SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing Pf6N2E2_3856 Lysine-arginine-ornithine-binding periplasmic protein precursor (TC 3.A.1.3.1) 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)

3tqlA Structure of the amino acid abc transporter, periplasmic amino acid- binding protein from coxiella burnetii. (see paper)
43% identity, 88% coverage: 25:246/251 of query aligns to 2:225/225 of 3tqlA

query
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3tqlA

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binding arginine: E9 (= E32), Y12 (= Y35), W48 (= W73), G65 (≠ S90), G66 (≠ S91), N68 (≠ S93), R73 (= R98), S89 (≠ Q114)

P02911 Lysine/arginine/ornithine-binding periplasmic protein; LAO-binding protein from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see 4 papers)
38% identity, 96% coverage: 12:251/251 of query aligns to 7:258/260 of P02911

query
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P02911

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D33 (≠ E32) binding ; binding ; binding ; 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 (= S90) binding ; binding ; mutation to A: Has no effect on the arginine and histidine binding affinity.
S92 (= S91) binding ; binding ; binding ; mutation to A: Decreases arginine and histidine binding affinity.
S94 (= S93) binding ; binding ; binding ; mutation to A: Decreases arginine and histidine binding affinity.
R99 (= R98) binding ; binding ; binding ; 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 ; binding ; binding
D183 (= D181) binding ; binding ; 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)
39% identity, 90% coverage: 25:251/251 of query aligns to 1:233/235 of 5owfA

query
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5owfA

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binding glutamine: Y11 (= Y35), F49 (≠ W73), S66 (= S90), S67 (= S91), S69 (= S93), R74 (= R98), 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)
39% identity, 90% coverage: 25:251/251 of query aligns to 4:236/238 of 1lstA

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1lstA

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binding lysine: Y14 (= Y35), F52 (≠ W73), S70 (= S91), S72 (= S93), R77 (= R98), L117 (≠ Q138), S120 (≠ T141), T121 (≠ L142), Q122 (≠ A143), D161 (= D181)

1lahE Structural bases for multiple ligand specificity of the periplasmic lysine-, arginine-, ornithine-binding protein (see paper)
39% identity, 90% coverage: 25:251/251 of query aligns to 4:236/238 of 1lahE

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Y

Y

binding L-ornithine: Y14 (= Y35), F52 (≠ W73), S70 (= S91), S72 (= S93), R77 (= R98), S120 (≠ T141), Q122 (≠ A143), D161 (= D181)

1lagE Structural bases for multiple ligand specificity of the periplasmic lysine-, arginine-, ornithine-binding protein (see paper)
39% identity, 90% coverage: 25:251/251 of query aligns to 4:236/238 of 1lagE

query
sites
1lagE

E

Q

K

T

L

V

K

R

M

I

G

G

I

T

E

D

A

T

Y
|
Y

P

A

P

P

F

F

N

S

K

K

D

D

A

A

S

K

G

G

Q

E

V

F

V

I

G

G

F

F

D

D

K

I

D

D

I

L

G

G

D

N

A

E

L

M

C

C

A

K

K

R

M

M

K

Q

V

V

E

K

C

C

E

T

V

W

V

V

T

A

S

S

N

D

W
x
F

D

D

G

A

I

L

I

I

P

P

A

S

L

L

M

K

A

A

K

K

F

I

D

D

F

A

L

I

I

I

S
|
S

L
|
L

S
|
S

V

I

N

T

D

D

E

K

R
|
R

K

Q

Q

Q

A

E

V

I

D

A

F

F

T

S

D

D

P

K

Y

L

Y

Y

S

A

N

A

K

D

L

S

Q

R

F

L

I

I

A

A

P

A

K

K

N

G

V

S

D

P

F

I

K

Q

V

P

D

T

K

L

E

E

S

S

L

L

K

K

G

G

K

K

V

H

I

V

G

G

A

V

Q
x
L

R

Q

S

G

T
x
S

L

T

A
x
Q

G

E

T

A

W

Y

L

A

E

N

D

D

E

N

L

W

-

R

-

T

-

K

G

G

S

V

D

D

I

V

T

V

A

A

K

-

L

-

Y

Y

D

A

T

N

Q

Q

E

D

N

L

A

I

Y

Y

L

S

D

D

L

L

T

T

S

A

G

G

R

R

V

L

D

D

A

A

I

A

L

L

A

Q

D
|
D

K

E

Y

V

V

A

N

A

Y

S

D

E

-

G

W

F

L

L

K

K

T

Q

E

P

A

A

G

G

R

K

A

E

Y

Y

E

A

F

F

K

A

G

G

D

P

P

S

V

V

V

K

E

D

-

K

-

Y

-

F

G

G

D

D

K

G

I

T

A

G

I

V

A

G

V

L

R

R

K

K

G

D

N

D

D

T

E

E

L

L

R

K

N

A

K

A

L

F

N

D

A

K

A

A

L

L

K

T

E

E

I

L

L

R

A

Q

D

D

G

G

T

T

Y

Y

K

D

K

K

I

M

N

A

D

K

K

K

Y

Y

F

F

P

D

F

F

S

N

I

V

Y

Y

binding histidine: Y14 (= Y35), F52 (≠ W73), S69 (= S90), S70 (= S91), L71 (= L92), S72 (= S93), R77 (= R98), L117 (≠ Q138), S120 (≠ T141), Q122 (≠ A143), D161 (= D181)

