SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing WP_013537942.1 NCBI__GCF_000185805.1:WP_013537942.1 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)

3e0iA Cu2+ substituted aquifex aeolicus kdo8ps in complex with pep (see paper)
60% identity, 97% coverage: 1:260/269 of query aligns to 3:261/263 of 3e0iA

query
sites
3e0iA

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binding copper (ii) ion: C10 (= C8), H184 (= H183), E221 (= E220)
binding phosphoenolpyruvate: K40 (= K38), K45 (= K43), Q98 (= Q96), P100 (= P98), A101 (= A99), K123 (= K121), R153 (= R151), H184 (= H183)
binding phosphate ion: R48 (= R46), S49 (= S47), K195 (≠ A194), S196 (= S195)

2a21A Aquifex aeolicus kdo8ps in complex with pep, po4, and zn2+ (see paper)
60% identity, 97% coverage: 1:260/269 of query aligns to 3:261/263 of 2a21A

query
sites
2a21A

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binding phosphoenolpyruvate: K40 (= K38), K45 (= K43), Q98 (= Q96), P100 (= P98), A101 (= A99), K123 (= K121), R153 (= R151), H184 (= H183)
binding phosphate ion: R48 (= R46), S49 (= S47), S196 (= S195)
binding zinc ion: C10 (= C8), H184 (= H183), E221 (= E220), D232 (= D231)

1jcyA Aquifex aeolicus kdo8p synthase in complex with r5p, pep and cadmium (see paper)
60% identity, 97% coverage: 1:260/269 of query aligns to 3:261/263 of 1jcyA

query
sites
1jcyA

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binding phosphoenolpyruvate: K40 (= K38), K45 (= K43), Q98 (= Q96), P100 (= P98), A101 (= A99), K123 (= K121), R153 (= R151), H184 (= H183)
binding ribose-5-phosphate: N47 (= N45), R48 (= R46), S49 (= S47), H184 (= H183), Q187 (= Q186), S196 (= S195)

1fwwA Aquifex aeolicus kdo8p synthase in complex with pep, a5p and cadmium (see paper)
60% identity, 97% coverage: 1:260/269 of query aligns to 3:261/263 of 1fwwA

query
sites
1fwwA

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binding arabinose-5-phosphate: N47 (= N45), R48 (= R46), S49 (= S47), H184 (= H183), S196 (= S195), D232 (= D231)
binding phosphoenolpyruvate: K40 (= K38), K45 (= K43), Q98 (= Q96), P100 (= P98), A101 (= A99), K123 (= K121), R153 (= R151), H184 (= H183)

1fwtA Aquifex aeolicus kdo8p synthase in complex with pep, e4p and cadmium (see paper)
60% identity, 97% coverage: 1:260/269 of query aligns to 3:261/263 of 1fwtA

query
sites
1fwtA

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L

L

G

G

R

D

A

K

S
|
S

G

G

D

M

R

R

R

E

F

F

V

I

P

F

Y

P

L

L

A

I

R

R

A

A

V

V

A

A

V

V

G

G

A

C

D

D

G

G

L

V

F

F

F

M

E

E

T

T

H

H

P

P

N

E

P

P

D

E

K

K

A

A

L

L

S

S

D

D

G

A

P

S

N

T

M

Q

V

L

P

P

L

L

N

S

G

Q

F

L

R

E

E

G

L

I

I

I

G

E

K

A

L

I

I

L

K

E

L

I

K

R

S

E

C

V

V

A

G

S

E

K

L

Y

F

Y

D

E

binding erythose-4-phosphate: N47 (= N45), R48 (= R46), S49 (= S47), S196 (= S195)
binding phosphoenolpyruvate: K40 (= K38), K45 (= K43), Q98 (= Q96), P100 (= P98), A101 (= A99), K123 (= K121), R153 (= R151), H184 (= H183)

2nx3D Structural and mechanistic changes along an engineered path from metallo to non-metallo kdo8p synthase (see paper)
60% identity, 97% coverage: 1:260/269 of query aligns to 2:260/262 of 2nx3D

