SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing WP_111607904.1 NCBI__GCF_003259225.1:WP_111607904.1 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)

P02911 Lysine/arginine/ornithine-binding periplasmic protein; LAO-binding protein from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see 4 papers)
36% identity, 99% coverage: 3:252/252 of query aligns to 1:258/260 of P02911

query
sites
P02911

L

M

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Y

D33 (≠ E34) binding L-arginine; binding L-lysine; binding L-ornithine; mutation to A: Decreases arginine and histidine binding affinity.
Y36 (≠ W37) mutation to A: Shows a drastic decrease in arginine and histidine binding affinity.
D52 (= D53) mutation to A: Shows a drastic decrease in arginine and histidine binding affinity.
C60 (= C61) modified: Disulfide link with 67
C67 (= C68) modified: Disulfide link with 60
F74 (≠ W75) mutation to A: Shows a drastic decrease in arginine and histidine binding affinity.
S91 (≠ A92) binding L-arginine; binding L-ornithine; mutation to A: Has no effect on the arginine and histidine binding affinity.
S92 (= S93) binding L-arginine; binding L-lysine; binding L-ornithine; mutation to A: Decreases arginine and histidine binding affinity.
S94 (= S95) binding L-arginine; binding L-lysine; binding L-ornithine; mutation to A: Decreases arginine and histidine binding affinity.
R99 (= R100) binding L-arginine; binding L-lysine; binding L-ornithine; mutation to A: Shows a drastic decrease in arginine and histidine binding affinity.
L139 (≠ Q138) mutation to K: Changes ligand specificity. Can bind glutamine. Still able to bind basic amino acids, however, with 1000-fold less affinity for arginine.; mutation to Q: Does not affect ligand preference.
T143 (≠ L142) binding L-arginine; binding L-lysine; binding L-ornithine
D183 (= D181) binding L-arginine; binding L-ornithine; mutation to A: Shows a drastic decrease in arginine and histidine binding affinity.

5owfA Structure of a lao-binding protein mutant with glutamine (see paper)
36% identity, 89% coverage: 29:252/252 of query aligns to 3:233/235 of 5owfA

query
sites
5owfA

V

V

R

R

F

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binding glutamine: Y11 (≠ W37), F49 (≠ W75), S66 (≠ A92), S67 (= S93), S69 (= S95), R74 (= R100), K114 (≠ Q138), S117 (≠ T141), T118 (≠ L142), D158 (= D181)

1lstA Three-dimensional structures of the periplasmic lysine-, arginine-, ornithine-binding protein with and without a ligand (see paper)
36% identity, 89% coverage: 29:252/252 of query aligns to 6:236/238 of 1lstA

query
sites
1lstA

V

V

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binding lysine: Y14 (≠ W37), F52 (≠ W75), S70 (= S93), S72 (= S95), R77 (= R100), L117 (≠ Q138), S120 (≠ T141), T121 (≠ L142), Q122 (≠ G143), D161 (= D181)

1lahE Structural bases for multiple ligand specificity of the periplasmic lysine-, arginine-, ornithine-binding protein (see paper)
36% identity, 89% coverage: 29:252/252 of query aligns to 6:236/238 of 1lahE

query
sites
1lahE

V

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D

D

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N

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K

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G

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N

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K

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binding L-ornithine: Y14 (≠ W37), F52 (≠ W75), S70 (= S93), S72 (= S95), R77 (= R100), S120 (≠ T141), Q122 (≠ G143), D161 (= D181)

1lagE Structural bases for multiple ligand specificity of the periplasmic lysine-, arginine-, ornithine-binding protein (see paper)
36% identity, 89% coverage: 29:252/252 of query aligns to 6:236/238 of 1lagE

query
sites
1lagE

V

V

R

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F

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F

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K

A

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G

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L

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R

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G

D

D

D

D

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E

L

L

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A

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A

L

F

N

D

K

K

A

A

L

L

D

T

Q

E

I

L

L

R

A

Q

D

D

G

G

T

T

Y

Y

Q

D

K

K

I

M

N

A

A

K

K

K

Y

Y

F

F

P

D

F

F

S

N

I

V

Y

Y

binding histidine: Y14 (≠ W37), F52 (≠ W75), S69 (≠ A92), S70 (= S93), L71 (≠ M94), S72 (= S95), R77 (= R100), L117 (≠ Q138), S120 (≠ T141), Q122 (≠ G143), D161 (= D181)

1lafE Structural bases for multiple ligand specificity of the periplasmic lysine-, arginine-, ornithine-binding protein (see paper)
36% identity, 89% coverage: 29:252/252 of query aligns to 6:236/238 of 1lafE

