SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing WP_104485187.1 NCBI__GCF_002936955.1:WP_104485187.1 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)
40% identity, 99% coverage: 3:256/257 of query aligns to 1:259/260 of P02911

query
sites
P02911

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D33 (≠ E32) binding L-arginine; binding L-lysine; binding L-ornithine; mutation to A: Decreases arginine and histidine binding affinity.
Y36 (= Y35) mutation to A: Shows a drastic decrease in arginine and histidine binding affinity.
D52 (= D51) mutation to A: Shows a drastic decrease in arginine and histidine binding affinity.
C60 (= C59) modified: Disulfide link with 67
C67 (= C66) modified: Disulfide link with 60
F74 (≠ W73) mutation to A: Shows a drastic decrease in arginine and histidine binding affinity.
S91 (≠ A90) binding L-arginine; binding L-ornithine; mutation to A: Has no effect on the arginine and histidine binding affinity.
S92 (= S91) binding L-arginine; binding L-lysine; binding L-ornithine; mutation to A: Decreases arginine and histidine binding affinity.
S94 (= S93) binding L-arginine; binding L-lysine; binding L-ornithine; mutation to A: Decreases arginine and histidine binding affinity.
R99 (= R98) 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 (= T142) binding L-arginine; binding L-lysine; binding L-ornithine
D183 (≠ N180) 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)
42% identity, 89% coverage: 27:256/257 of query aligns to 3:234/235 of 5owfA

query
sites
5owfA

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binding glutamine: Y11 (= Y35), F49 (≠ W73), S66 (≠ A90), S67 (= S91), S69 (= S93), R74 (= R98), K114 (≠ Q138), S117 (= S141), T118 (= T142), D158 (≠ N180)

1lstA Three-dimensional structures of the periplasmic lysine-, arginine-, ornithine-binding protein with and without a ligand (see paper)
42% identity, 89% coverage: 27:256/257 of query aligns to 6:237/238 of 1lstA

query
sites
1lstA

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binding lysine: Y14 (= Y35), F52 (≠ W73), S70 (= S91), S72 (= S93), R77 (= R98), L117 (≠ Q138), S120 (= S141), T121 (= T142), Q122 (≠ H143), D161 (≠ N180)

1lahE Structural bases for multiple ligand specificity of the periplasmic lysine-, arginine-, ornithine-binding protein (see paper)
42% identity, 89% coverage: 27:256/257 of query aligns to 6:237/238 of 1lahE

query
sites
1lahE

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binding L-ornithine: Y14 (= Y35), F52 (≠ W73), S70 (= S91), S72 (= S93), R77 (= R98), S120 (= S141), Q122 (≠ H143), D161 (≠ N180)

1lagE Structural bases for multiple ligand specificity of the periplasmic lysine-, arginine-, ornithine-binding protein (see paper)
42% identity, 89% coverage: 27:256/257 of query aligns to 6:237/238 of 1lagE

query
sites
1lagE

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K

K

Q

D

D

D

D

T

A

E

L

L

R

K

E

A

K

A

F

F

N

D

D

K

A

A

I

L

K

T

A

E

I

L

R

R

S

Q

N

D

G

G

V

T

Y

Y

Q

D

Q

K

I

M

Q

A

D

K

K

K

Y

Y

F

F

E

D

F

F

D

N

I

V

Y

Y

G

G

binding histidine: Y14 (= Y35), F52 (≠ W73), S69 (≠ A90), S70 (= S91), L71 (≠ M92), S72 (= S93), R77 (= R98), L117 (≠ Q138), S120 (= S141), Q122 (≠ H143), D161 (≠ N180)

1lafE Structural bases for multiple ligand specificity of the periplasmic lysine-, arginine-, ornithine-binding protein (see paper)
42% identity, 89% coverage: 27:256/257 of query aligns to 6:237/238 of 1lafE