1lafE Structural bases for multiple ligand specificity of the periplasmic lysine-, arginine-, ornithine-binding protein (see paper)
39% identity, 90% coverage: 25:251/251 of query aligns to 4:236/238 of 1lafE

query
sites
1lafE

E

Q

K

T

L

V

K

R

M

I

G

G

I

T

E
x
D

A

T

Y
|
Y

P

A

P

P

F

F

N

S

K

K

D

D

A

A

S

K

G

G

Q

E

V

F

V

I

G

G

F

F

D

D

K

I

D

D

I

L

G

G

D

N

A

E

L

M

C

C

A

K

K

R

M

M

K

Q

V

V

E

K

C

C

E

T

V

W

V

V

T

A

S

S

N

D

W
x
F

D

D

G

A

I

L

I

I

P

P

A

S

L

L

M

K

A

A

K

K

F

I

D

D

F

A

L

I

I

I

S
|
S

L

L

S
|
S

V

I

N

T

D

D

E

K

R
|
R

K

Q

Q

Q

A

E

V

I

D

A

F

F

T

S

D

D

P

K

Y

L

Y

Y

S

A

N

A

K

D

L

S

Q

R

F

L

I

I

A

A

P

A

K

K

N

G

V

S

D

P

F

I

K

Q

V

P

D

T

K

L

E

E

S

S

L

L

K

K

G

G

K

K

V

H

I

V

G

G

A

V

Q
x
L

R

Q

S

G

T
x
S

L
x
T

A
x
Q

G

E

T

A

W

Y

L

A

E

N

D

D

E

N

L

W

-

R

-

T

-

K

G

G

S

V

D

D

I

V

T

V

A

A

K

-

L

-

Y

Y

D

A

T

N

Q

Q

E

D

N

L

A

I

Y

Y

L

S

D

D

L

L

T

T

S

A

G

G

R

R

V

L

D

D

A

A

I

A

L

L

A

Q

D
|
D

K

E

Y

V

V

A

N

A

Y

S

D

E

-

G

W

F

L

L

K

K

T

Q

E

P

A

A

G

G

R

K

A

E

Y

Y

E

A

F

F

K

A

G

G

D

P

P

S

V

V

V

K

E

D

-

K

-

Y

-

F

G

G

D

D

K

G

I

T

A

G

I

V

A

G

V

L

R

R

K

K

G

D

N

D

D

T

E

E

L

L

R

K

N

A

K

A

L

F

N

D

A

K

A

A

L

L

K

T

E

E

I

L

L

R

A

Q

D

D

G

G

T

T

Y

Y

K

D

K

K

I

M

N

A

D

K

K

K

Y

Y

F

F

P

D

F

F

S

N

I

V

Y

Y

binding arginine: D11 (≠ E32), Y14 (= Y35), F52 (≠ W73), S69 (= S90), S70 (= S91), S72 (= S93), R77 (= R98), L117 (≠ Q138), S120 (≠ T141), T121 (≠ L142), Q122 (≠ A143), D161 (= D181)

P02910 Histidine-binding periplasmic protein; HBP from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see 2 papers)
38% identity, 90% coverage: 25:251/251 of query aligns to 26:258/260 of P02910

query
sites
P02910

E

Q

K

K

L

I

K

R

M

I

G

G

I

T

E

D

A

P

A

T

Y

Y

P

A

P

P

F

F

N
x
E

N

S

K
|
K

D

N

A

A

S

Q

G

G

Q
x
E

V

L

V

V

G

G

F

F

D

D

K

I

D

D

I

L

G

A

D

K

A

E

L

L

C

C

A

K

K

R

M

I

K

N

V

T

E

Q

C

C

E

T

V

F

V

V

T

E

S

N

N

P

W

L

D

D

G

A

I

L

I

I

P

P

A

S

L

L

M

K

A

A

K

K

F

I

D

D

F

A

L

I

I

M

S

S

L

L

S

S

V

I

N

T

D

E

E

K

R

R

K

Q

Q

Q

A

E

V

I

D

A

F

F

T

T

D

D

P

K

Y

L

Y

Y

S

A

N

A

K

D

L

S

Q

R

F

L

I

V

A

V

P

A

K

K

N

N

V

S

D

D

F

I

K

Q

V

P

D

T

K

V

E

A

S

S

L

L

K

K

G

G

K

K

V

R

I

V

G

G

A

V

Q

L

R

Q

S

G

T

T

L

T

A

Q

G

E

T

T

W

F

L

G

E

N

D

E

E

H

L

W

-

A

-

P

-

K

G

G

S

I

D

E

I

I

T

V

A

S

K

-

L

-

Y

Y

D

Q

T

G

Q

Q

E

D

N

N

A

I

Y

Y

L

S

D
|
D

L

L

T

T

S

A

G

G

R
|
R

V

I

D
|
D

A

A

I

A

L

F

A

Q

D

D

K

E

Y

V

V

A

N

A

Y

S

D

E

-

G

W

F

L

L

K

K

T

Q

E

P

A

V

G

G

R

K

A

D

Y

Y

E

K

F

F

K

-

G

G

D

G

P

P

V

A

V

V

E

K

G

D

D

E

K

K

I

L

-

F

-

G

-

V

-

G

-

T

A

G

I

M

A

G

V

L

R

R

K

K

G

E

N

D

D

N

E

E

L

L

R

R

N

E

K

A

L

L

N

N

A

K

A

A

L

F

K

A

E

E

I

M

L

R

A

A

D

D

G

G

T

T

Y

Y

K

E

K

K

I

L

N

A

D

K

K

K

Y

Y

F

F

P

D

F

F

S

D

I

V

Y

Y

E40 (≠ N39) mutation to K: Decrease in ATPase-inducing activity and histidine transport; when associated with K-47.
K42 (= K41) mutation to E: Increases ATPase-inducing activity and histidine transport; when associated with K-47.
E47 (≠ Q46) 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)
38% identity, 90% coverage: 25:251/251 of query aligns to 4:236/238 of 1hslA