query
sites
1lafE

V

V

R

R

F

I

V

G

T

T

E
x
D

G

T

A

T

W
x
Y

A

A

P

P

F

F

N

S

F

S

I

K

D

D

E

A

A

K

G

G

Q

E

P

F

Q

I

G

G

F

F

D

D

V

I

D

D

I

L

A

G

R

N

A

E

L

M

C

C

A

K

K

R

M

M

A

Q

A

V

D

K

C

C

E

T

I

W

L

V

T

A

Q

S

D

D

W
x
F

D

D

G

A

L

L

I

I

P

P

G

S

L

L

K

K

V

A

R

K

K

K

F

I

D

D

A

A

I

I

A
x
S

S
|
S

M

L

S
|
S

I

I

T

T

E

D

D

K

R
|
R

L

Q

K

Q

V

E

V

I

D

A

F

F

T

S

N

D

K

K

Y

L

Y

Y

S

A

G

A

G

D

L

S

R

R

F

L

M

I

G

A

R

A

V

K

E

G

D

S

N

P

F

I

D

Q

-

P

-

T

L

L

S

E

N

S

L

L

S

K

G

G

K

K

T

H

I

V

G

G

A

V

Q
x
L

R

Q

A

G

T
x
S

L
x
T

G
x
Q

A

E

Q

A

Y

Y

L

A

E

N

D

D

N

N

F

W

T

R

G

T

K

K

A

G

-

V

D

D

L

V

K

V

F

A

Y

Y

D

A

N

N

Q

Q

D

D

N

L

V

I

Y

Y

L

S

D

D

L

L

V

T

A

A

G

G

R

R

L

L

D

D

I

A

V

A

L

L

S

Q

D
|
D

E

E

L

V

P

A

T

A

Y

S

N

E

W

G

L

F

K

L

T

K

S

Q

E

P

S

A

G

G

A

K

K

E

F

Y

E

A

F

F

K

A

G

G

D

P

A

S

F

V

M

K

K

D

T

K

-

K

-

Y

-

F

-

G

D

D

N

G

I

T

G

G

I

V

A

G

V

L

R

R

K

K

G

D

D

D

D

T

K

E

L

L

K

K

E

A

K

A

L

F

N

D

K

K

A

A

L

L

D

T

Q

E

I

L

L

R

A

Q

D

D

G

G

T

T

Y

Y

Q

D

K

K

I

M

N

A

A

K

K

K

Y

Y

F

F

P

D

F

F

S

N

I

V

Y

Y

binding arginine: D11 (≠ E34), Y14 (≠ W37), F52 (≠ W75), S69 (≠ A92), S70 (= S93), S72 (= S95), R77 (= R100), L117 (≠ Q138), S120 (≠ T141), T121 (≠ L142), Q122 (≠ G143), D161 (= D181)

P02910 Histidine-binding periplasmic protein; HBP from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see 2 papers)
36% identity, 89% coverage: 28:252/252 of query aligns to 27:258/260 of P02910

query
sites
P02910

K

K

V

I

R

R

F

I

V

G

T

T

E

D

G

P

A

T

W

Y

A

A

P

P

F

F

N
x
E

F

S

I
x
K

D

N

E

A

A

Q

G

G

Q
x
E

P

L

Q

V

G

G

F

F

D

D

V

I

D

D

I

L

A

A

R

K

A

E

L

L

C

C

A

K

K

R

M

I

A

N

A

T

D

Q

C

C

E

T

I

F

L

V

T

E

Q

N

D

P

W

L

D

D

G

A

L

L

I

I

P

P

G

S

L

L

K

K

V

A

R

K

K

K

F

I

D

D

A

A

I

I

I

M

A

S

S

S

M

L

S

S

I

I

T

T

E

E

D

K

R

R

L

Q

K

Q

V

E

V

I

D

A

F

F

T

T

N

D

K

K

Y

L

Y

Y

S

A

G

A

G

D

L

S

R

R

F

L

M

V

G

-

R

-

V

V

E

A

D

K

N

N

F

S

D

D

L

I

-

Q

-

P

-

T

-

V

S

A

N

S

L

L

S

K

G

G

K

K

T

R

I

V

G

G

A

V

Q

L

R

Q

A

G

T

T

L

T

G

Q

A

E

Q

T

Y

F

L

G

E

N

D

E

N

H

F

W

T

A

G

P

K

K

A

G

-

I

D

E

L

I

K

V

F

S

Y

Y

D

Q

N

G

Q

Q

D

D

N

N

V

I

Y

Y

L

S

D
|
D

L

L

V

T

A

A

G

G

R
|
R

L

I

D
|
D

I

A

V

A

L

F

S

Q

D

D

E

E

L

V

P

A

T

A

Y

S

N

E

W

G

L

F

K

L

T

K

S

Q

E

P

S

V

G

G

A

K

K

D

F

Y

E

K

F

F

K

G

G

G

D

P

A

A

F

-

M

V

K

K

T

D

D

E

N

K

I

L

-

F

-

G

-

V

-

G

-

T

G

G

I

M

A

G

V

L

R

R

K

K

G

E

D

D

D

N

K

E

L

L

K

R

E

E

K

A

L

L

N

N

K

K

A

A

L

F

D

A

Q

E

I

M

L

R

A

A

D

D

G

G

T

T

Y

Y

Q

E

K

K

I

L

N

A

A

K

K

K

Y

Y

F

F

P

D

F

F

S

D

I

V

Y

Y

E40 (≠ N41) mutation to K: Decrease in ATPase-inducing activity and histidine transport; when associated with K-47.
K42 (≠ I43) mutation to E: Increases ATPase-inducing activity and histidine transport; when associated with K-47.
E47 (≠ Q48) mutation to K: Decrease in ATPase-inducing activity and histidine transport; when associated with K-40. Increases ATPase-inducing activity and histidine transport; when associated with E-42.
D171 (= D169) mutation D->A,N: Strong decrease in ATPase-inducing activity and histidine transport.
R176 (= R174) mutation R->D,S: Strong decrease in ATPase-inducing activity and histidine transport.
D178 (= D176) mutation to A: Slight decrease in ATPase-inducing activity and histidine transport.