query
sites
1lafE

V

V

R

R

I

I

A

G

V

T

E
x
D

G

T

A

T

Y
|
Y

P

A

P

P

Y

F

S

S

W

S

T

K

T

D

T

A

E

K

G

G

E

E

L

F

K

I

G

G

F

F

D

D

I

I

D

D

M

L

A

G

N

N

A

E

L

M

C

C

E

K

E

R

M

M

Q

Q

V

V

K

K

C

C

T

T

M

W

V

V

T

A

Q

S

E

D

W
x
F

D

D

G

A

M

L

I

I

P

P

S

S

L

L

L

K

A

A

R

K

K

K

F

I

D

D

A

A

I

I

V

I

A
x
S

S
|
S

M

L

S
|
S

I

I

T

T

E

D

E

K

R
|
R

K

Q

L

Q

K

E

V

I

D

A

F

F

T

S

D

D

K

K

Y

L

Y

Y

Q

A

I

A

S

D

S

S

R

R

F

L

V

I

A

A

K

A

Q

K

G

G

T

S

E

P

F

I

S

Q

F

P

D

T

K

L

A

E

G

S

L

L

K

K

G

G

K

K

S

H

V

V

G

G

V

V

Q
x
L

G

Q

S

G

S
|
S

T
|
T

H
x
Q

E

E

K

A

Y

Y

V

A

A

N

D

D

N

N

F

W

-

R

-

T

E

K

G

G

V

V

D

D

V

V

K

V

R

A

Y

Y

G

A

S

N

P

Q

E

D

N

L

A

I

F

Y

L

S

D

D

L

L

I

T

S

A

G

G

R

R

V

L

D

D

L

A

V

A

F

L

N

Q

N
x
D

I

E

P

V

A

A

I

A

E

S

S

E

G

G

L

F

L

L

E

K

K

Q

E

P

N

A

G

G

G

K

D

E

F

Y

A

A

F

F

T

A

G

G

P

P

L

S

I

V

T

K

D

D

K

K

E

K

W

Y

F

F

G

G

E

D

G

G

V

T

G

G

I

V

A

G

V

L

R

R

K

K

Q

D

D

D

D

T

A

E

L

L

R

K

E

A

K

A

F

F

N

D

D

K

A

A

I

L

K

T

A

E

I

L

R

R

S

Q

N

D

G

G

V

T

Y

Y

Q

D

Q

K

I

M

Q

A

D

K

K

K

Y

Y

F

F

E

D

F

F

D

N

I

V

Y

Y

G

G

binding arginine: D11 (≠ E32), Y14 (= Y35), F52 (≠ W73), S69 (≠ A90), S70 (= S91), S72 (= S93), R77 (= R98), L117 (≠ Q138), S120 (= S141), T121 (= T142), Q122 (≠ H143), D161 (≠ N180)

P02910 Histidine-binding periplasmic protein; HBP from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see 2 papers)
40% identity, 91% coverage: 25:257/257 of query aligns to 26:260/260 of P02910

query
sites
P02910

K

Q

Q

K

V

I

R

R

I

I

A

G

V

T

E

D

G

P

A

T

Y

Y

P

A

P

P

Y

F

S
x
E

W

S

T
x
K

T

N

T

A

E

Q

G

G

E
|
E

L

L

K

V

G

G

F

F

D

D

I

I

D

D

M

L

A

A

N

K

A

E

L

L

C

C

E

K

E

R

M

I

Q

N

V

T

K

Q

C

C

T

T

M

F

V

V

T

E

Q

N

E

P

W

L

D

D

G

A

M

L

I

I

P

P

S

S

L

L

L

K

A

A

R

K

K

K

F

I

D

D

A

A

I

I

V

M

A

S

S

S

M

L

S

S

I

I

T

T

E

E

E

K

R

R

K

Q

L

Q

K

E

V

I

D

A

F

F

T

T

D

D

K

K

Y

L

Y

Y

Q

A

I

A

S

D

S

S

R

R

F

L

V

V

A

V

K

A

Q

K

G

N

T

S

E

D

F

I

S

Q

F

P

D

T

K

V

A

A

G

S

L

L

K

K

G

G

K

K

S

R

V

V

G

G

V

V

Q

L

G

Q

S

G

S

T

T

T

H

Q

E

E

K

T

Y

F

V

G

A

N

D

E

N

H

F

W

-

A

-

P

E

K

G

G

V

I

D

E

V

I

K

V

R

S

Y

Y

G

Q

S

G

P

Q

E

D

N

N

A

I

F

Y

L

S

D
|
D

L

L

I

T

S

A

G

G

R
|
R

V

I

D
|
D

L

A

V

A

F

F

N

Q

N

D

I

E

P

V

A

A

I

A

E

S

S

E

G

G

L

F

L

L

E

K

K

Q

E

P

N

V

G

G

G

K

D

D

F

Y

A

K

F

F

T

G

G

G

P

P

L

A

I

V

T

K

D

D

K

E

E

K

W

L

F

F

G

G

E

V

G

G

V

T

G

G

I

M

A

G

V

L

R

R

K

K

Q

E

D

D

D

N

A

E

L

L

R

R

E

E

K

A

F

L

N

N

D

K

A

A

I

F

K

A

A

E

I

M

R

R

S

A

N

D

G

G

V

T

Y

Y

Q

E

Q

K

I

L

Q

A

D

K

K

K

Y

Y

F

F

E

D

F

F

D

D

I

V

Y

Y

G

G

E40 (≠ S39) mutation to K: Decrease in ATPase-inducing activity and histidine transport; when associated with K-47.
K42 (≠ T41) mutation to E: Increases ATPase-inducing activity and histidine transport; when associated with K-47.
E47 (= E46) 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 (= D168) mutation D->A,N: Strong decrease in ATPase-inducing activity and histidine transport.
R176 (= R173) mutation R->D,S: Strong decrease in ATPase-inducing activity and histidine transport.
D178 (= D175) 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)
40% identity, 91% coverage: 25:257/257 of query aligns to 4:238/238 of 1hslA