query
sites
1hslA

E

Q

K

K

L

I

K

R

M

I

G

G

I

T

E

D

A

P

A

T

Y
|
Y

P

A

P

P

F

F

N

E

N

S

K

K

D

N

A

A

S

Q

G

G

Q

E

V

L

V

V

G

G

F

F

D

D

K

I

D

D

I

L

G

A

D

K

A

E

L

L

C

C

A

K

K

R

M

I

K

N

V

T

E

Q

C

C

E

T

V

F

V

V

T

E

S

N

N

P

W
x
L

D

D

G

A

I

L

I

I

P

P

A

S

L

L

M

K

A

A

K

K

F

I

D

D

F

A

L

I

I

M

S
|
S

L
|
L

S
|
S

V

I

N

T

D

E

E

K

R
|
R

K

Q

Q

Q

A

E

V

I

D

A

F

F

T

T

D

D

P

K

Y

L

Y

Y

S

A

N

A

K

D

L

S

Q

R

F

L

I

V

A

V

P

A

K

K

N

N

V

S

D

D

F

I

K

Q

V

P

D

T

K

V

E

A

S

S

L

L

K

K

G

G

K

K

V

R

I

V

G

G

A

V

Q

L

R

Q

S

G

T
|
T

L
x
T

A

Q

G

E

T

T

W

F

L

G

E

N

D

E

E

H

L

W

-

A

-

P

-

K

G

G

S

I

D

E

I

I

T

V

A

S

K

-

L

-

Y

Y

D

Q

T

G

Q

Q

E

D

N

N

A

I

Y

Y

L

S

D

D

L

L

T

T

S

A

G

G

R

R

V

I

D

D

A

A

I

A

L

F

A

Q

D
|
D

K

E

Y

V

V

A

N

A

Y

S

D

E

-

G

W

F

L

L

K

K

T

Q

E

P

A

V

G

G

R

K

A

D

Y

Y

E

K

F

F

K

-

G

G

D

G

P

P

V

A

V

V

E

K

G

D

D

E

K

K

I

L

-

F

-

G

-

V

-

G

-

T

A

G

I

M

A

G

V

L

R

R

K

K

G

E

N

D

D

N

E

E

L

L

R

R

N

E

K

A

L

L

N

N

A

K

A

A

L

F

K

A

E

E

I

M

L

R

A

A

D

D

G

G

T

T

Y

Y

K

E

K

K

I

L

N

A

D

K

K

K

Y

Y

F

F

P

D

F

F

S

D

I

V

Y

Y

binding histidine: Y14 (= Y35), L52 (≠ W73), S69 (= S90), S70 (= S91), L71 (= L92), S72 (= S93), R77 (= R98), T120 (= T141), T121 (≠ L142), D161 (= D181)

P0AEU0 Histidine-binding periplasmic protein; HBP from Escherichia coli (strain K12) (see 3 papers)
37% identity, 90% coverage: 25:251/251 of query aligns to 26:258/260 of P0AEU0

query
sites
P0AEU0

E

Q

K

N

L

I

K

R

M

I

G

G

I

T

E

D

A

P

A

T

Y

Y

P

A

P

P

F

F

N

E

N

S

K

K

D

N

A

S

S

Q

G

G

Q

E

V

L

V

V

G

G

F

F

D

D

K

I

D

D

I

L

G

A

D

K

A

E

L

L

C
|
C

A

K

K

R

M

I

K

N

V

T

E

Q

C
|
C

E

T

V

F

V

V

T

E

S

N

N

P

W

L

D

D

G

A

I

L

I

I

P

P

A

S

L

L

M

K

A

A

K

K

F

I

D

D

F

A

L

I

I

M

S
|
S

L

L

S
|
S

V

I

N

T

D

E

E

K

R
|
R

K

Q

Q

Q

A

E

V

I

D

A

F

F

T

T

D

D

P

K

Y

L

Y

Y

S

A

N

A

K

D

L

S

Q

R

F

L

I

V

A

V

P

A

K

K

N

N

V

S

D

D

F

I

K

Q

V

P

D

T

K

V

E

E

S

S

L

L

K

K

G

G

K

K

V

R

I

V

G

G

A

V

Q

L

R

Q

S

G

T

T

L
x
T

A

Q

G

E

T

T

W

F

L

G

E

N

D

E

E

H

L

W

-

A

-

P

-

K

G

G

S

I

D

E

I

I

T

V

A

S

K

-

L

-

Y

Y

D

Q

T

G

Q

Q

E

D

N

N

A

I

Y

Y

L

S

D

D

L

L

T

T

S

A

G

G

R

R

V

I

D

D

A

A

I

A

L

F

A

Q

D
|
D

K

E

Y

V

V

A

N

A

Y

S

D

E

-

G

W

F

L

L

K

K

T

Q

E

P

A

V

G

G

R

K

A

D

Y

Y

E

K

F

F

K

-

G

G

D

G

P

P

V

S

V

V

E

K

G

D

D

E

K

K

I

L

-

F

-

G

-

V

-

G

-

T

A

G

I

M

A

G

V

L

R

R

K

K

G

E

N

D

D

N

E

E

L

L

R

R

N

E

K

A

L

L

N

N

A

K

A

A

L

F

K

A

E

E

I

M

L

R

A

A

D

D

G

G

T

T

Y

Y

K

E

K

K

I

L

N

A

D

K

K

K

Y

Y

F

F

P

D

F

F

S

D

I

V

Y

Y

C60 (= C59) modified: Disulfide link with 67
C67 (= C66) modified: Disulfide link with 60
S91 (= S90) binding
S92 (= S91) binding
S94 (= S93) binding
R99 (= R98) binding
T143 (≠ L142) binding
D183 (= D181) binding