Sites not aligning to the query:

1:22 signal peptide

1hslA Refined 1.89 angstroms structure of the histidine-binding protein complexed with histidine and its relationship with many other active transport(slash)chemosensory receptors (see paper)
35% identity, 89% coverage: 28:252/252 of query aligns to 5:236/238 of 1hslA

query
sites
1hslA

K

K

V

I

R

R

F

I

V

G

T

T

E

D

G

P

A

T

W
x
Y

A

A

P

P

F

F

N

E

F

S

I

K

D

N

E

A

A

Q

G

G

Q

E

P

L

Q

V

G

G

F

F

D

D

V

I

D

D

I

L

A

A

R

K

A

E

L

L

C

C

A

K

K

R

M

I

A

N

A

T

D

Q

C

C

E

T

I

F

L

V

T

E

Q

N

D

P

W
x
L

D

D

G

A

L

L

I

I

P

P

G

S

L

L

K

K

V

A

R

K

K

K

F

I

D

D

A

A

I

I

I

M

A
x
S

S
|
S

M
x
L

S
|
S

I

I

T

T

E

E

D

K

R
|
R

L

Q

K

Q

V

E

V

I

D

A

F

F

T

T

N

D

K

K

Y

L

Y

Y

S

A

G

A

G

D

L

S

R

R

F

L

M

V

G

-

R

-

V

V

E

A

D

K

N

N

F

S

D

D

L

I

-

Q

-

P

-

T

-

V

S

A

N

S

L

L

S

K

G

G

K

K

T

R

I

V

G

G

A

V

Q

L

R

Q

A

G

T
|
T

L
x
T

G

Q

A

E

Q

T

Y

F

L

G

E

N

D

E

N

H

F

W

T

A

G

P

K

K

A

G

-

I

D

E

L

I

K

V

F

S

Y

Y

D

Q

N

G

Q

Q

D

D

N

N

V

I

Y

Y

L

S

D

D

L

L

V

T

A

A

G

G

R

R

L

I

D

D

I

A

V

A

L

F

S

Q

D
|
D

E

E

L

V

P

A

T

A

Y

S

N

E

W

G

L

F

K

L

T

K

S

Q

E

P

S

V

G

G

A

K

K

D

F

Y

E

K

F

F

K

G

G

G

D

P

A

A

F

V

M

K

K

D

T

E

D

K

-

L

-

F

-

G

-

V

N

G

I

T

G

G

I

M

A

G

V

L

R

R

K

K

G

E

D

D

D

N

K

E

L

L

K

R

E

E

K

A

L

L

N

N

K

K

A

A

L

F

D

A

Q

E

I

M

L

R

A

A

D

D

G

G

T

T

Y

Y

Q

E

K

K

I

L

N

A

A

K

K

K

Y

Y

F

F

P

D

F

F

S

D

I

V

Y

Y

binding histidine: Y14 (≠ W37), L52 (≠ W75), S69 (≠ A92), S70 (= S93), L71 (≠ M94), S72 (= S95), R77 (= R100), T120 (= T141), T121 (≠ L142), D161 (= D181)

P0AEU0 Histidine-binding periplasmic protein; HBP from Escherichia coli (strain K12) (see 3 papers)
35% identity, 89% coverage: 29:252/252 of query aligns to 28:258/260 of P0AEU0

query
sites
P0AEU0

V

I

R

R

F

I

V

G

T

T

E

D

G

P

A

T

W

Y

A

A

P

P

F

F

N

E

F

S

I

K

D

N

E

S

A

Q

G

G

Q

E

P

L

Q

V

G

G

F

F

D

D

V

I

D

D

I

L

A

A

R

K

A

E

L

L

C
|
C

A

K

K

R

M

I

A

N

A

T

D

Q

C
|
C

E

T

I

F

L

V

T

E

Q

N

D

P

W

L

D

D

G

A

L

L

I

I

P

P

G

S

L

L

K

K

V

A

R

K

K

K

F

I

D

D

A

A

I

I

I

M

A
x
S

S
|
S

M

L

S
|
S

I

I

T

T

E

E

D

K

R
|
R

L

Q

K

Q

V

E

V

I

D

A

F

F

T

T

N

D

K

K

Y

L

Y

Y

S

A

G

A

G

D

L

S

R

R

F

L

M

V

G

-

R

-

V

V

E

A

D

K

N

N

F

S

D

D

L

I

-

Q

-

P

-

T

-

V

S

E

N

S

L

L

S

K

G

G

K

K

T

R

I

V

G

G

A

V

Q

L

R

Q

A

G

T

T

L
x
T

G

Q

A

E

Q

T

Y

F

L

G

E

N

D

E

N

H

F

W

T

A

G

P

K

K

A

G

-

I

D

E

L

I

K

V

F

S

Y

Y

D

Q

N

G

Q

Q

D

D

N

N

V

I

Y

Y

L

S

D

D

L

L

V

T

A

A

G

G

R

R

L

I

D

D

I

A

V

A

L

F

S

Q

D
|
D

E

E

L

V

P

A

T

A

Y

S

N

E

W

G

L

F

K

L

T

K

S

Q

E

P

S

V

G

G

A

K

K

D

F

Y

E

K

F

F

K

G

G

G

D

P

A

S

F

V

M

K

K

D

T

E

D

K

-

L

-

F

-

G

-

V

N

G

I

T

G

G

I

M

A

G

V

L

R

R

K

K

G

E

D

D

D

N

K

E

L

L

K

R

E

E

K

A

L

L

N

N

K

K

A

A

L

F

D

A

Q

E

I

M

L

R

A

A

D

D

G

G

T

T

Y

Y

Q

E

K

K

I

L

N

A

A

K

K

K

Y

Y

F

F

P

D

F

F

S

D

I

V

Y

Y

C60 (= C61) modified: Disulfide link with 67
C67 (= C68) modified: Disulfide link with 60
S91 (≠ A92) binding L-histidine
S92 (= S93) binding L-histidine
S94 (= S95) binding L-histidine
R99 (= R100) binding L-histidine
T143 (≠ L142) binding L-histidine
D183 (= D181) binding L-histidine

Sites not aligning to the query:

1:22 signal peptide

4zv2A An ancestral arginine-binding protein bound to glutamine (see paper)
37% identity, 87% coverage: 29:247/252 of query aligns to 6:223/225 of 4zv2A

query
sites
4zv2A

V

L

R

R

F

V

V

G

T

T

E
|
E

G

A

A

T

W
x
F

A

P

P

P

F

F

N

G

F

F

I

K

D

D

E

E

A

N

G

G

Q

K

P

L

Q

V

G

G

F

F

D

D

V

I

D

D

I

L

A

A

R

K

A

A

L

I

C

A

A

K

K

K

M

L

A

G

A

V

D

K

C

V

E

E

I

F

L

K

T

P

Q

M

D

D

W
x
F

D

D

G

G

L

I

I

I

P

P

G

A

L

L

K

Q

V

S

R

G

K

K

F

I

D

D

A

V

I

V

I

I

A

A

S
x
G

M
|
M

S
x
T

I

I

T

T

E

E

D

E

R
|
R

L

K

K

K

V

Q

V

V

D

D

F

F

T

S

N

D

K

P

Y

Y

Y

F

S

E

G

A

G

G

L

Q

R

A

F

I

M

V

G

V

R

K

V

K

E

G

D

N

N

D

F

S

-

I

-

K

D

S

L

L

S

E

N

D

L

L

S

K

G

G

K

K

T

K

I

V

G

G

A

V

Q

Q

R

L

A

G

T
x
S

L
x
T

G

S

A

E

Q

Q

Y

H

L

V

E

K

D

K

N

V

F

A

T

A

G

G

K

-

A

V

D

K

L

V

K

K

F

K

Y

F

D

D

N

N

Q

F

D

S

N

E

V

A

Y

F

L

Q

D

E

L

L

V

K

A

S

G

G

R

R

L

V

D

D

I

A

V

V

L

V

S

T

D
|
D

E

N

L

A

P

V

T

A

Y

L

N

A

W

Y

L

V

K

K

T

Q

S

N

E

P

S

N

G

-

A

A

K

G

F

V

E

K

F

I

K

V

G

G

D

E

A

T

F

F

M

-

K

S

T

G

D

E

N

P

I

Y

G

G

I

I

A

A

V

V

R

R

K

K

G

G

D

N

D

S

K

E

L

L

K

L

E

E

K

K

L

I

N

N

K

K

A

A

L

L

D

E

Q

E

I

M

L

K

A

K

D

D

G

G

T

T

Y

Y

Q

D

K

K

I

I

N

Y

A

E

K

K

Y

W

F

F

binding glutamine: E11 (= E34), F14 (≠ W37), F52 (≠ W75), G70 (≠ S93), M71 (= M94), T72 (≠ S95), R77 (= R100), S120 (≠ T141), T121 (≠ L142), D159 (= D181)

4zv1A An ancestral arginine-binding protein bound to arginine (see paper)
36% identity, 87% coverage: 29:247/252 of query aligns to 6:225/226 of 4zv1A

query
sites
4zv1A

V

L

R

R

F

V

V

G

T

T

E
|
E

G

A

A

T

W
x
F

A

P

P

P

F

F

N

G

F

F

I

K

D

D

E

E

A

N

G

G

Q

K

P

L

Q

V

G

G

F

F

D

D

V

I

D

D

I

L

A

A

R

K

A

A

L

I

C

A

A

K

K

K

M

L

A

G

A

V

D

K

C

V

E

E

I

F

L

K

T

P

Q

M

D

D

W
x
F

D

D

G

G

L

I

I

I

P

P

G

A

L

L

K

Q

V

S

R

G

K

K

F

I

D

D

A

V

I

V

I

I

A
|
A

S
x
G

M
|
M

S
x
T

I

I

T

T

E

E

D

E

R
|
R

L

K

K

K

V

Q

V

V

D

D

F

F

T

S

N

D

K

P

Y

Y

Y

F

S

E

G

A

G

G

L

Q

R

A

F

I

M

V

G

V

R

K

V

K

E

G

D

N

N

D

F

S

-

I

-

K

D

S

L

L

S

E

N

D

L

L

S

K

G

G

K

K

T

K

I

V

G

G

A

V

Q
|
Q

R

L

A

G

T
x
S

L
x
T

G

S

A

E

Q

Q

Y

H

L

V

E

K

D

K

N

V

F

A

T

K

-

D

G

A

K

G

A

V

D

K

L

V

K

K

F

K

Y

F

D

D

N

N

Q

F

D

S

N

E

V

A

Y

F

L

Q

D

E

L

L

V

K

A

S

G

G

R

R

L

V

D

D

I

A

V

V

L

V

S

T

D
|
D

E

N

L

A

P

V

T

A

Y

L

N

A

W

Y

L

V

K

K

T

Q

S

N

E

P

S

N

G

-

A

A

K

G

F

V

E

K

F

I

K

V

G

G

D

E

A

T

F

F

M

-

K

S

T

G

D

E

N

P

I

Y

G

G

I

I

A

A

V

V

R

R

K

K

G

G

D

N

D

S

K

E

L

L

K

L

E

E

K

K

L

I

N

N

K

K

A

A

L

L

D

E

Q

E

I

M

L

K

A

K

D

D

G

G

T

T

Y

Y

Q

D

K

K

I

I

N

Y

A

E

K

K

Y

W

F

F

binding arginine: E11 (= E34), F14 (≠ W37), F52 (≠ W75), A69 (= A92), G70 (≠ S93), M71 (= M94), T72 (≠ S95), R77 (= R100), Q117 (= Q138), S120 (≠ T141), T121 (≠ L142), D161 (= D181)