query
sites
1hslA

K

Q

Q

K

V

I

R

R

I

I

A

G

V

T

E

D

G

P

A

T

Y
|
Y

P

A

P

P

Y

F

S

E

W

S

T

K

T

N

T

A

E

Q

G

G

E

E

L

L

K

V

G

G

F

F

D

D

I

I

D

D

M

L

A

A

N

K

A

E

L

L

C

C

E

K

E

R

M

I

Q

N

V

T

K

Q

C

C

T

T

M

F

V

V

T

E

Q

N

E

P

W
x
L

D

D

G

A

M

L

I

I

P

P

S

S

L

L

L

K

A

A

R

K

K

K

F

I

D

D

A

A

I

I

V

M

A
x
S

S
|
S

M
x
L

S
|
S

I

I

T

T

E

E

E

K

R
|
R

K

Q

L

Q

K

E

V

I

D

A

F

F

T

T

D

D

K

K

Y

L

Y

Y

Q

A

I

A

S

D

S

S

R

R

F

L

V

V

A

V

K

A

Q

K

G

N

T

S

E

D

F

I

S

Q

F

P

D

T

K

V

A

A

G

S

L

L

K

K

G

G

K

K

S

R

V

V

G

G

V

V

Q

L

G

Q

S

G

S
x
T

T
|
T

H

Q

E

E

K

T

Y

F

V

G

A

N

D

E

N

H

F

W

-

A

-

P

E

K

G

G

V

I

D

E

V

I

K

V

R

S

Y

Y

G

Q

S

G

P

Q

E

D

N

N

A

I

F

Y

L

S

D

D

L

L

I

T

S

A

G

G

R

R

V

I

D

D

L

A

V

A

F

F

N

Q

N
x
D

I

E

P

V

A

A

I

A

E

S

S

E

G

G

L

F

L

L

E

K

K

Q

E

P

N

V

G

G

G

K

D

D

F

Y

A

K

F

F

T

G

G

G

P

P

L

A

I

V

T

K

D

D

K

E

E

K

W

L

F

F

G

G

E

V

G

G

V

T

G

G

I

M

A

G

V

L

R

R

K

K

Q

E

D

D

D

N

A

E

L

L

R

R

E

E

K

A

F

L

N

N

D

K

A

A

I

F

K

A

A

E

I

M

R

R

S

A

N

D

G

G

V

T

Y

Y

Q

E

Q

K

I

L

Q

A

D

K

K

K

Y

Y

F

F

E

D

F

F

D

D

I

V

Y

Y

G

G

binding histidine: Y14 (= Y35), L52 (≠ W73), S69 (≠ A90), S70 (= S91), L71 (≠ M92), S72 (= S93), R77 (= R98), T120 (≠ S141), T121 (= T142), D161 (≠ N180)

P0AEU0 Histidine-binding periplasmic protein; HBP from Escherichia coli (strain K12) (see 3 papers)
39% identity, 91% coverage: 25:257/257 of query aligns to 26:260/260 of P0AEU0

query
sites
P0AEU0

K

Q

Q

N

V

I

R

R

I

I

A

G

V

T

E

D

G

P

A

T

Y

Y

P

A

P

P

Y

F

S

E

W

S

T

K

T

N

T

S

E

Q

G

G

E

E

L

L

K

V

G

G

F

F

D

D

I

I

D

D

M

L

A

A

N

K

A

E

L

L

C
|
C

E

K

E

R

M

I

Q

N

V

T

K

Q

C
|
C

T

T

M

F

V

V

T

E

Q

N

E

P

W

L

D

D

G

A

M

L

I

I

P

P

S

S

L

L

L

K

A

A

R

K

K

K

F

I

D

D

A

A

I

I

V

M

A
x
S

S
|
S

M

L

S
|
S

I

I

T

T

E

E

E

K

R
|
R

K

Q

L

Q

K

E

V

I

D

A

F

F

T

T

D

D

K

K

Y

L

Y

Y

Q

A

I

A

S

D

S

S

R

R

F

L

V

V

A

V

K

A

Q

K

G

N

T

S

E

D

F

I

S

Q

F

P

D

T

K

V

A

E

G

S

L

L

K

K

G

G

K

K

S

R

V

V

G

G

V

V

Q

L

G

Q

S

G

S

T

T
|
T

H

Q

E

E

K

T

Y

F

V

G

A

N

D

E

N

H

F

W

-

A

-

P

E

K

G

G

V

I

D

E

V

I

K

V

R

S

Y

Y

G

Q

S

G

P

Q

E

D

N

N

A

I

F

Y

L

S

D

D

L

L

I

T

S

A

G

G

R

R

V

I

D

D

L

A

V

A

F

F

N

Q

N
x
D

I

E

P

V

A

A

I

A

E

S

S

E

G

G

L

F

L

L

E

K

K

Q

E

P

N

V

G

G

G

K

D

D

F

Y

A

K

F

F

T

G

G

G

P

P

L

S

I

V

T

K

D

D

K

E

E

K

W

L

F

F

G

G

E

V

G

G

V

T

G

G

I

M

A

G

V

L

R

R

K

K

Q

E

D

D

D

N

A

E

L

L

R

R

E

E

K

A

F

L

N

N

D

K

A

A

I

F

K

A

A

E

I

M

R

R

S

A

N

D

G

G

V

T

Y

Y

Q

E

Q

K

I

L

Q

A

D

K

K

K

Y

Y

F

F

E

D

F

F

D

D

I

V

Y

Y

G

G

C60 (= C59) modified: Disulfide link with 67
C67 (= C66) modified: Disulfide link with 60
S91 (≠ A90) binding L-histidine
S92 (= S91) binding L-histidine
S94 (= S93) binding L-histidine
R99 (= R98) binding L-histidine
T143 (= T142) binding L-histidine
D183 (≠ N180) binding L-histidine

Sites not aligning to the query:

1:22 signal peptide

3tqlA Structure of the amino acid abc transporter, periplasmic amino acid- binding protein from coxiella burnetii. (see paper)
45% identity, 87% coverage: 27:250/257 of query aligns to 4:225/225 of 3tqlA