query
sites
2nx3D

M

F

I

L

V

V

I

I

A

A

G

G

P

P

C
x
N

V

A

I

I

E

E

D

S

K

E

G

E

T

L

V

L

F

L

E

K

V

V

A

G

R

E

A

E

V

I

K

K

E

R

L

L

Q

S

S

E

L

K

Y

F

P

K

E

E

H

V

T

E

F

F

I

V

F

F

K

K

A

S

S

S

F

F

D

D

K
|
K

A

A

N
|
N

R
|
R

S
|
S

S

S

L

I

D

H

S

S

F

F

R

R

G

G

P

H

G

G

L

L

E

E

R

Y

G

G

L

V

E

K

V

A

L

L

K

R

E

K

V

V

K

K

E

E

L

F

G

G

L

L

P

K

V

I

T

T

D

D

I

I

H

H

E

E

P

S

W

W

Q

Q

A

A

E

E

K

P

V

V

A

A

E

E

V

V

A

A

D

D

V

I

I

I

Q
|
Q

I

I

P
|
P

A
|
A

F

F

L

L

C

C

R

R

Q

Q

T

T

D

D

L

L

V

L

A

A

G

K

T

T

G

G

K

R

T

A

V

V

N

N

I

V

K
|
K

K

K

G

G

Q

Q

F

F

M

L

A

A

P

P

W

W

D

D

M

T

E

K

N

N

A

V

V

V

E

E

K

K

V

L

R

K

R

F

S

G

G

G

G

A

R

K

E

E

V

I

W

Y

V

L

T

T

E

E

R
|
R

G

G

T

T

F

F

G

G

Y

Y

N

N

L

L

V

V

D

D

F

F

R

R

S

S

I

L

P

P

V

I

M

M

E

K

E

Q

F

W

A

A

D

-

K

K

V

V

V

I

F

Y

D

D

A

A

T

T

H
|
H

S

S

V

V

Q

Q

R

L

P

P

G

G

L

L

G

G

R

D

A
x
K

S
|
S

G

G

D

M

R

R

R

E

F

F

V

I

P

F

Y

P

L

L

A

I

R

R

A

A

V

V

A

A

V

V

G

G

A

C

D

D

G

G

L

V

F

F

F

M

E

E

T

T

H

H

P

P

N

E

P

P

D

E

K

K

A

A

L

L

S

S

D
|
D

G

A

P

P

N

T

M

A

V

L

P

P

L

L

N

S

G

Q

F

L

R

E

E

G

L

I

I

I

G

E

K

A

L

I

I

L

K

E

L

I

K

R

S

E

C

V

V

A

G

S

E

K

L

Y

F

Y

D

E

binding (2r,4r,5r,6r,7r)-2,4,5,6,7-pentahydroxy-2,8-bis(phosphonooxy)octanoic acid: N9 (≠ C8), K44 (= K43), N46 (= N45), R47 (= R46), S48 (= S47), Q97 (= Q96), P99 (= P98), A100 (= A99), K122 (= K121), R152 (= R151), H183 (= H183), K194 (≠ A194), S195 (= S195), D231 (= D231)

2nx1A Structural and mechanistic changes along an engineered path from metallo to non-metallo kdo8p synthase (see paper)
59% identity, 97% coverage: 1:260/269 of query aligns to 3:261/263 of 2nx1A

query
sites
2nx1A

M

F

I

L

V

V

I

I

A

A

G

G

P

P

C

N

V

A

I

I

E

E

D

S

K

E

G

E

T

L

V

L

F

L

E

K

V

V

A

G

R

E

A

E

V

I

K

K

E

R

L

L

Q

S

S

E

L

K

Y

F

P

K

E

E

H

V

T

E

F

F

I

V

F

F

K
|
K

A

S

S

S

F

F

D

D

K
|
K

A

A

N
|
N

R
|
R

S
|
S

S

S

L

I

D

H

S

S

F

F

R

R

G

G

P

H

G

G

L

L

E

E

R

Y

G

G

L

V

E

K

V

A

L

L

K

R

E

K

V

V

K

K

E

E

L

F

G

G

L

L

P

K

V

I

T

T

D

D

I

I

H

H

E

E

P

S

W

W

Q

Q

A

A

E

E

K

P

V

V

A

A

E

E

V

V

A

A

D

D

V

I

I

I

Q
|
Q

I

I

P
|
P

A
|
A

F

F

L

L

C

C

R

R

Q

Q

T

T

D

D

L

L

V

L

A

A

G

K

T

T

G

G

K

R

T

A

V

V

N

N

I

V

K
|
K

K

K

G

G

Q

Q

F

F

M

L

A

A

P

P

W

W

D

D

M

T

E

K

N

N

A

V

V

V

E

E

K

K

V

L

R

K

R

F

S

G

G

G

G

A

R

K

E

E

V

I

W

Y

V

L

T

T

E

E

R
|
R

G

G

T

T

F

F

G

G

Y

Y

N

N

L

L

V

V

D

D

F

F

R

R

S

S

I

L

P

P

V

I

M

M

E

K

E

Q

F

W

A

A

D

-

K

K

V

V

V

I

F

Y

D

D

A

A

T

T

H
|
H

S

S

V

V

Q

Q

R

L

P

P

G

G

L

L

G

G

R

D

A

K

S
|
S

G

G

D

M

R

R

R

E

F

F

V

I

P

F

Y

P

L

L

A

I

R

R

A

A

V

V

A

A

V

V

G

G

A

C

D

D

G

G

L

V

F

F

F

M

E

E

T

T

H

H

P

P

N

E

P

P

D

E

K

K

A

A

L

L

S

S

D
|
D

G

A

P

S

N

T

M

Q

V

L

P

P

L

L

N

S

G

Q

F

L

R

E

E

G

L

I

I

I

G

E

K

A

L

I

I

L

K

E

L

I

K

R

S

E

C

V

V

A

G

S

E

K

L

Y

F

Y

D

E

binding phosphoenolpyruvate: K40 (= K38), Q98 (= Q96), P100 (= P98), A101 (= A99), K123 (= K121), R153 (= R151), H184 (= H183)
binding 5-O-phosphono-beta-D-ribofuranose: K45 (= K43), N47 (= N45), R48 (= R46), S49 (= S47), S196 (= S195), D232 (= D231)