3tqlA Structure of the amino acid abc transporter, periplasmic amino acid- binding protein from coxiella burnetii. (see paper)
38% identity, 88% coverage: 26:247/252 of query aligns to 1:225/225 of 3tqlA

query
sites
3tqlA

A

T

D

D

K

T

V

I

R

K

F

F

V

A

T

T

E
|
E

G

A

A

T

W
x
Y

A

P

P

P

F

Y

N

V

F

Y

I

M

D

-

E

-

A

G

G

G

Q

Q

P

V

Q

E

G

G

F

F

D

G

V

A

D

D

I

I

A

V

R

K

A

A

L

V

C

C

A

K

K

Q

M

M

A

Q

A

A

D

V

C

C

E

T

I

I

L

S

T

N

Q

Q

D

P

W
|
W

D

D

G

S

L

L

I

I

P

P

G

S

L

L

K

K

V

L

R

G

K

K

F

F

D

D

A

A

I

L

I

F

A
x
G

S
x
G

M

M

S
x
N

I

I

T

T

E

T

D

A

R
|
R

L

Q

K

K

V

E

V

V

D

D

F

F

T

T

N

D

K

P

Y

Y

S

T

G

N

G

S

L

V

R
x
S

F

F

M

I

G

A

R

D

V

K

E

N

D

T

N

P

F

L

D

T

L

L

S

S

-

K

-

Q

N

G

L

L

S

K

G

G

K

K

T

I

I

I

G

G

A

V

Q

Q

R

G

A

G

T

T

L

T

G

F

A

D

Q

S

Y

Y

L

L

E

Q

D

D

N

S

F

F

T

G

G

N

K

S

A

I

D

T

L

I

K

Q

F

R

Y

Y

D

P

N

S

Q

E

D

E

N

D

V

A

Y

L

L

M

D

D

L

L

V

T

A

S

G

G

R

R

L

V

D

D

I

A

V

V

L

V

S

G

D

D

E

T

L

P

P

L

T

I

Y

K

N

Q

W

W

L

L

K

K

T

-

S

-

E

Q

S

N

G

G

A

R

K

R

-

E

F

Y

E

V

F

L

K

I

G

G

D

K

A

P

F

V

M

N

K

D

T

P

D

N

-

Y

-

F

-

G

-

K

N

G

I

V

G

G

I

I

A

A

V

V

R

K

K

K

G

G

D

N

D

Q

K

A

L

L

K

L

E

L

K

K

L

L

N

N

K

K

A

A

L

L

D

A

Q

A

I

I

L

K

A

A

D

N

G

G

T

V

Y

Y

Q

A

K

A

I

I

N

V

A

Q

K

K

Y

Y

F

F

binding arginine: E9 (= E34), Y12 (≠ W37), W48 (= W75), G65 (≠ A92), G66 (≠ S93), N68 (≠ S95), R73 (= R100), S89 (≠ R116)

8hqrA Crystal structure of the arginine-/lysine-binding protein sar11_1210 from 'candidatus pelagibacter ubique' htcc1062 bound to arginine
34% identity, 88% coverage: 27:249/252 of query aligns to 8:263/267 of 8hqrA

query
sites
8hqrA

D

D

K

K

V

I

R

K

F

I

V

G

T

T

E
|
E

G

G

A

A

W
x
Y

A

P

P

P

F

W

N

N

F

S

I

K

D

D

E

A

A

S

G

G

Q

A

P

L

Q

I

G

G

F

F

D

E

V

V

D

E

I

L

A

A

R

E

A

E

L

L

C

C

A

K

K

I

M

M

A

G

A

R

D

E

C

C

E

T

I

I

L

V

T

E

Q

Q

D

D

W
|
W

D

D

G

G

L

M

I

I

P

P

G

A

L

L

K

L

V

M

R

R

K

K

F

F

D

D

A

A

I

I

I

M

A
|
A

S
x
G

M

M

S
|
S

I

I

T

T

E

A

D

E

R
|
R

L

Q

K

K

V

T

V

I

D

T

F

F

T

S

N

Q

K

G

Y

Y

Y

A

-

D

-
x
E

-

V

-

A

-

L

-

A

-

V

-

M

-

K

S

G

G

S

L

L

R

E

F

S

M

M

G

D

R

T

V

P

E

E

D

G

-

I

N

N

F

L

D

T

L

L

S

G

N

G

-

S

-

A

-

V

-

K

-

T

-

L

-

K

-

T

-

L

-

T

-

A

L

L

S

A

G

G

K

K

T

T

I

V

G

C

A

T

Q
|
Q

R

T

A

G

T
|
T

L
x
I

G

H

A

Q

Q

N

Y

F

L

L

E

E

D

S

N

G

F

D

T

V

G

G

K

K

A

V

D

N

L

V

K

R

F

T

Y

Y

D

K

N

T

Q

Q

D

D

N

E

V

V

Y

N

L

L

D

D

L

L

V

T

A

S

G

G

R

R

L

C

D

D

I

V

V

A

L

L

S

A

D

A

E

A

L

V

P

A

T

F

Y

T

N

D

W

Y

L

A

K

D

T

K

S

S

E

G

S

K

G

P

A

V

K

V

F

L

-

V

-

G

-

P

E

T

F

F

K

S

G

G

D

G

A

A

F

F

M

-

K

-

T

G

D

N

N

G

I

V

G

G

I

V

A

G

V

I

R

R

K

Q

G

G

D

G

D

D

-

D

-

A

-

I

-

G

-

T

-

R

-

D

-

A

K

K

L

L

K

L

E

K

K

D

L

F

N

N

K

K

A

A

L

I

D

N

Q

T

I

A

L

R

A

K

D

Q

G

G

T

I

Y

I

Q

S

K

K

I

L

N

A

A

I

K

K

Y

H

F

F

P

G

F

F

binding arginine: E15 (= E34), Y18 (≠ W37), W56 (= W75), A73 (= A92), G74 (≠ S93), S76 (= S95), R81 (= R100), E94 (vs. gap), Q143 (= Q138), T146 (= T141), I147 (≠ L142)