Sites not aligning to the query:

1:22 signal peptide

4zv2A An ancestral arginine-binding protein bound to glutamine (see paper)
38% identity, 88% coverage: 27:246/251 of query aligns to 6:223/225 of 4zv2A

query
sites
4zv2A

L

L

K

R

M

V

G

G

I

T

E
|
E

A

A

A

T

Y
x
F

P

P

F

F

N

G

N

F

K

K

D

D

A

E

S

N

G

G

Q

K

V

L

V

V

G

G

F

F

D

D

K

I

D

D

I

L

G

A

D

K

A

A

L

I

C

A

A

K

K

K

M

L

K

G

V

V

E

K

C

V

E

E

V

F

V

K

T

P

S

M

N

D

W
x
F

D

D

G

G

I

I

P

P

A

A

L

L

M

Q

A

S

K

G

K

K

F

I

D

D

F

V

L

V

I

I

S

A

S
x
G

L
x
M

S
x
T

V

I

N

T

D

E

E

E

R
|
R

K

K

Q

K

A

Q

V

V

D

D

F

F

T

S

D

D

P

P

Y

Y

Y

F

S

E

N

A

K

G

L

Q

Q

A

F

I

I

V

A

V

P

K

K

K

N

G

V

N

D

D

F

S

K

I

V

K

D

S

K

L

E

E

S

D

L

L

K

K

G

G

K

K

V

K

I

V

G

G

A

V

Q

Q

R

L

S

G

T
x
S

L
x
T

A

S

G

E

T

Q

W

H

L

V

E

K

D

-

E

K

L

V

G

A

S

A

D

G

I

V

T

K

A

V

K

K

L

K

Y

F

D

D

T

N

Q

F

E

S

N

E

A

A

Y

F

L

Q

D

E

L

L

T

K

S

S

G

G

R

R

V

V

D

D

A

A

I

V

L

V

A

T

D
|
D

K

N

Y

A

V

V

N

A

Y

L

D

A

W

Y

L

V

K

K

T

Q

E

N

A

P

G

N

R

A

A

G

Y

V

E

K

F

I

K

V

G

G

D

E

P

-

V

T

V

F

E

S

G

G

D

E

K

P

I

Y

A

G

I

I

A

A

V

V

R

R

K

K

G

G

N

N

D

S

E

E

L

L

R

L

N

E

K

K

L

I

N

N

A

K

A

A

L

L

K

E

E

E

I

M

L

K

A

K

D

D

G

G

T

T

Y

Y

K

D

K

K

I

I

N

Y

D

E

K

K

Y

W

F

F

binding glutamine: E11 (= E32), F14 (≠ Y35), F52 (≠ W73), G70 (≠ S91), M71 (≠ L92), T72 (≠ S93), R77 (= R98), S120 (≠ T141), T121 (≠ L142), D159 (= D181)

4zv1A An ancestral arginine-binding protein bound to arginine (see paper)
38% identity, 88% coverage: 27:246/251 of query aligns to 6:225/226 of 4zv1A

query
sites
4zv1A

L

L

K

R

M

V

G

G

I

T

E
|
E

A

A

A

T

Y
x
F

P

P

F

F

N

G

N

F

K

K

D

D

A

E

S

N

G

G

Q

K

V

L

V

V

G

G

F

F

D

D

K

I

D

D

I

L

G

A

D

K

A

A

L

I

C

A

A

K

K

K

M

L

K

G

V

V

E

K

C

V

E

E

V

F

V

K

T

P

S

M

N

D

W
x
F

D

D

G

G

I

I

P

P

A

A

L

L

M

Q

A

S

K

G

K

K

F

I

D

D

F

V

L

V

I

I

S
x
A

S
x
G

L
x
M

S
x
T

V

I

N

T

D

E

E

E

R
|
R

K

K

Q

K

A

Q

V

V

D

D

F

F

T

S

D

D

P

P

Y

Y

Y

F

S

E

N

A

K

G

L

Q

Q

A

F

I

I

V

A

V

P

K

K

K

N

G

V

N

D

D

F

S

K

I

V

K

D

S

K

L

E

E

S

D

L

L

K

K

G

G

K

K

V

K

I

V

G

G

A

V

Q
|
Q

R

L

S

G

T
x
S

L
x
T

A

S

G

E

T

Q

W

H

L

V

E

K

D

-

E

K

L

V

G

A

S

K

D

D

-

A

-

G

I

V

T

K

A

V

K

K

L

K

Y

F

D

D

T

N

Q

F

E

S

N

E

A

A

Y

F

L

Q

D

E

L

L

T

K

S

S

G

G

R

R

V

V

D

D

A

A

I

V

L

V

A

T

D
|
D

K

N

Y

A

V

V

N

A

Y

L

D

A

W

Y

L

V

K

K

T

Q

E

N

A

P

G

N

R

A

A

G

Y

V

E

K

F

I

K

V

G

G

D

E

P

-

V

T

V

F

E

S

G

G

D

E

K

P

I

Y

A

G

I

I

A

A

V

V

R

R

K

K

G

G

N

N

D

S

E

E

L

L

R

L

N

E

K

K

L

I

N

N

A

K

A

A

L

L

K

E

E

E

I

M

L

K

A

K

D

D

G

G

T

T

Y

Y

K

D

K

K

I

I

N

Y

D

E

K

K

Y

W

F

F

binding arginine: E11 (= E32), F14 (≠ Y35), F52 (≠ W73), A69 (≠ S90), G70 (≠ S91), M71 (≠ L92), T72 (≠ S93), R77 (= R98), Q117 (= Q138), S120 (≠ T141), T121 (≠ L142), D161 (= D181)