1pckA Aquifex aeolicus kdo8ps in complex with z-methyl-pep (see paper)
58% identity, 97% coverage: 1:260/269 of query aligns to 3:256/258 of 1pckA

query
sites
1pckA

M

F

I

L

V

V

I

I

A

A

G

G

P

P

C

C

V

A

I

I

E

E

D

S

K

E

G

E

T

L

V

L

F

L

E

K

V

V

A

G

R

E

A

E

V

I

K

K

E

R

L

L

Q

S

S

E

L

K

Y

F

P

K

E

E

H

V

T

E

F

F

I

V

F

F

K
|
K

A

S

S

S

F

F

D

D

K
|
K

A

A

N
|
N

R

R

S

S

L

I

D

H

S

S

F

F

R

R

G

G

P

H

G

G

L

L

E

E

R

Y

G

G

L

V

E

K

V

A

L

L

K

R

E

K

V

V

K

K

E

E

L

F

G

G

L

L

P

K

V

I

T

T

D

D

I

I

H

H

E

E

P

S

W

W

Q

Q

A

A

E

E

K

P

V

V

A

A

E

E

V

V

A

A

D

D

V

I

I

I

Q
|
Q

I

I

P
|
P

A
|
A

F

F

L

L

C

C

R

R

Q

Q

T

T

D

D

L

L

V

L

A

A

G

K

T

T

G

G

K

R

T

A

V

V

N

N

I

V

K
|
K

K

K

G

G

Q

Q

F

F

M

L

A

A

P

P

W

W

D

D

M

T

E

K

N

N

A

V

V

V

E

E

K

K

V

L

R

K

R

F

S

G

G

G

G

A

R

K

E

E

V

I

W

Y

V

L

T

T

E

E

R
|
R

G

G

T

T

F

F

G

G

Y

Y

N

N

L

L

V

V

D

D

F

F

R

R

S

S

I

L

P

P

V

I

M

M

E

K

E

Q

F

W

A

A

D

-

K

K

V

V

V

I

F

Y

D

D

A

A

T

T

H
|
H

S

S

V

V

Q

Q

R

L

P

P

G

G

L

L

G

G

R

M

A

-

S

-

G

-

D

-

R

R

R

E

F

F

V

I

P

F

Y

P

L

L

A

I

R

R

A

A

V

V

A

A

V

V

G

G

A

C

D

D

G

G

L

V

F

F

F

M

E

E

T

T

H

H

P

P

N

E

P

P

D

E

K

K

A

A

L

L

S

S

D

D

G

A

P

S

N

T

M

Q

V

L

P

P

L

L

N

S

G

Q

F

L

R

E

E

G

L

I

I

I

G

E

K

A

L

I

I

L

K

E

L

I

K

R

S

E

C

V

V

A

G

S

E

K

L

Y

F

Y

D

E

binding 2-(phosphonooxy)butanoic acid: K40 (= K38), K45 (= K43), N47 (= N45), Q98 (= Q96), P100 (= P98), A101 (= A99), K123 (= K121), R153 (= R151), H184 (= H183)

3e12A Cu2+ substituted aquifex aeolicus kdo8ps in complex with kdo8p (see paper)
58% identity, 97% coverage: 1:260/269 of query aligns to 3:256/258 of 3e12A