5orgA Structure of the periplasmic binding protein (pbp) occj from a. Tumefaciens b6 in complex with octopine. (see paper)
33% identity, 87% coverage: 29:247/252 of query aligns to 6:250/257 of 5orgA

query
sites
5orgA

V

I

R

T

F

I

V

A

T

T

E
|
E

G

G

A

G

W
x
Y

A

A

P

P

F

W

N

N

F

F

I

S

D

G

E

P

A

G

G

G

Q

K

P

L

Q

D

G

G

F

F

D

E

V

I

D

D

I

L

A

A

R

N

A

A

L

L

C

C

A

E

K

K

M

M

A

K

A

A

D

K

C

C

E

Q

I

I

L

V

T

A

Q

Q

D

N

W
|
W

D

D

G

G

L

I

I

M

P

P

G

S

L

L

K

T

V

G

R

K

K

K

F

Y

D

D

A

A

I

I

I

M

A
|
A

S
x
A

M
|
M

S
|
S

I

V

T

T

E

P

D

K

R
|
R

L

Q

K

E

V

V

V

I

D

G

F

F

T

S

N

I

K

P

Y

Y

Y

A

S

A

G

G

-

I

-
x
N

G

G

L

F

R

A

F

V

M

M

G

G

-

D

-

S

-

K

-

L

-

A

-

E

-

M

-

P

R

G

V

L

E

G

D

E

N

T

F

Y

D

S

L

L

-

D

-

S

-

Q

-

A

-

D

-

A

-

K

-

A

-

I

-

A

-

D

-

I

-

S

S

S

N

F

L

L

S

N

G

G

K

T

T

T

I

V

G

G

A

V

Q
|
Q

R

G

A

S

T
|
T

L
x
T

G

A

A

S

Q

T

Y

F

L

L

E

D

D

K

N

Y

F

F

T

K

G

G

K

S

A

V

D

D

L

I

K

K

F

E

Y

Y

D

K

N

S

Q

V

D

E

N

E

V

H

Y

N

L

L

D

D

L

L

V

T

A

S

G

G

R

R

L

L

D

D

I

A

V

V

L

L

S

A

D
x
N

E

A

L

T

P

V

T

L

Y

A

N

A

W

A

L

I

K

E

T

K

S

P

E

E

-

M

S

K

G

G

A

A

K

K

F

L

E

V

-

G

-

P

-

L

F

F

K

S

G

G

D

G

A

E

F

F

M

-

K

-

T

-

D

G

N

V

I

V

G

A

I

V

A

G

V

L

R

R

K

K

G

E

D

D

D

T

K

A

L

L

K

K

E

A

K

D

L

F

N

D

K

A

A

A

L

I

D

K

Q

A

I

A

L

S

A

E

D

D

G

G

T

T

Y

I

Q

K

K

T

I

L

N

S

A

L

K

K

Y

W

F

F

binding octopine: E11 (= E34), Y14 (≠ W37), W52 (= W75), A69 (= A92), A70 (≠ S93), M71 (= M94), S72 (= S95), R77 (= R100), N92 (vs. gap), Q140 (= Q138), T143 (= T141), T144 (≠ L142), N183 (≠ D181)

2y7iA Structural basis for high arginine specificity in salmonella typhimurium periplasmic binding protein stm4351. (see paper)
34% identity, 88% coverage: 25:247/252 of query aligns to 4:227/228 of 2y7iA

query
sites
2y7iA

A

S

A

A

D

R

K

T

V

L

R
x
H

F

F

V

G

T

T

E

S

G

A

A

T

W
x
Y

A

A

P

P

F

Y

N
x
E

F

F

I

V

D
|
D

E

A

A
x
D

G

N

Q

K

P

I

Q

V

G

G

F

F

D

D

V

I

D

D

I

V

A

A

R

N

A

A

L

V

C

C

A

K

K

E

M

M

A

Q

A

A

D

E

C

C

E

S

I

F

L

T

T

N

Q

Q

D

S

W
x
F

D
|
D

G

S

L

L

I

I

P

P

G

S

L

L

K

R

V

F

R

K

K

K

F

F

D
|
D

A

A

I

V

I

I

A
|
A

S
x
G

M

M

S
x
D

I

M

T

T

E

P

D

K

R
|
R

L

E

K

Q

V

Q

V

V

D

S

F

F

T

S

N

Q

K

P

Y

Y

S

E

G

G

-

L

G

S

L

A

R

V

F

V

M

V

G

T

R

R

V

K

E

G

D

A

N

Y

F

H

D

T

L

F

S

A

N

D

L

L

S

K

G

G

K

K

T

K

I

V

G

G

A

L

Q
x
E

R

N

A

G

T
|
T

L
x
T

G

H

A

Q

Q

R

Y

Y

L

L

E

Q

D

D

N

K

F

Q

T

Q

G

A

K

I

A

T

D

P

L

V

K

A

F

-

Y

Y

D
|
D

N

S

Q

Y

D

L

N

N

V

A

Y

F

L

T

D

D

L

L

V

K

A

N

G

N

R

R

L

L

D

E

I

G

V

V

L

F

S

G

D
|
D

E

V

L

A

P

A

T

I

Y

G

N

K

W

W

L

L

K

K

T

N

S

N

E

P

S

D

G

Y

A

A

K

I

F

M

-

D

E

E

F

R

K

A

G

S

D

D

A

P

F

D

M

Y

K

Y

T

G

D

K

N

G

I

L

G

G

I

I

A

A

V

V

R

R

K

K

G

D

D

N

D

D

K

A

L

L

K

L

E

Q

K

E

L

I

N

N

K

A

A

A

L

L

D

D

Q

K

I

V

L

K

A

A

D

S

G

P

T

E

Y

Y

Q

A

K

Q

I

M

N

Q

A

E

K

K

Y

W

F

F

binding arginine: Y16 (≠ W37), E20 (≠ N41), F54 (≠ W75), A71 (= A92), G72 (≠ S93), D74 (≠ S95), R79 (= R100), E118 (≠ Q138), T121 (= T141), T122 (≠ L142), D160 (= D181)
binding zinc ion: H9 (≠ R30), D23 (= D44), D25 (≠ A46), D55 (= D76), D67 (= D88), D140 (= D161)