2y7iA Structural basis for high arginine specificity in salmonella typhimurium periplasmic binding protein stm4351. (see paper)
33% identity, 90% coverage: 20:246/251 of query aligns to 1:227/228 of 2y7iA

query
sites
2y7iA

S

A

A

S

M

V

A

S

V

A

E

R

K

T

L

L

K
x
H

M

F

G

G

I

T

E

S

A

A

A

T

Y
|
Y

P

A

P

P

F

Y

N
x
E

N

F

K

V

D
|
D

A

A

S
x
D

G

N

Q

K

V

I

V

V

G

G

F

F

D

D

K

I

D

D

I

V

G

A

D

N

A

A

L

V

C

C

A

K

K

E

M

M

K

Q

V

A

E

E

C

C

E

S

V

F

V

T

T

N

S

Q

N

S

W
x
F

D
|
D

G

S

I

L

I

I

P

P

A

S

L

L

M

R

A

F

K

K

F

F

D
|
D

F

A

L

V

I

I

S
x
A

S
x
G

L

M

S
x
D

V

M

N

T

D

P

E

K

R
|
R

K

E

Q

Q

A

Q

V

V

D

S

F

F

T

S

D

Q

P

P

Y

Y

S

E

N

G

K

L

L

S

Q

A

F

V

I

V

A

V

P

T

K

R

N

K

V

G

D

A

F

Y

K

H

V

T

D

F

K

A

E

D

S

-

L

L

K

K

G

G

K

K

V

K

I

V

G

G

A

L

Q
x
E

R

N

S

G

T
|
T

L
x
T

A

H

G

Q

T

R

W

Y

L

L

E

Q

D

D

E

K

L

Q

G

Q

S

A

D

-

I

I

T

T

A

P

K

V

L

A

Y

Y

D
|
D

T

S

Q

Y

E

L

N

N

A

A

Y

F

L

T

D

D

L

L

T

K

S

N

G

N

R

R

V

L

D

E

A

G

I

V

L

F

A

G

D
|
D

K

V

Y

A

V

A

N

I

Y

G

D

K

W

W

L

L

K

K

T

N

E

N

A

P

G

D

R

Y

A

A

Y

I

-

M

-

D

E

E

F

R

K

A

G

S

D

D

P

P

V

D

V

Y

E

Y

G

G

D

K

K

G

I

L

A

G

I

I

A

A

V

V

R

R

K

K

G

D

N

N

D

D

E

A

L

L

R

L

N

Q

K

E

L

I

N

N

A

A

L

L

K

D

E

K

I

V

L

K

A

A

D

S

G

P

T

E

Y

Y

K

A

K

Q

I

M

N

Q

D

E

K

K

Y

W

F

F

binding arginine: Y16 (= Y35), E20 (≠ N39), F54 (≠ W73), A71 (≠ S90), G72 (≠ S91), D74 (≠ S93), R79 (= R98), E118 (≠ Q138), T121 (= T141), T122 (≠ L142), D160 (= D181)
binding zinc ion: H9 (≠ K28), D23 (= D42), D25 (≠ S44), D55 (= D74), D67 (= D86), D140 (= D161)

5orgA Structure of the periplasmic binding protein (pbp) occj from a. Tumefaciens b6 in complex with octopine. (see paper)
30% identity, 90% coverage: 22:246/251 of query aligns to 1:250/257 of 5orgA

query
sites
5orgA

M

M

A

Q

V

E

E

K

K

S

L

I

K

T

M

I

G

A

I

T

E
|
E

A

G

Y
|
Y

P

A

P

P

F

W

N

N

N

F

K

S

D

G

A

P

S

G

G

G

Q

K

V

L

V

D

G

G

F

F

D

E

K

I

D

D

I

L

G

A

D

N

A

A

L

L

C

C

A

E

K

K

M

M

K

K

V

A

E

K

C

C

E

Q

V

I

V

V

T

A

S

Q

N

N

W
|
W

D

D

G

G

I

I

I

M

P

P

A

S

L

L

M

T

A

G

K

K

F

Y

D

D

F

A

L

I

I

M

S
x
A

L
x
M

S
|
S

V

V

N

T

D

P

E

K

R
|
R

K

Q

Q

E

A

V

V

I

D

G

F

F

T

S

D

I

P

P

Y

Y

Y

A

S

A

-

G

-

I

-
x
N

-

G

-

F

-

A

-

V

-

M

-

G

-

D

N

S

K

K

L

L

Q

A

F

E

I

M

A

P

P

G

K

L

N

G

V

E

D

T

F

Y

K

S

V

L

D

D

K

S

E

Q

S

A

-

D

-

A

-

K

-

A

-

I

-

A

-

D

-

I

-

S

-

F

L

L

K

N

G

G

K

T

V

T

I

V

G

G

A

V

Q
|
Q

R

G

S

S

T
|
T

L
x
T

A

A

G

S

T

T

W

F

L

L

E

D

D

K

E

Y

L

F

G

K

S

G

D

S

I

V

T

D

A

I

K

K

L

E

Y

Y

D

K

T

S

Q

V

E

E

N

E

A

H

Y

N

L

L

D

D

L

L

T

T

S

S

G

G

R

R

V

L

D

D

A

A

I

V

L

L

A

A

D
x
N

K

A

Y

T

V

V

N

L

Y

A

D

A

W

A

L

I

K

E

T

K

E

P

A

E

G

M

R

K

A

G

Y

A

E

K

F

L

K

V

G

G

D

-

P

P

V

L

V

F

E

S

G

G

D

G

K

E

-

F

-

G

-

V

I

V

A

A

I

V

A

G

V

L

R

R

K

K

G

E

N

D

D

T

E

A

L

L

R

K

N

A

K

D

L

F

N

D

A

A

L

I

K

K

E

A

I

A

L

S

A

E

D

D

G

G

T

T

Y

I

K

K

K

T

I

L

N

S

D

L

K

K

Y

W

F

F

binding octopine: E11 (= E32), Y14 (= Y35), W52 (= W73), A69 (≠ S90), A70 (≠ S91), M71 (≠ L92), S72 (= S93), R77 (= R98), N92 (vs. gap), Q140 (= Q138), T143 (= T141), T144 (≠ L142), N183 (≠ D181)