query
sites
3e12A

M

F

I

L

V

V

I

I

A

A

G

G

P

P

C
|
C

V

A

I

I

E

E

D

S

K

E

G

E

T

L

V

L

F

L

E

K

V

V

A

G

R

E

A

E

V

I

K

K

E

R

L

L

Q

S

S

E

L

K

Y

F

P

K

E

E

H

V

T

E

F

F

I

V

F

F

K
|
K

A

S

S

S

F

F

D

D

K
|
K

A

A

N
|
N

R
|
R

S
|
S

S

S

L

I

D

H

S

S

F

F

R

R

G

G

P

H

G

G

L

L

E

E

R

Y

G

G

L

V

E

K

V

A

L

L

K

R

E

K

V

V

K

K

E

E

L

F

G

G

L

L

P

K

V

I

T

T

D

D

I

I

H

H

E

E

P

S

W

W

Q

Q

A

A

E

E

K

P

V

V

A

A

E

E

V

V

A

A

D

D

V

I

I

I

Q
|
Q

I

I

P
|
P

A
|
A

F

F

L

L

C

C

R

R

Q

Q

T

T

D

D

L

L

V

L

A

A

G

K

T

T

G

G

K

R

T

A

V

V

N

N

I

V

K
|
K

K

K

G

G

Q

Q

F

F

M

L

A

A

P

P

W

W

D

D

M

T

E

K

N

N

A

V

V

V

E

E

K

K

V

L

R

K

R

F

S

G

G

G

G

A

R

K

E

E

V

I

W

Y

V

L

T

T

E

E

R
|
R

G

G

T

T

F

F

G

G

Y

Y

N

N

L

L

V

V

D

D

F

F

R

R

S

S

I

L

P

P

V

I

M

M

E

K

E

Q

F

W

A

A

D

-

K

K

V

V

V

I

F

Y

D

D

A

A

T

T

H
|
H

S

S

V

V

Q

Q

R

L

P

P

G

G

L

-

G

-

R

-

A

-

S

-

G

G

D

M

R

R

R

E

F

F

V

I

P

F

Y

P

L

L

A

I

R

R

A

A

V

V

A

A

V

V

G

G

A

C

D

D

G

G

L

V

F

F

F

M

E
|
E

T

T

H

H

P

P

N

E

P

P

D

E

K

K

A

A

L

L

S

S

D
|
D

G

A

P

S

N

T

M

Q

V

L

P

P

L

L

N

S

G

Q

F

L

R

E

E

G

L

I

I

I

G

E

K

A

L

I

I

L

K

E

L

I

K

R

S

E

C

V

V

A

G

S

E

K

L

Y

F

Y

D

E

binding copper (ii) ion: C10 (= C8), H184 (= H183), E216 (= E220), D227 (= D231)
binding 3-deoxy-8-O-phosphono-D-manno-oct-2-ulosonic acid: K40 (= K38), K45 (= K43), N47 (= N45), R48 (= R46), S49 (= S47), Q98 (= Q96), K123 (= K121), H184 (= H183), D227 (= D231)
binding phosphate ion: P100 (= P98), A101 (= A99), K123 (= K121), R153 (= R151)

1pe1A Aquifex aeolicus kdo8ps in complex with cadmium and 2-pga (see paper)
58% identity, 97% coverage: 1:260/269 of query aligns to 4:256/258 of 1pe1A

query
sites
1pe1A

M

F

I

L

V

V

I

I

A

A

G

G

P

P

C

C

V

A

I

I

E

E

D

S

K

E

G

E

T

L

V

L

F

L

E

K

V

V

A

G

R

E

A

E

V

I

K

K

E

R

L

L

Q

S

S

E

L

K

Y

F

P

K

E

E

H

V

T

E

F

F

I

V

F

F

K
|
K

A

S

S

S

F

F

D

D

K

K

A

A

N

N

R

R

S

S

L

I

D

H

S

S

F

F

R

R

G

G

P

H

G

G

L

L

E

E

R

Y

G

G

L

V

E

K

V

A

L

L

K

R

E

K

V

V

K

K

E

E

L

F

G

G

L

L

P

K

V

I

T

T

D
|
D

I

I

H

H

E

E

P

S

W

W

Q

Q

A

A

E

E

K

P

V

V

A

A

E

E

V

V

A

A

D

D

V

I

I

I

Q
|
Q

I

I

P
|
P

A
|
A

F

F

L

L

C

C

R

R

Q

Q

T

T

D

D

L

L

V

L

A

A

G

K

T

T

G

G

K

R

T

A

V

V

N

N

I

V

K
|
K

K

K

G

G

Q

Q

F

F

M

L

A

A

P

P

W

W

D

D

M

T

E

K

N

N

A

V

V

V

E

E

K

K

V

L

R

K

R

F

S

G

G

G

G

A

R

K

E

E

V

I

W

Y

V

L

T

T

E

E

R
|
R

G

G

T

T

F

F

G

G

Y

Y

N

N

L

L

V

V

D

D

F

F

R

R

S

S

I

L

P

P

V

I

M

M

E

K

E

Q

F

W

A

A

D

-

K

K

V

V

V

I

F

Y

D

D

A

A

T

T

H
|
H

S

S

V

V

Q

Q

R

L

P

P

G

G

G

-

L

-

G

-

R

-

A

-

S

-

G

G

D

M

R

R

R

E

F

F

V

I

P

F

Y

P

L

L

A

I

R

R

A

A

V

V

A

A

V

V

G

G

A

C

D

D

G

G

L

V

F

F

F

M

E

E

T

T

H

H

P

P

N

E

P

P

D

E

K

K

A

A

L

L

S

S

D

D

G

A

P

S

N

T

M

Q

V

L

P

P

L

L

N

S

G

Q

F

L

R

E

E

G

L

I

I

I

G

E

K

A

L

I

I

L

K

E

L

I

K

R

S

E

C

V

V

A

G

S

E

K

L

Y

F

Y

D

E

binding 2-phosphoglyceric acid: K41 (= K38), D81 (= D78), Q99 (= Q96), P101 (= P98), A102 (= A99), K124 (= K121), R154 (= R151), H185 (= H183)

1pcwA Aquifex aeolicus kdo8ps in complex with cadmium and app, a bisubstrate inhibitor (see paper)
58% identity, 97% coverage: 1:260/269 of query aligns to 3:255/257 of 1pcwA