query
sites
3tqlA

V

I

R

K

I

F

A

A

V

T

E
|
E

G

A

A

T

Y
|
Y

P

P

Y

Y

S

V

W

Y

T

M

T

-

E

G

G

G

E

Q

L

V

K

E

G

G

F

F

D

G

I

A

D

D

M

I

A

V

N

K

A

A

L

V

C

C

E

K

E

Q

M

M

Q

Q

V

A

K

V

C

C

T

T

M

I

V

S

T

N

Q

Q

E

P

W
|
W

D

D

G

S

M

L

I

I

P

P

S

S

L

L

L

K

A

L

R

G

K

K

F

F

D

D

A

A

I

L

V

F

A
x
G

S
x
G

M

M

S
x
N

I

I

T

T

E

T

E

A

R
|
R

K

Q

L

K

K

E

V

V

D

D

F

F

T

T

D

D

K

P

Y

Y

Q

T

I

N

S

S

S

V

R
x
S

F

F

V

I

A

A

K

D

Q

K

G

N

T

T

E

P

F

L

S

T

F

L

D

S

K

K

A

Q

G

G

L

L

K

K

G

G

K

K

S

I

V

I

G

G

V

V

Q

Q

G

G

S

G

S

T

T

T

H

F

E

D

K

S

Y

Y

V

L

A

Q

D

D

N

S

F

F

-

G

E

N

G

S

V

I

D

T

V

I

K

Q

R

R

Y

Y

G

P

S

S

P

E

E

E

N

D

A

A

F

L

L

M

D

D

L

L

I

T

S

S

G

G

R

R

V

V

D

D

L

A

V

V

F

V

N

G

N

D

I

T

P

P

A

L

I

I

E

K

S

Q

G

W

L

L

L

-

E

-

K

K

E

Q

N

N

G

G

-

R

G

R

D

E

F

Y

A

V

F

L

T

I

G

G

P

K

L

P

I

V

T

N

D

D

K

P

E

N

W

Y

F

F

G

G

E

K

G

G

V

V

G

G

I

I

A

A

V

V

R

K

K

K

Q

G

D

N

D

Q

A

A

L

L

R

L

E

L

K

K

F

L

N

N

D

K

A

A

I

L

K

A

A

A

I

I

R

K

S

A

N

N

G

G

V

V

Y

Y

Q

A

I

I

Q

V

D

Q

K

K

Y

Y

F

F

binding arginine: E9 (= E32), Y12 (= Y35), W48 (= W73), G65 (≠ A90), G66 (≠ S91), N68 (≠ S93), R73 (= R98), S89 (≠ R114)

2y7iA Structural basis for high arginine specificity in salmonella typhimurium periplasmic binding protein stm4351. (see paper)
37% identity, 88% coverage: 25:250/257 of query aligns to 6:227/228 of 2y7iA

query
sites
2y7iA

K

R

Q

T

V

L

R
x
H

I

F

A

G

V

T

E

S

G

A

A

T

Y
|
Y

P

A

P

P

Y

Y

S
x
E

W

F

T

V

T
x
D

T

A

E
x
D

G

N

E

K

L

I

K

V

G

G

F

F

D

D

I

I

D

D

M

V

A

A

N

N

A

A

L

V

C

C

E

K

E

E

M

M

Q

Q

V

A

K

E

C

C

T

S

M

F

V

T

T

N

Q

Q

E

S

W
x
F

D
|
D

G

S

M

L

I

I

P

P

S

S

L

L

L

R

A

F

R

K

K

K

F

F

D
|
D

A

A

I

V

V

I

A
|
A

S
x
G

M

M

S
x
D

I

M

T

T

E

P

E

K

R
|
R

K

E

L

Q

K

Q

V

V

D

S

F

F

T

S

D

Q

K

P

Y

Y

Q

E

-

G

I

L

S

S

S

A

R

V

F

V

V

V

A

T

K

R

Q

K

G

G

T

A

E

Y

F

H

S

T

F

F

D

-

K

-

A

A

G

D

L

L

K

K

G

G

K

K

S

K

V

V

G

G

V

L

Q
x
E

G

N

S

G

S
x
T

T
|
T

H

H

E

Q

K

R

Y

Y

V

L

A

Q

D

D

N

K

F

Q

E

Q

G

A

V

I

D

T

V

P

K

V

R

A

Y

Y

G
x
D

S

S

P

Y

E

L

N

N

A

A

F

F

L

T

D

D

L

L

I

K

S

N

G

N

R

R

V

L

D

E

L

G

V

V

F

F

N

G

N
x
D

I

V

P

A

A

A

I

I

E

G

S

K

G

W

L

L

L

-

E

-

K

-

E

K

N

N

G

N

G

P

D

D

F

Y

A

A

F

I

T

M

G

D

P

E

L

R

I

A

T

S

D

D

K

P

E

D

W

Y

F

Y

G

G

E

K

G

G

V

L

G

G

I

I

A

A

V

V

R

R

K

K

Q

D

D

N

D

D

A

A

L

L

R

L

E

Q

K

E

F

I

N

N

D

A

A

A

I

L

K

D

A

K

I

V

R

K

S

A

N

S

G

P

V

E

Y

Y

Q

A

Q

Q

I

M

Q

Q

D

E

K

K

Y

W

F

F

binding arginine: Y16 (= Y35), E20 (≠ S39), F54 (≠ W73), A71 (= A90), G72 (≠ S91), D74 (≠ S93), R79 (= R98), E118 (≠ Q138), T121 (≠ S141), T122 (= T142), D160 (≠ N180)
binding zinc ion: H9 (≠ R28), D23 (≠ T42), D25 (≠ E44), D55 (= D74), D67 (= D86), D140 (≠ G160)