3vvfA Crystal structure of ttc0807 complexed with arginine (see paper)
32% identity, 88% coverage: 26:246/251 of query aligns to 18:234/241 of 3vvfA

query
sites
3vvfA

K

E

L

I

K

R

M

I

G

G

I

T

E
|
E

A

G

A

A

Y
x
F

P

P

F

F

N

N

N

Y

K

F

D

D

A

E

S

R

G

N

Q

Q

V

L

V

T

G

G

F

F

D

E

K

V

D

D

I

L

G

G

D

N

A

A

L

I

C

A

A

E

K

R

M

L

K

G

V

L

E

K

C

P

E

R

V

W

V

I

T

A

S

Q

N

S

W
x
F

D

D

G

T

I

L

P

I

A

Q

L

L

M

N

A

Q

K

G

K

R

F

F

D

D

F

F

L

V

I

I

S
x
A

S
|
S

L
x
H

S
x
G

V

I

N

T

D

E

E

E

R
|
R

K

A

Q

R

A

A

V

V

D

D

F

F

T

T

D

N

P

P

Y

H

Y

Y

S

C

N

T

K

G

L

G

Q

V

F

I

I

V

A

S

P

R

K

K

N

G

V

G

D

P

F

R

K

T

V

A

D

-

K

-

E

K

S

D

L

L

K

Q

G

G

K

K

V

V

I

V

G

G

A

V

Q
|
Q

R

V

S

G

T
|
T

L

-

A

-

G

-

T
|
T

W
x
Y

L

M

E

E

-

A

D

Q

E

K

L

I

G

P

S

G

D

I

I

K

T

E

A

V

K

R

L

T

Y

Y

D

Q

T

R

Q

D

E

P

N

D

A

A

Y

L

L

Q

D

D

L

L

T

L

S

A

G

G

R

R

V

I

D

D

A

T

I

W

L

I

A

T

D

D

K

R

Y

F

V

V

N

A

Y

K

D

E

W

A

L

I

K

K

T

E

E

R

A

K

G

L

R

E

A

N

Y

T

E

L

F

Q

K

V

G

G

D

E

P

L

V

V

V

F

E

Q

G

-

D
x
E

K

R

I

V

A

A

I

M

A

A

V

V

R

A

K

K

G

G

N

N

D

K

E

S

L

L

R

L

N

D

K

A

L

L

N

N

A

R

A

A

L

L

K

A

E

E

I

L

L

M

A

Q

D

D

G

G

T

T

Y

Y

K

A

K

R

I

I

N

S

D

Q

K

K

Y

W

F

F

binding arginine: E24 (= E32), F27 (≠ Y35), F65 (≠ W73), A82 (≠ S90), S83 (= S91), H84 (≠ L92), G85 (≠ S93), R90 (= R98), Q128 (= Q138), T131 (= T141), T132 (= T145), Y133 (≠ W146), E196 (≠ D208)

3vveA Crystal structure of ttc0807 complexed with lysine (see paper)
32% identity, 88% coverage: 26:246/251 of query aligns to 18:234/241 of 3vveA

query
sites
3vveA

K

E

L

I

K

R

M

I

G

G

I

T

E
|
E

A

G

A

A

Y
x
F

P

P

F

F

N

N

N

Y

K

F

D

D

A

E

S

R

G

N

Q

Q

V

L

V

T

G

G

F

F

D

E

K

V

D

D

I

L

G

G

D

N

A

A

L

I

C

A

A

E

K

R

M

L

K

G

V

L

E

K

C

P

E

R

V

W

V

I

T

A

S

Q

N

S

W
x
F

D

D

G

T

I

L

P

I

A

Q

L

L

M

N

A

Q

K

G

K

R

F

F

D

D

F

F

L

V

I

I

S

A

S
|
S

L
x
H

S

G

V

I

N

T

D

E

E

E

R
|
R

K

A

Q

R

A

A

V

V

D

D

F

F

T

T

D

N

P

P

Y

H

Y

Y

S

C

N

T

K

G

L

G

Q

V

F

I

I

V

A

S

P

R

K

K

N

G

V

G

D

P

F

R

K

T

V

A

D

-

K

-

E

K

S

D

L

L

K

Q

G

G

K

K

V

V

I

V

G

G

A

V

Q
|
Q

R

V

S

G

T
|
T

L

-

A

-

G

-

T
|
T

W
x
Y

L

M

E

E

-

A

D

Q

E

K

L

I

G

P

S

G

D

I

I

K

T

E

A

V

K

R

L

T

Y

Y

D

Q

T

R

Q

D

E

P

N

D

A

A

Y

L

L

Q

D

D

L

L

T

L

S

A

G

G

R

R

V

I

D

D

A

T

I

W

L

I

A

T

D

D

K

R

Y

F

V

V

N

A

Y

K

D

E

W

A

L

I

K

K

T

E

E

R

A

K

G

L

R

E

A

N

Y

T

E

L

F

Q

K

V

G

G

D

E

P

L

V

V

V

F

E

Q

G

-

D
x
E

K

R

I

V

A

A

I

M

A

A

V

V

R

A

K

K

G

G

N

N

D

K

E

S

L

L

R

L

N

D

K

A

L

L

N

N

A

R

A

A

L

L

K

A

E

E

I

L

L

M

A

Q

D

D

G

G

T

T

Y

Y

K

A

K

R

I

I

N

S

D

Q

K

K

Y

W

F

F

binding lysine: E24 (= E32), F27 (≠ Y35), F65 (≠ W73), S83 (= S91), H84 (≠ L92), R90 (= R98), Q128 (= Q138), T131 (= T141), T132 (= T145), Y133 (≠ W146), E196 (≠ D208)