query
sites
1pcwA

M

F

I

L

V

V

I

I

A

A

G

G

P

P

C

C

V

A

I

I

E

E

D

S

K

E

G

E

T

L

V

L

F

L

E

K

V

V

A

G

R

E

A

E

V

I

K

K

E

R

L

L

Q

S

S

E

L

K

Y

F

P

K

E

E

H

V

T

E

F

F

I

V

F

F

K

K

A

S

S

S

F

F

D

D

K
|
K

A

A

N
|
N

R
|
R

S
|
S

S

S

L

I

D

H

S

S

F

F

R

R

G

G

P

H

G

G

L

L

E

E

R

Y

G

G

L

V

E

K

V

A

L

L

K

R

E

K

V

V

K

K

E

E

L

F

G

G

L

L

P

K

V

I

T

T

D

D

I

I

H

H

E

E

P

S

W

W

Q

Q

A

A

E

E

K

P

V

V

A

A

E

E

V

V

A

A

D

D

V

I

I

I

Q

Q

I

I

P
|
P

A
|
A

F

F

L

L

C

C

R

R

Q

Q

T

T

D

D

L

L

V

L

A

A

G

K

T

T

G

G

K

R

T

A

V

V

N

N

I

V

K
|
K

K

K

G

G

Q

Q

F

F

M

L

A

A

P

P

W

W

D

D

M

T

E

K

N

N

A

V

V

V

E

E

K

K

V

L

R

K

R

F

S

G

G

G

G

A

R

K

E

E

V

I

W

Y

V

L

T

T

E

E

R
|
R

G

G

T

T

F

F

G

G

Y

Y

N

N

L

L

V

V

D

D

F

F

R

R

S

S

I

L

P

P

V

I

M

M

E

K

E

Q

F

W

A

A

D

-

K

K

V

V

V

I

F

Y

D

D

A

A

T

T

H
|
H

S

S

V

V

Q
|
Q

R

L

P

P

G

G

G

-

L

-

G

-

R

-

A

-

S

-

G

G

D

M

R

R

R

E

F

F

V

I

P

F

Y

P

L

L

A

I

R

R

A

A

V

V

A

A

V

V

G

G

A

C

D

D

G

G

L

V

F

F

F

M

E

E

T

T

H

H

P

P

N

E

P

P

D

E

K

K

A

A

L

L

S

S

D
|
D

G

A

P

S

N

T

M

Q

V

L

P

P

L

L

N

S

G

Q

F

L

R

E

E

G

L

I

I

I

G

E

K

A

L

I

I

L

K

E

L

I

K

R

S

E

C

V

V

A

G

S

E

K

L

Y

F

Y

D

E

binding 1-deoxy-6-o-phosphono-1-[(phosphonomethyl)amino]-l-threo-hexitol: K45 (= K43), N47 (= N45), R48 (= R46), S49 (= S47), P100 (= P98), A101 (= A99), K123 (= K121), R153 (= R151), H184 (= H183), Q187 (= Q186), D226 (= D231)

1jcxA Aquifex aeolicus kdo8p synthase in complex with api and cadmium (see paper)
57% identity, 97% coverage: 1:260/269 of query aligns to 3:253/255 of 1jcxA

query
sites
1jcxA

M

F

I

L

V

V

I

I

A

A

G

G

P

P

C

C

V

A

I

I

E

E

D

S

K

E

G

E

T

L

V

L

F

L

E

K

V

V

A

G

R

E

A

E

V

I

K

K

E

R

L

L

Q

S

S

E

L

K

Y

F

P

K

E

E

H

V

T

E

F

F

I

V

F

F

K
|
K

A

S

S

S

F

F

D

D

K
|
K

A

A

N
|
N

R
|
R

S
|
S

S

S

L

I

D

H

S

S

F

F

R

R

G

G

P

H

G

G

L

L

E

E

R

Y

G

G

L

V

E

K

V

A

L

L

K

R

E

K

V

V

K

K

E

E

L

F

G

G

L

L

P

K

V

I

T

T

D

D

I

I

H

H

E

E

P

S

W

W

Q

Q

A

A

E

E

K

P

V

V

A

A

E

E

V

V

A

A

D

D

V

I

I

I

Q
|
Q

I

I

P
|
P

A
|
A

F

F

L

L

C

C

R

R

Q

Q

T

T

D

D

L

L

V

L

A

A

G

K

T

T

G

G

K

R

T

A

V

V

N

N

I

V

K
|
K

K

K

G

G

Q

Q

F

F

M

L

A

A

P

P

W

W

D

D

M

T

E

K

N

N

A

V

V

V

E

E

K

K

V

L

R

K

R

F

S

G

G

G

G

A

R

K

E

E

V

I

W

Y

V

L

T

T

E

E

R
|
R

G

G

T

T

F

F

G

G

Y

Y

N

N

L

L

V

V

D

D

F

F

R

R

S

S

I

L

P

P

V

I

M

M

E

K

E

Q

F

W

A

A

D

-

K

K

V

V

V

I

F

Y

D

D

A

A

T

T

H
|
H

S

S

V

V

Q
|
Q

R

L

P

P

G

G

G

M

L

-

G

-

R

-

A

-

S

-

G

-

D

-

R

R

R

E

F

F

V

I

P

F

Y

P

L

L

A

I

R

R

A

A

V

V

A

A

V

V

G

G

A

C

D

D

G

G

L

V

F
|
F

F

M

E
|
E

T

T

H

H

P

P

N

E

P

P

D

E

K

K

A

A

L

L

S

S

D

D

G

A

P

S

N

T

M

Q

V

L

P

P

L

L

N

S

G

Q

F

L

R

E

E

G

L

I

I

I

G

E

K

A

L

I

I

L

K

E

L

I

K

R

S

E

C

V

V

A

G

S

E

K

L

Y

F

Y

D

E

binding {[(2,2-dihydroxy-ethyl)-(2,3,4,5-tetrahydroxy-6-phosphonooxy-hexyl)-amino]-methyl}-phosphonic acid: K40 (= K38), K45 (= K43), N47 (= N45), R48 (= R46), S49 (= S47), Q98 (= Q96), P100 (= P98), A101 (= A99), K123 (= K121), R153 (= R151), H184 (= H183), Q187 (= Q186), F211 (= F218), E213 (= E220)