5orgA Structure of the periplasmic binding protein (pbp) occj from a. Tumefaciens b6 in complex with octopine. (see paper)
37% identity, 89% coverage: 25:254/257 of query aligns to 4:254/257 of 5orgA

query
sites
5orgA

K

K

Q

S

V

I

R

T

I

I

A

A

V

T

E
|
E

G

G

A

G

Y
|
Y

P

A

P

P

Y

W

S

N

W

F

T

S

T

G

T

P

E

G

G

G

E

K

L

L

K

D

G

G

F

F

D

E

I

I

D

D

M

L

A

A

N

N

A

A

L

L

C

C

E

E

E

K

M

M

Q

K

V

A

K

K

C

C

T

Q

M

I

V

V

T

A

Q

Q

E

N

W
|
W

D

D

G

G

M

I

I

M

P

P

S

S

L

L

L

T

A

G

R

K

K

K

F

Y

D

D

A

A

I

I

V

M

A
|
A

S
x
A

M
|
M

S
|
S

I

V

T

T

E

P

E

K

R
|
R

K

Q

L

E

K

V

V

I

D

G

F

F

T

S

D

I

K

P

Y

Y

Y

A

Q

A

I

G

S

I

S
x
N

R

G

F

F

-

A

-

V

-

M

-

G

-

D

-

S

-

K

-

L

-

A

-

E

V

M

A

P

K

G

Q

L

G

G

T

E

E

T

F

Y

S

S

F

L

D

D

K

S

A

Q

G

A

-

D

-

A

-

K

-

A

-

I

-

A

-

D

-

I

-

S

-

F

L

L

K

N

G

G

K

T

S

T

V

V

G

G

V

V

Q
|
Q

G

G

S

S

S
x
T

T
|
T

H

A

E

S

K

T

Y

F

V

L

A

D

D

K

N

Y

F

F

E

K

G

G

-

S

V

V

D

D

V

I

K

K

R

E

Y

Y

G

K

S

S

P

V

E

E

N

E

A

H

F

N

L

L

D

D

L

L

I

T

S

S

G

G

R

R

V

L

D

D

L

A

V

V

F

L

N

A

N
|
N

I

A

P

T

A

V

I

L

E

A

S

A

G

A

L

I

L

E

E

K

K

P

E

E

N

M

G

K

G

G

D

A

F

-

A

K

F

L

T

V

G

G

P

P

L

L

I

F

T

S

D

G

K

G

E

E

W

-

F

F

G

G

E

V

G

-

V

V

G

A

I

V

A

G

V

L

R

R

K

K

Q

E

D

D

D

T

A

A

L

L

R

K

E

A

K

D

F

F

N

D

D

A

A

A

I

I

K

K

A

A

I

A

R

S

S

E

N

D

G

G

V

T

Y

I

Q

K

Q

T

I

L

Q

S

D

L

K

K

Y

W

F

F

E

K

F

V

D

D

I

V

binding octopine: E11 (= E32), Y14 (= Y35), W52 (= W73), A69 (= A90), A70 (≠ S91), M71 (= M92), S72 (= S93), R77 (= R98), N92 (≠ S113), Q140 (= Q138), T143 (≠ S141), T144 (= T142), N183 (= N180)

4zv2A An ancestral arginine-binding protein bound to glutamine (see paper)
38% identity, 87% coverage: 27:250/257 of query aligns to 6:223/225 of 4zv2A

query
sites
4zv2A

V

L

R

R

I

V

A

G

V

T

E
|
E

G

A

A

T

Y
x
F

P

P

Y

F

S

G

W

F

T

K

T

D

T

E

E

N

G

G

E

K

L

L

K

V

G

G

F

F

D

D

I

I

D

D

M

L

A

A

N

K

A

A

L

I

C

A

E

K

M

L

Q

G

V

V

K

K

C

V

T

E

M

F

V

K

T

P

Q

M

E

D

W
x
F

D

D

G

G

M

I

I

I

P

P

S

A

L

L

L

Q

A

S

R

G

K

K

F

I

D

D

A

V

I

V

V

I

A

A

S
x
G

M
|
M

S
x
T

I

I

T

T

E

E

R
|
R

K

K

L

K

K

Q

V

V

D

D

F

F

T

S

D

D

K

P

Y

Y

Y

F

Q

E

I

A

S

G

S

Q

R

A

F

I

V

V

A

V

K

K

Q

K

G

G

T

N

E

D

F

S

S

I

F

K

D

S

K

L

A

E

G

D

L

L

K

K

G

G

K

K

S

K

V

V

G

G

V

V

Q

Q

G

L

S

G

S
|
S

T
|
T

H

S

E

E

K

Q

Y

H

V

V

A

K

D

K

N

V

F

A

E

A

G

G

V

V

D

K

V

V

K

K

R

K

Y

F

G

D

S

N

P

F

E

S

N

E

A

A

F

F

L

Q

D

E

L

L

I

K

S

S

G

G

R

R

V

V

D

D

L

A

V

V

F

V

N

T

N
x
D

I

N

P

A

A

V

I

A

E

L

S

A

G

Y

L

V

L

K

E

Q

K

N

E

P

N

N

G

-

D

-

F

-

A

-

F

-

T

A

G

G

P

V

L

K

I

I

T

V

D

G

K

E

E

T

W

F

F

S

G

G

E

E

G

P

V

Y

G

G

I

I

A

A

V

V

R

R

K

K

Q

G

D

N

D

S

A

E

L

L

R

L

E

E

K

K

F

I

N

N

D

K

A

A

I

L

K

E

A

E

I

M

R

K

S

K

N

D

G

G

V

T

Y

Y

Q

D

Q

K

I

I

Q

Y

D

E

K

K

Y

W

F

F

binding glutamine: E11 (= E32), F14 (≠ Y35), F52 (≠ W73), G70 (≠ S91), M71 (= M92), T72 (≠ S93), R77 (= R98), S120 (= S141), T121 (= T142), D159 (≠ N180)