3vvdA Crystal structure of ttc0807 complexed with ornithine (see paper)
32% identity, 88% coverage: 26:246/251 of query aligns to 18:234/241 of 3vvdA

query
sites
3vvdA

K

E

L

I

K

R

M

I

G

G

I

T

E
|
E

A

G

A

A

Y

F

P

P

F

F

N

N

N

Y

K

F

D

D

A

E

S

R

G

N

Q

Q

V

L

V

T

G

G

F

F

D

E

K

V

D

D

I

L

G

G

D

N

A

A

L

I

C

A

A

E

K

R

M

L

K

G

V

L

E

K

C

P

E

R

V

W

V

I

T

A

S

Q

N

S

W
x
F

D

D

G

T

I

L

P

I

A

Q

L

L

M

N

A

Q

K

G

K

R

F

F

D

D

F

F

L

V

I

I

S

A

S
|
S

L
x
H

S
x
G

V

I

N

T

D

E

E

E

R
|
R

K

A

Q

R

A

A

V

V

D

D

F

F

T

T

D

N

P

P

Y

H

Y

Y

S

C

N

T

K

G

L

G

Q

V

F

I

I

V

A

S

P

R

K

K

N

G

V

G

D

P

F

R

K

T

V

A

D

-

K

-

E

K

S

D

L

L

K

Q

G

G

K

K

V

V

I

V

G

G

A

V

Q
|
Q

R

V

S

G

T
|
T

L

-

A

-

G

-

T
|
T

W
x
Y

L

M

E

E

-

A

D

Q

E

K

L

I

G

P

S

G

D

I

I

K

T

E

A

V

K

R

L

T

Y

Y

D

Q

T

R

Q

D

E

P

N

D

A

A

Y

L

L

Q

D

D

L

L

T

L

S

A

G

G

R

R

V

I

D

D

A

T

I

W

L

I

A

T

D

D

K

R

Y

F

V

V

N

A

Y

K

D

E

W

A

L

I

K

K

T

E

E

R

A

K

G

L

R

E

A

N

Y

T

E

L

F

Q

K

V

G

G

D

E

P

L

V

V

V

F

E

Q

G

-

D
x
E

K

R

I

V

A

A

I

M

A

A

V

V

R

A

K

K

G

G

N

N

D

K

E

S

L

L

R

L

N

D

K

A

L

L

N

N

A

R

A

A

L

L

K

A

E

E

I

L

L

M

A

Q

D

D

G

G

T

T

Y

Y

K

A

K

R

I

I

N

S

D

Q

K

K

Y

W

F

F

binding L-ornithine: E24 (= E32), F65 (≠ W73), S83 (= S91), H84 (≠ L92), G85 (≠ S93), R90 (= R98), Q128 (= Q138), T131 (= T141), T132 (= T145), Y133 (≠ W146), E196 (≠ D208)

3vv5A Crystal structure of ttc0807 complexed with (s)-2-aminoethyl-l- cysteine (aec) (see paper)
32% identity, 88% coverage: 26:246/251 of query aligns to 14:230/237 of 3vv5A

query
sites
3vv5A

K

E

L

I

K

R

M

I

G

G

I

T

E
|
E

A

G

A

A

Y
x
F

P

P

F

F

N
|
N

N

Y

K

F

D

D

A

E

S

R

G

N

Q

Q

V

L

V

T

G

G

F

F

D

E

K

V

D

D

I

L

G

G

D

N

A

A

L

I

C

A

A

E

K

R

M

L

K

G

V

L

E

K

C

P

E

R

V

W

V

I

T

A

S

Q

N

S

W
x
F

D

D

G

T

I

L

P

I

A

Q

L

L

M

N

A

Q

K

G

K

R

F

F

D

D

F

F

L

V

I

I

S
x
A

S
|
S

L

H

S
x
G

V

I

N

T

D

E

E

E

R
|
R

K

A

Q

R

A

A

V

V

D

D

F

F

T

T

D

N

P

P

Y

H

Y

Y

S

C

N

T

K

G

L

G

Q

V

F

I

I

V

A

S

P

R

K

K

N

G

V

G

D

P

F

R

K

T

V

A

D

-

K

-

E

K

S

D

L

L

K

Q

G

G

K

K

V

V

I

V

G

G

A

V

Q

Q

R

V

S

G

T
|
T

L

-

A

-

G

-

T
|
T

W
x
Y

L

M

E

E

-

A

D

Q

E

K

L

I

G

P

S

G

D

I

I

K

T

E

A

V

K

R

L

T

Y

Y

D

Q

T

R

Q

D

E

P

N

D

A

A

Y

L

L

Q

D

D

L

L

T

L

S

A

G

G

R

R

V

I

D

D

A

T

I

W

L

I

A

T

D

D

K

R

Y

F

V

V

N

A

Y

K

D

E

W

A

L

I

K

K

T

E

E

R

A

K

G

L

R

E

A

N

Y

T

E

L

F

Q

K

V

G

G

D

E

P

L

V

V

V

F

E

Q

G

-

D

E

K

R

I

V

A

A

I

M

A

A

V

V

R

A

K

K

G

G

N

N

D

K

E

S

L

L

R

L

N

D

K

A

L

L

N

N

A

R

A

A

L

L

K

A

E

E

I

L

L

M

A

Q

D

D

G

G

T

T

Y

Y

K

A

K

R

I

I

N

S

D

Q

K

K

Y

W

F

F

binding l-thialysine: E20 (= E32), F23 (≠ Y35), N27 (= N39), F61 (≠ W73), A78 (≠ S90), S79 (= S91), G81 (≠ S93), R86 (= R98), T127 (= T141), T128 (= T145), Y129 (≠ W146)