4z1dA Structure of pep and zinc bound kdo8ps from h.Pylori (see paper)
50% identity, 94% coverage: 2:253/269 of query aligns to 3:254/256 of 4z1dA

query
sites
4z1dA

I

V

V

L

I

I

A

A

G

G

P

P

C
|
C

V

V

I

I

E

E

D

S

K

L

G

E

T

N

V

L

F

R

E

S

V

I

A

A

R

T

A

K

V

L

K

Q

E

P

L

L

Q

A

S

N

L

-

Y

N

P

E

E

R

H

L

T

D

F

F

I

Y

F

F

K
|
K

A

A

S

S

F

F

D

D

K

K

A

A

N

N

R

R

S

T

S

S

L

L

D

E

S

S

F

Y

R

R

G

G

P

P

G

G

L

L

E

E

R

K

G

G

L

L

E

E

V

M

L

L

K

Q

E

T

V

I

K

K

E

E

L

F

G

G

L

Y

P

K

V

I

T

L

T

T

D

D

I

V

H

H

E

E

P

S

W

Y

Q

Q

A

A

E

S

K

V

V

A

A

A

E

K

V

V

A

A

D

D

V

I

I

L

Q
|
Q

I

I

P
|
P

A
|
A

F

F

L

L

C

C

R

R

Q

Q

T

T

D

D

L

L

L

I

V

V

A

E

A

V

A

S

G

Q

T

T

G

N

K

A

T

I

V

V

N

N

I

I

K
|
K

K

K

G

G

Q

Q

F

F

M

M

A

N

P

P

W

K

D

D

M

M

E

Q

N

Y

A

S

V

V

E

L

K

K

V

A

R

L

R

K

S

T

G

R

G

D

R

K

E

S

-

I

-

Q

-

S

-

P

-

T

-

Y

-

E

-

T

-

A

-

L

-

K

-

N

-

G

V

V

W

W

V

L

T

C

E

E

R
|
R

G

G

T

S

F

F

G

G

Y

Y

N

G

N

N

L

L

V

V

D

D

F

M

R

R

S

S

I

L

P

K

V

I

M

M

E

R

E

E

F

F

A

A

D

-

K

P

V

V

V

I

F

F

D

D

A

A

T

T

H
|
H

S

S

V

V

Q

Q

R

M

P

P

G

S

G

-

L

-

G

-

R

-

A

-

S

-

G

-

D

-

R

-

F

F

V

A

P

P

Y

I

L

L

A

A

R

R

A

A

V

A

A

A

V

V

G

G

A

I

D

D

G

G

L

L

F

F

F

A

E
|
E

T

T

H

H

P

V

N

D

P

P

D

K

K

N

A

A

L

L

S

S

D
|
D

G

G

P

A

N

N

M

M

V

L

P

K

L

P

N

D

G

E

F

L

R

E

E

Q

L

L

I

V

G

T

K

D

L

M

I

L

K

K

L

I

K

Q

S

N

binding phosphoenolpyruvate: K38 (= K38), Q96 (= Q96), P98 (= P98), A99 (= A99), K121 (= K121), R164 (= R151), H195 (= H183)
binding zinc ion: C9 (= C8), H195 (= H183), E221 (= E220), D232 (= D231)

3undB Substrate-bound crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from burkholderia pseudomallei (see paper)
54% identity, 80% coverage: 35:248/269 of query aligns to 53:268/284 of 3undB