4zv1A An ancestral arginine-binding protein bound to arginine (see paper)
37% identity, 87% coverage: 27:250/257 of query aligns to 6:225/226 of 4zv1A

query
sites
4zv1A

V

L

R

R

I

V

A

G

V

T

E
|
E

G

A

A

T

Y
x
F

P

P

Y

F

S

G

W

F

T

K

T

D

T

E

E

N

G

G

E

K

L

L

K

V

G

G

F

F

D

D

I

I

D

D

M

L

A

A

N

K

A

A

L

I

C

A

E

K

M

L

Q

G

V

V

K

K

C

V

T

E

M

F

V

K

T

P

Q

M

E

D

W
x
F

D

D

G

G

M

I

I

I

P

P

S

A

L

L

L

Q

A

S

R

G

K

K

F

I

D

D

A

V

I

V

V

I

A
|
A

S
x
G

M
|
M

S
x
T

I

I

T

T

E

E

R
|
R

K

K

L

K

K

Q

V

V

D

D

F

F

T

S

D

D

K

P

Y

Y

Y

F

Q

E

I

A

S

G

S

Q

R

A

F

I

V

V

A

V

K

K

Q

K

G

G

T

N

E

D

F

S

S

I

F

K

D

S

K

L

A

E

G

D

L

L

K

K

G

G

K

K

S

K

V

V

G

G

V

V

Q
|
Q

G

L

S

G

S
|
S

T
|
T

H

S

E

E

K

Q

Y

H

V

V

A

K

D

K

N

V

F

A

E

K

-

D

-

A

G

G

V

V

D

K

V

V

K

K

R

K

Y

F

G

D

S

N

P

F

E

S

N

E

A

A

F

F

L

Q

D

E

L

L

I

K

S

S

G

G

R

R

V

V

D

D

L

A

V

V

F

V

N

T

N
x
D

I

N

P

A

A

V

I

A

E

L

S

A

G

Y

L

V

L

K

E

Q

K

N

E

P

N

N

G

-

D

-

F

-

A

-

F

-

T

A

G

G

P

V

L

K

I

I

T

V

D

G

K

E

E

T

W

F

F

S

G

G

E

E

G

P

V

Y

G

G

I

I

A

A

V

V

R

R

K

K

Q

G

D

N

D

S

A

E

L

L

R

L

E

E

K

K

F

I

N

N

D

K

A

A

I

L

K

E

A

E

I

M

R

K

S

K

N

D

G

G

V

T

Y

Y

Q

D

Q

K

I

I

Q

Y

D

E

K

K

Y

W

F

F

binding arginine: E11 (= E32), F14 (≠ Y35), F52 (≠ W73), A69 (= A90), G70 (≠ S91), M71 (= M92), T72 (≠ S93), R77 (= R98), Q117 (= Q138), S120 (= S141), T121 (= T142), D161 (≠ N180)

5itoA Structure of the periplasmic binding protein m117n-noct from a. Tumefaciens in complex with octopine (see paper)
31% identity, 90% coverage: 23:253/257 of query aligns to 1:252/255 of 5itoA

query
sites
5itoA

E

D

W

Y

K

K

Q

S

V

I

R

T

I

I

A

A

V

T

E
|
E

G

G

A

S

Y
|
Y

P

A

P

P

Y

Y

S

N

W

F

T

K

T

D

T

A

E

G

G

G

E

K

L

L

K

I

G

G

F

F

D

D

I

I

D

D

M

L

A

G

N

N

A

D

L

L

C

C

E

K

E

R

M

M

Q

N

V

I

K

E

C

C

T

K

M

F

V

V

T

E

Q

Q

E

A

W
|
W

D

D

G

G

M

I

I

I

P

P

S

S

L

L

L

T

A

A

R

G

K

R

F

Y

D

D

A

A

I

I

V

M

A
|
A

S
x
A

M

M

S
x
G

I

I

T

Q

E

P

E

A

R
|
R

K

E

L

K

K

V

V

I

D

A

F

F

T

S

D

R

K

P

Y

Y

Y

L

Q

L

I

T

S

P

S

N

R

T

F

F

V

L

-

T

-

A

-

D

-

S

-

P

-

L

-

K

-

T

-

Q

-

V

-

A

-

I

-

E

-

N

-

L

-

P

-

L

-

D

-

N

-

I

-

T

A

P

K

E

Q

Q

G

K

T

A

E

E

F

L

S

D

F

K

D

F

K

T

A

K

G

I

L

F

K

E

G

G

K

V

S

K

V

F

G

G

V

V

Q
|
Q

G

A

S

G

S
x
T

T
x
S

H
|
H

E

E

K

A

Y

F

V

M

A

K

D

Q

N

M

F

M

E

P

G

S

V

V

D

Q

V

I

K

S

R

T

Y

Y

G

D

S

T

P

I

E

D

N

N

A

V

F

V

L

M

D

D

L

L

I

K

S

A

G

G

R

R

V

I

D

D

L

A

V

S

F

L

N

A

N
x
S

I

V

P

S

A

F

I

L

E

K

S

P

G

-

L

L

L

T

E

D

K

K

E

P

N

D

G

N

G

K

D

D

F

L

A

K

F

M

T

F

G

G

P

P

L

R

I

M

T

T

D

G

K

G

E

-

W

L

F

F

G

G

E

K

G

G

V

V

G

G

I

V

A

G

V

I

R

R

K

K

Q

E

D

D

D

A

A

D

L

L

R

K

E

A

K

L

F

F

N

D

D

K

A

A

I

I

K

D

A

A

I

A

R

I

S

A

N

D

G

G

V

T

Y

V

Q

Q

Q

K

I

L

Q

S

D

Q

K

Q

Y

W

F

F

E

G

F

Y

D

D

binding octopine: E10 (= E32), Y13 (= Y35), W51 (= W73), A68 (= A90), A69 (≠ S91), G71 (≠ S93), R76 (= R98), Q139 (= Q138), T142 (≠ S141), S143 (≠ T142), H144 (= H143), S181 (≠ N180)