3vv5A Crystal structure of ttc0807 complexed with (s)-2-aminoethyl-l- cysteine (aec) (see paper)
32% identity, 90% coverage: 22:247/252 of query aligns to 8:230/237 of 3vv5A

query
sites
3vv5A

S

E

V

I

Q

K

A

R

A

S

D

G

K

E

V

I

R

R

F

I

V

G

T

T

E
|
E

G

G

A

A

W
x
F

A

P

P

P

F

F

N
|
N

F

Y

I

F

D

D

E

E

A

R

G

N

Q

Q

P

L

Q

T

G

G

F

F

D

E

V

V

D

D

I

L

A

G

R

N

A

A

L

I

C

A

A

E

K

R

M

L

A

G

A

L

D

K

C

P

E

R

I

W

L

I

T

A

Q

Q

D

S

W
x
F

D

D

G

T

L

L

I

L

P

I

G

Q

L

L

K

N

V

Q

R

G

K

R

F

F

D

D

A

F

I

V

I

I

A
|
A

S
|
S

M

H

S
x
G

I

I

T

T

E

E

D

E

R
|
R

L

A

K

R

V

A

V

V

D

D

F

F

T

T

N

N

K

P

Y

H

Y

Y

S

C

G

T

G

G

L

G

R

V

F

I

M

V

G

S

R

R

V

K

E

G

D

G

N

P

F

R

D

T

L

A

S

K

N

D

L

L

S

Q

G

G

K

K

T

V

I

V

G

G

A

V

Q

Q

R

-

A

-

T

-

L

V

G

G

A
x
T

Q
x
T

Y
|
Y

L

M

E

E

-

A

D

Q

N

K

F

I

T

P

G

G

K

I

A

K

D

E

L

V

K

R

F

T

Y

Y

D

Q

N

R

Q

D

D

P

N

D

V

A

Y

L

L

Q

D

D

L

L

V

L

A

A

G

G

R

R

L

I

D

D

I

T

V

W

L

I

S

T

D

D

E

R

L

F

P

V

T

A

Y

K

N

E

W

A

L

I

K

K

T

E

S

R

E

K

S

L

G

E

A

N

K

T

F

L

E

Q

F

V

K

G

G

E

D

L

A

V

F

F

M

Q

K

-

T

-

D

E

N

R

I

V

G

A

I

M

A

A

V

V

R

A

K

K

G

G

D

N

D

K

K

S

L

L

K

L

E

D

K

A

L

L

N

N

K

R

A

A

L

L

D

A

Q

E

I

L

L

M

A

Q

D

D

G

G

T

T

Y

Y

Q

A

K

R

I

I

N

S

A

Q

K

K

Y

W

F

F

binding l-thialysine: E20 (= E34), F23 (≠ W37), N27 (= N41), F61 (≠ W75), A78 (= A92), S79 (= S93), G81 (≠ S95), R86 (= R100), T127 (≠ A144), T128 (≠ Q145), Y129 (= Y146)

3vvfA Crystal structure of ttc0807 complexed with arginine (see paper)
32% identity, 90% coverage: 22:247/252 of query aligns to 12:234/241 of 3vvfA