query
sites
3undB

F

F

I

V

F

F

K
|
K

A

A

S

S

F

F

D

D

K
|
K

A

A

N
|
N

R
|
R

S
|
S

S

S

L

I

D

H

S

S

F

Y

R

R

G

G

P

V

G

G

L

L

E

D

R

E

G

G

L

L

E

K

V

I

L

F

K

A

E

E

V

V

K

K

E

A

E

R

L

F

G

G

L

V

P

P

V

V

T

I

T

T

D

D

I

V

H

H

E

E

P

A

W

E

Q

Q

A

A

E

A

K

P

V

V

A

A

E

E

V

I

A

A

D

D

V

V

I

L

Q
|
Q

I

V

P
|
P

A
|
A

F

F

L

L

C

A

R

R

Q

Q

T

T

D

D

L

L

L

V

V

V

A

A

A

I

A

A

G

K

T

A

G

G

K

K

T

P

V

V

N

N

I

V

K
|
K

K

K

G

P

Q

Q

F

F

M

M

A

S

P

P

W

T

D

Q

M

L

E

K

N

H

A

V

V

V

E

S

K

K

V

C

R

G

R

E

S

V

G

G

G

N

R

D

E

R

V

V

W

M

V

L

T

C

E

E

R
|
R

G

G

T

S

F

F

G

G

Y

Y

N

D

N

N

L

L

V

V

D

D

F

M

R

L

S

G

I

F

P

R

V

Q

M

M

E

A

E

E

F

T

A

T

D

G

-

G

-

C

K

P

V

V

V

I

F

F

D

D

A

V

T

T

H
|
H

S

S

V

L

Q
|
Q

R

C

P
x
R

G

D

G

P

L

L

G

G

R

D

A
|
A

S
|
S

G

G

D

R

R

R

F

Q

V

V

P

L

Y

D

L

L

A

A

R

R

A

A

A

G

V

I

A

A

V

V

G

G

A

I

D

A

G

G

L

L

F

F

F

L

E

E

T

A

H

H

P

P

N

D

P

P

D

D

K

R

A

A

L

R

S
x
C

D
|
D

G

G

P

P

N

S

M

A

V

L

P

P

L

L

N

H

G

Q

F

L

R

E

E

G

L

L

I

L

G

S

K

Q

L

M

binding arabinose-5-phosphate: K61 (= K43), N63 (= N45), R64 (= R46), S65 (= S47), H203 (= H183), Q206 (= Q186), R208 (≠ P188), A214 (= A194), S215 (= S195), C250 (≠ S230), D251 (= D231)
binding 3-deoxy-8-O-phosphono-D-manno-oct-2-ulosonic acid: K56 (= K38), K61 (= K43), N63 (= N45), R64 (= R46), S65 (= S47), K139 (= K121), H203 (= H183), R208 (≠ P188), A214 (= A194), S215 (= S195), D251 (= D231)
binding phosphoenolpyruvate: K56 (= K38), Q114 (= Q96), P116 (= P98), A117 (= A99), K139 (= K121), R169 (= R151), H203 (= H183)

Sites not aligning to the query:

binding arabinose-5-phosphate: 27

1g7vA Crystal structures of kdo8p synthase in its binary complexes with the mechanism-based inhibitor (see paper)
51% identity, 76% coverage: 35:238/269 of query aligns to 52:257/284 of 1g7vA

query
sites
1g7vA

F

Y

I

V

F

F

K

K

A

A

S

S

F

F

D

D

K
|
K

A

A

N
|
N

R
|
R

S

S

L

I

D

H

S

S

F

Y

R

R

G

G

P

P

G

G

L

L

E

E

R

E

G

G

L

M

E

K

V

I

L

F

K

Q

E

E

V

L

K

K

E

Q

E

T

L

F

G

G

L

V

P

K

V

I

T

I

T

T

D

D

I

V

H

H

E

E

P

P

W

S

Q

Q

A

A

E

Q

K

P

V

V

A

A

E

D

V

V

A

V

D

D

V

V

I

I

Q

Q

I

L

P

P

A

A

F
|
F

L

L

C

A

R

R

Q

Q

T

T

D

D

L

L

L

V

V

E

A

A

A

M

A

A

G

K

T

T

G

G

K

A

T

V

V

I

N

N

I

V

K

K

G

P

Q

Q

F

F

M

V

A

S

P

P

W

G

D

Q

M

M

E

G

N

N

A

I

V

V

E

D

K

K

V

F

R

K

R

E

S

G

G

G

G

N

R

E

E

K

V

V

W

I

V

L

T

C

E

D

R
|
R

G

G

T

A

T

N

F

F

G

G

Y

Y

N

D

N

N

L

L

V

V

D

D

F

M

R

L

S

G

I

F

P

S

V

I

M

M

E

K

F

V

A

S

-

G

-

N

D

S

K

P

V

V

V

I

F

F

D

D

A

V

T

T

H
|
H

S

A

V

L

Q
|
Q

R

C

P

R

G

D

G

P

L

F

G

G

R

A

A

A

S

S

G

G

D

R

R

R

R

A

F

Q

V

V

P

A

Y

E

L

L

A

A

R

R

A

A

A

G

V

M

A

A

V

V

G

G

A

L

D

A

G

G

L

L

F

F

F

I

E

E

T

A

H

H

P

P

N

D

P

P

D

E

K

H

A
|
A

L

K

S

C

D
|
D

G
|
G

P
|
P

N

S

M

A

V

L

P

P

L

L

active site: K60 (= K43), D250 (= D231)
binding {[(2,2-dihydroxy-ethyl)-(2,3,4,5-tetrahydroxy-6-phosphonooxy-hexyl)-amino]-methyl}-phosphonic acid: N62 (= N45), R63 (= R46), F117 (= F100), R168 (= R151), H202 (= H183), Q205 (= Q186), A247 (= A228), G251 (= G232), P252 (= P233)

Sites not aligning to the query:

active site: 26

1g7uA Crystal structures of kdo8p synthase in its binary complex with substrate phosphoenol pyruvate (see paper)
49% identity, 80% coverage: 35:248/269 of query aligns to 52:267/284 of 1g7uA