5ovzA High resolution structure of the pbp noct in complex with nopaline (see paper)
31% identity, 90% coverage: 23:253/257 of query aligns to 1:252/259 of 5ovzA

query
sites
5ovzA

E

D

W

Y

K

K

Q

S

V

I

R

T

I

I

A

A

V

T

E
|
E

G

G

A

S

Y
|
Y

P

A

P

P

Y

Y

S

N

W

F

T

K

T

D

T

A

E

G

G

G

E

K

L

L

K

I

G

G

F

F

D

D

I

I

D

D

M

L

A

G

N

N

A

D

L

L

C

C

E

K

E

R

M

M

Q

N

V

I

K

E

C

C

T

K

M

F

V

V

T

E

Q

Q

E

A

W
|
W

D

D

G

G

M

I

I

I

P

P

S

S

L

L

L

T

A

A

R

G

K

R

F

Y

D

D

A

A

I

I

V

M

A
|
A

S
x
A

M

M

S
x
G

I

I

T

Q

E

P

E

A

R
|
R

K

E

L

K

K

V

V

I

D

A

F

F

T

S

D

R

K

P

Y

Y

Y

L

Q

L

I

T

S

P

S
x
M

R

T

F

F

V

L

-

T

-

A

-

D

-

S

-

P

-

L

-

K

-

T

-

Q

-

V

-

A

-

I

-

E

-

N

-

L

-

P

-

L

-

D

-

N

-

I

-

T

A

P

K

E

Q

Q

G

K

T

A

E

E

F

L

S

D

F

K

D

F

K

T

A

K

G

I

L

F

K

E

G

G

K

V

S

K

V

F

G

G

V

V

Q
|
Q

G

A

S

G

S
x
T

T
x
S

H
|
H

E

E

K

A

Y

F

V

M

A

K

D

Q

N

M

F

M

E

P

G

S

V

V

D

Q

V

I

K

S

R

T

Y

Y

G

D

S

T

P

I

E

D

N

N

A

V

F

V

L

M

D

D

L

L

I

K

S

A

G

G

R

R

V

I

D

D

L

A

V

S

F

L

N

A

N
x
S

I

V

P

S

A

F

I

L

E

K

S

P

G

-

L

L

L

T

E

D

K

K

E

P

N

D

G

N

G

K

D

D

F

L

A

K

F

M

T

F

G

G

P

P

L

R

I

M

T

T

D

G

K

G

E

-

W

L

F

F

G

G

E

K

G

G

V
|
V

G

G

I

V

A

G

V

I

R

R

K

K

Q

E

D

D

D

A

A

D

L

L

R

K

E

A

K

L

F

F

N

D

D

K

A

A

I

I

K

D

A

A

I

A

R

I

S

A

N

D

G

G

V

T

Y

V

Q

Q

Q

K

I

L

Q

S

D

Q

K

Q

Y

W

F

F

E

G

F

Y

D

D

binding N-[(1S)-4-carbamimidamido-1-carboxybutyl]-D-glutamic acid: E10 (= E32), Y13 (= Y35), W51 (= W73), A68 (= A90), A69 (≠ S91), G71 (≠ S93), R76 (= R98), M91 (≠ S113), Q139 (= Q138), T142 (≠ S141), S143 (≠ T142), H144 (= H143), S181 (≠ N180), V213 (= V214)

5otcA Structure of the periplasmic binding protein (pbp) noct from agrobacterium tumefaciens c58 in complex with noroctopinic acid. (see paper)
31% identity, 89% coverage: 24:253/257 of query aligns to 1:251/256 of 5otcA

