G

G
|
G

N

S

G

G

I
|
I

S

T

D

L

E

E

F

Y

G

S

V

P

A

L

R

R

H

H

L

A

V

N

N

N

L

L

E

E

V

S

V

V

N

L

T
|
T

Y
|
Y

E
|
E

G

G

T
|
T

H

S

D
x
E

V
x
M

H

H

A

L

L

L

I

S

L

I

G

G

R
x
K

A

A

Q

L

T

T

G

G

I

K

Q

A

A

A

F

F

active site: L135 (= L139), T136 (= T140), A246 (= A251), E367 (= E372), K379 (≠ R384)
binding dihydroflavine-adenine dinucleotide: F133 (= F137), L135 (= L139), T136 (= T140), G141 (= G145), S142 (= S146), W166 (= W170), I167 (= I171), T168 (= T172), R272 (= R277), V274 (≠ Q279), F275 (= F280), L279 (= L284), Y282 (≠ N287), T340 (≠ D345), L341 (≠ M346), G344 (= G349), I347 (= I352), T365 (= T370), Y366 (= Y371), T369 (= T374), E371 (≠ D376), M372 (≠ V377)

2ix5A Short chain specific acyl-coa oxidase from arabidopsis thaliana, acx4 in complex with acetoacetyl-coa (see paper)
35% identity, 95% coverage: 19:392/393 of query aligns to 39:412/415 of 2ix5A

query
sites
2ix5A

L

L

T

T

E

P

E

E

R

Q

M

A

V

I

Q

R

G

K

S

K

A

V

A

R

Q

E

F

C

A

M

A

E

D

K

K

E

L

V

A

A

P

P

R

I

V

M

L

T

E

E

A

Y

F

W

R

E

H

K

E

A

Q

E

T

F

D

P

P

F

A

H

I

I

F

T

R

P

E

K

M

L

G

G

E

A

T

M

G

G

L

V

L

A

G

G

A

G

T

S

I

I

P

-

E

K

A

G

Y

Y

G

G

G

C

S

P

G

G

L

L

N

S

Y

I

V

T

C

A

Y

N

G

A

L

I

I

A

A

T

R

A

E

E

V

I

E

A

R

R

I

V

D

D

S

A

G

S

Y

C

R

S

S

T

M

F

M

I

S

L

V

V

Q

H

S

S

L

L

V

G

M

M

V

L

P

T

I

I

Y

A

E

L

F

C

G

G

N

S

E

E

A

A

T

Q

R

K

Q

E

K

K

Y

Y

L

L

P

P

K

S

L

L

A

A

S

Q

G

L

E

N

Y

T

I

V

G

A

C

C

F

W

G

A

L
|
L

T
|
T

E

E

P

P

N

D

H

N

G
|
G

S
|
S

D

D

P
x
A

G
x
S

S

G

M

L

V

G

T

T

R

T

A

A

K

T

K

K

V

V

D

E

G

G

Y

W

R

K

L

I

S

N

G

G

S

Q

K

K

M

R

W
|
W

I

I

T

G

N

N

S

S

P

T

I

F

A

A

D

D

V

L

F

L

V

I

W

F

A

A

K

R

D

N

D

T

A

T

-

T

G

N

E

Q

I

I

R

N

G

G

F

F

V

I

L

V

E

K

K

K

G

D

W

A

E

P

G

G

L

L

S

K

A

A

P

T

T

K

I

I

H

P

G

N

K

K

V

I

G

G

L

L

R

R

A

M

S

V

I

Q

T
x
N

G

G

E

D

I

I

V

L

M

L

D

Q

N

N

V

V

F

F

C

V

P

P

E

D

E

E

N

D

A

R

F

L

P

P

D

G

V

V

R

N

G

S

L
x
F

K

Q

G

D

P

T

F

S

T

K

C

V

L
|
L

N

A

S

V

A
x
S

R
|
R

Y

V

G

M

I

V

S

A

W

W

G

Q

A

P

L

I

G

G

A

I

A

S

E

M

F

G

C

I

W

Y

H

D

T

M

A

C

R

H

Q

R

Y

Y

T

L

L

K

D

E

R
|
R

Q

K

Q

Q

F
|
F

G

G

R

A

P

P

L
|
L

A

A

N
x
F

Q

Q

L
|
L

I
x
N

Q

Q

K

Q

K

K

L

L

A

V

D

Q

M

M

Q

L

T

G

E

N

I

V

T

Q

L

A

A

M

L

F

Q

L

G

M

C

G

L

W

R

R

L

L

G

C

R

K

M

L

K

Y

D

E

E

T

G

G

T

Q

A

M

A

T

V

P

E

G

I

Q

T

A

S

S

I

L

M

G

K

K

R

A

N

W

S

I

C

S

G

S

K

K

A

A

L

R

D

E

I

T

A

A

R

S

M

L

A

G

R

R

D
x
E

M
x
L

L

L

G
|
G

N

N

G

G

I

I

S

L

D

A

E

D

F

F

G

L

V

V

A

A

R

K

H

A

L

F

V

C

N

D

L

L

E

E

V

P

V

I

N

Y

T

T

Y
|
Y

E
|
E

G
|
G

T
|
T

H

Y

D
|
D

V
x
I

H

N

A

T

L

L

I

V

L

T

G

G

R
|
R

A

E

Q

V

T

T

G

G

I

I

Q

A

A

S

F

F

active site: L158 (= L139), T159 (= T140), S271 (≠ A251), E392 (= E372), R404 (= R384)
binding acetoacetyl-coenzyme a: S165 (= S146), A167 (≠ P148), S168 (≠ G149), F261 (≠ L241), L268 (= L248), R272 (= R252), E392 (= E372), G393 (= G373), R404 (= R384)
binding flavin-adenine dinucleotide: L158 (= L139), T159 (= T140), G164 (= G145), S165 (= S146), W189 (= W170), N239 (≠ T219), R297 (= R277), F300 (= F280), L304 (= L284), F307 (≠ N287), L309 (= L289), N310 (≠ I290), E365 (≠ D345), L366 (≠ M346), G368 (= G348), G369 (= G349), Y391 (= Y371), T394 (= T374), D396 (= D376), I397 (≠ V377)

2ix6A Short chain specific acyl-coa oxidase from arabidopsis thaliana, acx4 (see paper)
35% identity, 95% coverage: 19:392/393 of query aligns to 39:412/416 of 2ix6A

query
sites
2ix6A

L

L

T

T

E

P

E

E

R

Q

M

A

V

I

Q

R

G

K

S

K

A

V

A

R

Q

E

F

C

A

M

A

E

D

K

K

E

L

V

A

A

P

P

R

I

V

M

L

T

E

E

A

Y

F

W

R

E

H

K

E

A

Q

E

T

F

D

P

P

F

A

H

I

I

F

T

R

P

E

K

M

L

G

G

E

A

T

M

G

G

L

V

L

A

G

G

A

G

T

S

I

I

P

-

E

K

A

G

Y

Y

G

G

G

C

S

P

G

G

L

L

N

S

Y

I

V

T

C

A

Y

N

G

A

L

I

I

A

A

T

R

A

E

E

V

I

E

A

R

R

I

V

D

D

S

A

G

S

Y

C

R

S

S

T

M

F

M

I

S

L

V

V

Q

H

S

S

L

L

V

G

M

M

V

L

P

T

I

I

Y

A