query
sites
1g7uA

F

Y

I

V

F

F

K

K

A

A

S

S

F

F

D

D

K

K

A

A

N

N

R

R

S

S

L

I

D

H

S

S

F

Y

R

R

G

G

P

P

G

G

L

L

E

E

R

E

G

G

L

M

E

K

V

I

L

F

K

Q

E

E

V

L

K

K

E

Q

E

T

L

F

G

G

L

V

P

K

V

I

T

I

T

T

D

D

I

V

H

H

E

E

P

P

W

S

Q

Q

A

A

E

Q

K

P

V

V

A

A

E

D

V

V

A

V

D

D

V

V

I

I

Q

Q

I

L

P

P

A

A

F
|
F

L

L

C

A

R

R

Q

Q

T

T

D

D

L

L

L

V

V

E

A

A

A

M

A

A

G

K

T

T

G

G

K

A

T

V

V

I

N

N

I

V

K

K

G

P

Q

Q

F

F

M

V

A

S

P

P

W

G

D

Q

M

M

E

G

N

N

A

I

V

V

E

D

K

K

V

F

R

K

R

E

S

G

G

G

G

N

R

E

E

K

V

V

W

I

V

L

T

C

E

D

R
|
R

G

G

T

A

T

N

F

F

G

G

Y

Y

N

D

N

N

L

L

V

V

D

D

F

M

R

L

S

G

I

F

P

S

V

I

M

M

E

K

F

V

A

S

-

G

-

N

D

S

K

P

V

V

V

I

F

F

D

D

A

V

T

T

H
|
H

S

A

V

L

Q

Q

R

C

P

R

G

D

G

P

L

F

G

V

R

A

A

A

S

S

G

G

D

R

R

R

R

A

F

Q

V

V

P

A

Y

E

L

L

A

A

R

R

A

A

A

G

V

M

A

A

V

V

G

G

A

L

D

A

G

G

L

L

F

F

F

I

E

E

T

A

H

H

P

P

N

D

P

P

D

E

K

H

A

A

L

K

S

C

D

D

G

G

P

P

N

S

M

A

V

L

P

P

L

L

N

A

G

K

F

L

R

E

E

P

L

F

I

L

G

K

K

Q

L

M

binding phosphoenolpyruvate: F117 (= F100), R168 (= R151), H202 (= H183)

1x6uA Kdo8p synthase in it's binary complex with the product kdo8p (see paper)
47% identity, 80% coverage: 35:248/269 of query aligns to 52:255/272 of 1x6uA

query
sites
1x6uA

F

Y

I

V

F

F

K
|
K

A

A

S

S

F

F

D

D

K
|
K

A

A

N
|
N

R

R

S

S

L

I

D

H

S

S

F

Y

R

R

G

G

P

P

G

G

L

L

E

E

R

E

G

G

L

M

E

K

V

I

L

F

K

Q

E

E

V

L

K

K

E

Q

E

T

L

F

G

G

L

V

P

K

V

I

T

I

T

T

D

D

I

V

H

H

E

E

P

P

W

S

Q

Q

A

A

E

Q

K

P

V

V

A

A

E

D

V

V

A

V

D

D

V

V

I

I

Q
|
Q

I

L

P

P

A

A

F
|
F

L

L

C

A

R

R

Q

Q

T

T

D

D

L

L

L

V

V

E

A

A

A

M

A

A

G

K

T

T

G

G

K

A

T

V

V

I

N

N

I

V

K
|
K

K

K

G

P

Q

Q

F

F

M

V

A

S

P

P

W

G

D

Q

M

M

E

G

N

N

A

I

V

V

E

D

K

K

V

F

R

K

R

E

S

G

G

G

G

N

R

E

E

K

V

V

W

I

V

L

T

C

E

D

R

R

G

G

T

A

T

N

F

F

G

G

Y

Y

N

D

N

N

L

L

V

V

D

D

F

M

R

L

S

G

I

F

P

S

V

I

M

M

E

K

F

V

A

S

-

G

-

N

D

S

K

P

V

V

V

I

F

F

D
|
D

A

V

T

T

H
|
H

S

A

V

L

Q

Q

R

R

P

A

G

Q

G

-

L

-

G

-

R

-

A

-

S

-

G

-

D

-

R

-

F

-

V

V

P

A

Y

E

L

L

A

A

R

R

A

A

A

G

V

M

A

A

V

V

G

G

A

L

D

A

G

G

L

L

F
|
F

F

I

E
|
E

T

A

H

H

P

P

N

D

P

P

D

E

K

H

A

A

L

K

S

C

D
|
D

G

G

P
|
P

N

S

M

A

V

L

P

P

L

L

N

A

G

K

F

L

R

E

E

P

L

F

I

L

G

K

K

Q

L

M

active site: K60 (= K43), D238 (= D231)
binding 3-deoxy-8-O-phosphono-alpha-D-manno-oct-2-ulopyranosonic acid: K55 (= K38), N62 (= N45), Q113 (= Q96), F117 (= F100), K138 (= K121), D199 (= D180), H202 (= H183), F225 (= F218), E227 (= E220), P240 (= P233)

Sites not aligning to the query:

active site: 26
binding 3-deoxy-8-O-phosphono-alpha-D-manno-oct-2-ulopyranosonic acid: 26

1phwA Crystal structure of kdo8p synthase in its binary complex with substrate analog 1-deoxy-a5p (see paper)
47% identity, 80% coverage: 35:248/269 of query aligns to 52:255/272 of 1phwA

query
sites
1phwA

F

Y

I

V

F

F

K

K

A

A

S

S

F

F

D

D

K
|
K

A

A

N

N

R

R

S

S

L

I

D

H

S

S

F

Y

R

R

G

G

P

P

G

G

L

L

E

E

R

E

G

G

L

M

E

K

V

I

L

F

K

Q

E

E

V

L

K

K

E

Q

E

T

L

F

G

G

L

V

P

K

V

I

T

I

T

T

D

D

I

V

H

H

E

E

P

P

W

S

Q

Q

A

A

E

Q

K

P

V

V

A

A

E

D

V

V

A

V

D

D

V

V

I

I

Q

Q

I

L

P
|
P