query
sites
3vvfA

S

E

V

I

Q

K

A

R

A

S

D

G

K

E

V

I

R

R

F

I

V

G

T

T

E
|
E

G

G

A

A

W
x
F

A

P

P

P

F

F

N

N

F

Y

I

F

D

D

E

E

A

R

G

N

Q

Q

P

L

Q

T

G

G

F

F

D

E

V

V

D

D

I

L

A

G

R

N

A

A

L

I

C

A

A

E

K

R

M

L

A

G

A

L

D

K

C

P

E

R

I

W

L

I

T

A

Q

Q

D

S

W
x
F

D

D

G

T

L

L

I

L

P

I

G

Q

L

L

K

N

V

Q

R

G

K

R

F

F

D

D

A

F

I

V

I

I

A
|
A

S
|
S

M
x
H

S
x
G

I

I

T

T

E

E

D

E

R
|
R

L

A

K

R

V

A

V

V

D

D

F

F

T

T

N

N

K

P

Y

H

Y

Y

S

C

G

T

G

G

L

G

R

V

F

I

M

V

G

S

R

R

V

K

E

G

D

G

N

P

F

R

D

T

L

A

S

K

N

D

L

L

S

Q

G

G

K

K

T

V

I

V

G

G

A

V

Q
|
Q

R

-

A

-

T

-

L

V

G

G

A
x
T

Q
x
T

Y
|
Y

L

M

E

E

-

A

D

Q

N

K

F

I

T

P

G

G

K

I

A

K

D

E

L

V

K

R

F

T

Y

Y

D

Q

N

R

Q

D

D

P

N

D

V

A

Y

L

L

Q

D

D

L

L

V

L

A

A

G

G

R

R

L

I

D

D

I

T

V

W

L

I

S

T

D

D

E

R

L

F

P

V

T

A

Y

K

N

E

W

A

L

I

K

K

T

E

S

R

E

K

S

L

G

E

A

N

K

T

F

L

E

Q

F

V

K

G

G

E

D

L

A

V

F

F

M

Q

K

-

T

-

D
x
E

N

R

I

V

G

A

I

M

A

A

V

V

R

A

K

K

G

G

D

N

D

K

K

S

L

L

K

L

E

D

K

A

L

L

N

N

K

R

A

A

L

L

D

A

Q

E

I

L

L

M

A

Q

D

D

G

G

T

T

Y

Y

Q

A

K

R

I

I

N

S

A

Q

K

K

Y

W

F

F

binding arginine: E24 (= E34), F27 (≠ W37), F65 (≠ W75), A82 (= A92), S83 (= S93), H84 (≠ M94), G85 (≠ S95), R90 (= R100), Q128 (= Q138), T131 (≠ A144), T132 (≠ Q145), Y133 (= Y146), E196 (≠ D209)

3vveA Crystal structure of ttc0807 complexed with lysine (see paper)
32% identity, 90% coverage: 22:247/252 of query aligns to 12:234/241 of 3vveA

query
sites
3vveA

S

E

V

I

Q

K

A

R

A

S

D

G

K

E

V

I

R

R

F

I

V

G

T

T

E
|
E

G

G

A

A

W
x
F

A

P

P

P

F

F

N

N

F

Y

I

F

D

D

E

E

A

R

G

N

Q

Q

P

L

Q

T

G

G

F

F

D

E

V

V

D

D

I

L

A

G

R

N

A

A

L

I

C

A

A

E

K

R

M

L

A

G

A

L

D

K

C

P

E

R

I

W

L

I

T

A

Q

Q

D

S

W
x
F

D

D

G

T

L

L

I

L

P

I

G

Q

L

L

K

N

V

Q

R

G

K

R

F

F

D

D

A

F

I

V

I

I

A

A

S
|
S

M
x
H

S

G

I

I

T

T

E

E

D

E

R
|
R

L

A

K

R

V

A

V

V

D

D

F

F

T

T

N

N

K

P

Y

H

Y

Y

S

C

G

T

G

G

L

G

R

V

F

I

M

V

G

S

R

R

V

K

E

G

D

G

N

P

F

R

D

T

L

A

S

K

N

D

L

L

S

Q

G

G

K

K

T

V

I

V

G

G

A

V

Q
|
Q

R

-

A

-

T

-

L

V

G

G

A
x
T

Q
x
T

Y
|
Y

L

M

E

E

-

A

D

Q

N

K

F

I

T

P

G

G

K

I

A

K

D

E

L

V

K

R

F

T

Y

Y

D

Q

N

R

Q

D

D

P

N

D

V

A

Y

L

L

Q

D

D

L

L

V

L

A

A

G

G

R

R

L

I

D

D

I

T

V

W

L

I

S

T

D

D

E

R

L

F

P

V

T

A

Y

K

N

E

W

A

L

I

K

K

T

E

S

R

E

K

S

L

G

E

A

N

K

T

F

L

E

Q

F

V

K

G

G

E

D

L

A

V

F

F

M

Q

K

-

T

-

D
x
E

N

R

I

V

G

A

I

M

A

A

V

V

R

A

K

K

G

G

D

N

D

K

K

S

L

L

K

L

E

D

K

A

L

L

N

N

K

R

A

A

L

L

D

A

Q

E

I

L

L

M

A

Q

D

D

G

G

T

T

Y

Y

Q

A

K

R

I

I

N

S

A

Q

K

K

Y

W

F

F

binding lysine: E24 (= E34), F27 (≠ W37), F65 (≠ W75), S83 (= S93), H84 (≠ M94), R90 (= R100), Q128 (= Q138), T131 (≠ A144), T132 (≠ Q145), Y133 (= Y146), E196 (≠ D209)

3vvdA Crystal structure of ttc0807 complexed with ornithine (see paper)
32% identity, 90% coverage: 22:247/252 of query aligns to 12:234/241 of 3vvdA

query
sites
3vvdA

S

E

V

I

Q

K

A

R

A

S

D

G

K

E

V

I

R

R

F

I

V

G

T

T

E
|
E

G

G

A

A

W

F

A

P

P

P

F

F

N

N

F

Y

I

F

D

D

E

E

A

R

G

N

Q

Q

P

L

Q

T

G

G

F

F

D

E

V

V

D

D

I

L

A

G

R

N

A

A

L

I

C

A

A

E

K

R

M

L

A

G

A

L

D

K

C

P

E

R

I

W

L

I

T

A

Q

Q

D

S

W
x
F

D

D

G

T

L

L

I

L

P

I

G

Q

L

L

K

N

V

Q

R

G

K

R

F

F

D

D

A

F

I

V

I

I

A

A

S
|
S

M
x
H

S
x
G

I

I

T

T

E

E

D

E

R
|
R

L

A

K

R

V

A

V

V

D

D

F

F

T

T

N

N

K

P

Y

H

Y

Y

S

C

G

T

G

G

L

G

R

V

F

I

M

V

G

S

R

R

V

K

E

G

D

G

N

P

F

R

D

T

L

A

S

K

N

D

L

L

S

Q

G

G

K

K

T

V

I

V

G

G

A

V

Q
|
Q

R

-

A

-

T

-

L

V

G

G

A
x
T

Q
x
T

Y
|
Y

L

M

E

E

-

A

D

Q

N

K

F

I

T

P

G

G

K

I

A

K

D

E

L

V

K

R

F

T

Y

Y

D

Q

N

R

Q

D

D

P

N

D

V

A

Y

L

L

Q

D

D

L

L

V

L

A

A

G

G

R

R

L

I

D

D

I

T

V

W

L

I

S

T

D

D

E

R

L

F

P

V