query
sites
5otcA

W

Y

K

K

Q

S

V

I

R

T

I

I

A

A

V

T

E
|
E

G

G

A

S

Y
|
Y

P

A

P

P

Y

Y

S

N

W

F

T

K

T

D

T

A

E

G

G

G

E

K

L

L

K

I

G

G

F

F

D

D

I

I

D

D

M

L

A

G

N

N

A

D

L

L

C

C

E

K

E

R

M

M

Q

N

V

I

K

E

C

C

T

K

M

F

V

V

T

E

Q

Q

E

A

W
|
W

D

D

G

G

M

I

I

I

P

P

S

S

L

L

L

T

A

A

R

G

K

R

F

Y

D

D

A

A

I

I

V

M

A

A

S
x
A

M

M

S
x
G

I

I

T

Q

E

P

E

A

R
|
R

K

E

L

K

K

V

V

I

D

A

F

F

T

S

D

R

K

P

Y

Y

Y

L

Q

L

I

T

S

P

S

M

R

T

F

F

V

L

-

T

-

A

-

D

-

S

-

P

-

L

-

K

-

T

-

Q

-

V

-

A

-

I

-

E

-

N

-

L

-

P

-

L

-

D

-

N

-

I

-

T

A

P

K

E

Q

Q

G

K

T

A

E

E

F

L

S

D

F

K

D

F

K

T

A

K

G

I

L

F

K

E

G

G

K

V

S

K

V

F

G

G

V

V

Q
|
Q

G

A

S

G

S
x
T

T
x
S

H
|
H

E

E

K

A

Y

F

V

M

A

K

D

Q

N

M

F

M

E

P

G

S

V

V

D

Q

V

I

K

S

R

T

Y

Y

G

D

S

T

P

I

E

D

N

N

A

V

F

V

L

M

D

D

L

L

I

K

S

A

G

G

R

R

V

I

D

D

L

A

V

S

F

L

N

A

N
x
S

I

V

P

S

A

F

I

L

E

K

S

P

G

-

L

L

L

T

E

D

K

K

E

P

N

D

G

N

G

K

D

D

F

L

A

K

F

M

T

F

G

G

P

P

L

R

I

M

T

T

D

G

K

G

E

-

W

L

F

F

G

G

E

K

G

G

V

V

G

G

I

V

A

G

V

I

R

R

K

K

Q

E

D

D

D

A

A

D

L

L

R

K

E

A

K

L

F

F

N

D

D

K

A

A

I

I

K

D

A

A

I

A

R

I

S

A

N

D

G

G

V

T

Y

V

Q

Q

Q

K

I

L

Q

S

D

Q

K

Q

Y

W

F

F

E

G

F

Y

D

D

binding (2~{S})-5-azanyl-2-(2-hydroxy-2-oxoethylamino)pentanoic acid: E9 (= E32), Y12 (= Y35), W50 (= W73), A68 (≠ S91), G70 (≠ S93), R75 (= R98), Q138 (= Q138), T141 (≠ S141), S142 (≠ T142), H143 (= H143), S180 (≠ N180)

5otaA Structure of the periplasmic binding protein (pbp) noct from agrobacterium tumefaciens c58 in complex with octopinic acid (see paper)
31% identity, 89% coverage: 24:253/257 of query aligns to 1:251/254 of 5otaA

query
sites
5otaA

W

Y

K

K

Q

S

V

I

R

T

I

I

A

A

V

T

E
|
E

G

G

A

S

Y
|
Y

P

A

P

P

Y

Y

S

N

W

F

T

K

T

D

T

A

E

G

G

G

E

K

L

L

K

I

G

G

F

F

D

D

I

I

D

D

M

L

A

G

N

N

A

D

L

L

C

C

E

K

E

R

M

M

Q

N

V

I

K

E

C

C

T

K

M

F

V

V

T

E

Q

Q

E

A

W
|
W

D

D

G

G

M

I

I

I

P

P

S

S

L

L

L

T

A

A

R

G

K

R

F

Y

D

D

A

A

I

I

V

M

A

A

S
x
A

M

M

S
x
G

I

I

T

Q

E

P

E

A

R
|
R

K

E

L

K

K

V

V

I

D

A

F

F

T

S

D

R

K

P

Y

Y

Y

L

Q

L

I

T

S

P

S
x
M

R

T

F

F

V

L

-

T

-

A

-

D

-

S

-

P

-

L

-

K

-

T

-

Q

-

V

-

A

-

I

-

E

-

N

-

L

-

P

-

L

-

D

-

N

-

I

-

T

A

P

K

E

Q

Q

G

K

T

A

E

E

F

L

S

D

F

K

D

F

K

T

A

K

G

I

L

F

K

E

G

G

K

V

S

K

V

F

G

G

V

V

Q
|
Q

G

A

S

G

S
x
T

T
x
S

H
|
H

E

E

K

A

Y

F

V

M

A

K

D

Q

N

M

F

M

E

P

G

S

V

V

D

Q

V

I

K

S

R

T

Y

Y

G

D

S

T

P

I

E

D

N

N

A

V

F

V

L

M

D

D

L

L

I

K

S

A

G

G

R

R

V

I

D

D

L

A

V

S

F

L

N

A

N
x
S

I

V

P

S

A

F

I

L

E

K

S

P

G

-

L

L

L

T

E

D

K

K

E

P

N

D

G

N

G

K

D

D

F

L

A

K

F

M

T

F

G

G

P

P

L

R

I

M

T

T

D

G

K

G

E

-

W

L

F

F

G

G

E

K

G

G

V

V

G

G

I

V

A

G

V

I

R

R

K

K

Q

E

D

D

D

A

A

D

L

L

R

K

E

A

K

L

F

F

N

D

D

K

A

A

I

I

K

D

A

A

I

A

R

I

S

A

N

D

G

G

V

T

Y

V

Q

Q

Q

K

I

L

Q

S

D

Q

K

Q

Y

W

F

F

E

G

F

Y

D

D

binding (2~{S})-5-azanyl-2-[[(2~{R})-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]pentanoic acid: E9 (= E32), Y12 (= Y35), W50 (= W73), A68 (≠ S91), G70 (≠ S93), R75 (= R98), M90 (≠ S113), Q138 (= Q138), T141 (≠ S141), S142 (≠ T142), H143 (= H143), S180 (≠ N180)

5ot9A Structure of the periplasmic binding protein (pbp) noct from a.Tumefaciens c58 in complex with histopine. (see paper)
31% identity, 89% coverage: 24:253/257 of query aligns to 1:251/254 of 5ot9A

query
sites
5ot9A

W

Y

K

K

Q

S

V

I

R

T

I

I

A

A

V

T

E
|
E

G

G

A

S

Y
|
Y

P

A

P

P

Y

Y

S

N

W

F

T

K

T

D

T

A

E

G

G

G

E

K

L

L

K

I

G

G

F

F

D

D

I

I

D

D

M

L

A

G

N

N

A

D

L

L

C

C

E

K

E

R

M

M

Q

N

V

I

K

E

C

C

T

K

M

F

V

V

T

E

Q

Q

E

A

W
|
W

D

D

G

G

M

I

I

I

P

P

S

S

L

L