8hqrA Crystal structure of the arginine-/lysine-binding protein sar11_1210 from 'candidatus pelagibacter ubique' htcc1062 bound to arginine
29% identity, 90% coverage: 24:248/251 of query aligns to 7:263/267 of 8hqrA

query
sites
8hqrA

V

M

E

D

K

K

L

I

K

K

M

I

G

G

I

T

E
|
E

A

G

A

A

Y
|
Y

P

P

F

W

N

N

N

S

K

K

D

D

A

A

S

S

G

G

Q

A

V

L

V

I

G

G

F

F

D

E

K

V

D

E

I

L

G

A

D

E

A

E

L

L

C

C

A

K

K

I

M

M

K

G

V

R

E

E

C

C

E

T

V

I

V

V

T

E

S

Q

N

D

W
|
W

D

D

G

G

I

M

I

I

P

P

A

A

L

L

M

L

A

M

K

R

K

K

F

F

D

D

F

A

L

I

I

M

S
x
A

S
x
G

L

M

S
|
S

V

I

N

T

D

A

E

E

R
|
R

K

Q

Q

K

A

T

V

I

D

T

F

F

T

S

D

Q

P

G

Y

Y

Y

A

-

D

-
x
E

-

V

-

A

-

L

-

A

-

V

-

M

-

K

-

G

S

S

N

S

K

L

L

E

Q

S

F

M

I

D

A

T

P

P

K

E

N

G

V

I

D

N

F

L

K

T

V

L

D

G

K

G

E

S

S

A

L

V

K

K

-

K

-

T

-

L

-

K

-

T

-

L

-

T

-

A

-

L

-

A

G

G

K

K

V

T

I

V

G

C

A

T

Q
|
Q

R

T

S

G

T
|
T

L
x
I

A

H

G

Q

T

N

W

F

L

L

E

E

D

S

E

G

L

D

G

V

S

G

D

K

I

V

T

N

A

V

K

R

L

T

Y

Y

D

K

T

T

Q

Q

E

D

N

E

A

V

Y

N

L

L

D

D

L

L

T

T

S

S

G

G

R

R

V

C

D

D

A

V

I

A

L

L

A

A

D

A

K

A

Y

V

V

A

N

F

Y

T

D

D

W

Y

L

-

K

-

T

-

E

-

A

-

G

-

R

-

A

-

Y

A

E

D

F

K

K

S

G

G

D

K

P

P

V

V

E

L

-

V

-

G

-

P

-

T

-

F

-

S

-

G

-

A

-

F

G

G

D

N

K

G

I

V

A

G

I

V

A

G

V

I

R

R

K

Q

G

G

N

G

D

D

E

D

-

A

-

I

-

G

-

T

-

R

-

D

-

A

-

K

L

L

R

L

N

K

K

D

L

F

N

N

A

K

A

A

L

I

K

N

E

T

I

A

L

R

A

K

D

Q

G

G

T

I

Y

I

K

S

K

K

I

L

N

A

D

I

K

K

Y

H

F

F

P

G

F

F

binding arginine: E15 (= E32), Y18 (= Y35), W56 (= W73), A73 (≠ S90), G74 (≠ S91), S76 (= S93), R81 (= R98), E94 (vs. gap), Q143 (= Q138), T146 (= T141), I147 (≠ L142)

3i6vA Crystal structure of a periplasmic his/glu/gln/arg/opine family- binding protein from silicibacter pomeroyi in complex with lysine
32% identity, 88% coverage: 27:246/251 of query aligns to 2:211/218 of 3i6vA

query
sites
3i6vA

L

V

K

R

M

M

G

G

I

T

E
|
E

A

G

A

A

Y
|
Y

P

P

F

Y

N

N

N

F

K

I

D

N

A

D

S

A

G

G

Q

E

V

V

V

D

G

G

F

F

D

E

K

R

D

E

I

L

G

G

D

D

A

E

L

L

C

C

A

K

K

R

M

A

K

G

V

L

E

T

C

C

E

E

V

W

V

V

T

K

S

N

N

D

W
|
W

D

D

G

S

I

I

P

P

A

N

L

L

M

V

A

S

K

G

K

N

F

Y

D

D

F

T

L

I

I

I

S

A

S
x
G

L
x
M

S
|
S

V

I

N

T

D

D

E

E

R
|
R

K

D

Q

E

A

V

V

I

D

D

F

F

T

T

D

Q

P

N

Y

Y

Y

-

S

-

N

-

K

-

L

-

Q

-

F

-

I

I

A

P

P

P

K

T

N

A

V

S

D

S

F

Y

-

V

-

A

K

T

V

S

D

D

K

G

E

A

S

D

L

L

K

S

G

G

K

-

V

I

I

V

G

A

A

A

Q
|
Q

R

T

S

A

T
|
T

L
x
I

A
x
Q

G

A

T

G

W

Y

L

I

E

A

D

E

E

-

L

-

G

-

S

S

D

G

I

A

T

T

A

L

K

V

L

E

Y

F

D

A

T

T

Q

P

E

E

N

E

A

T

Y

I

L

A

D

A

L

V

T

R

S

N

G

G

R

E

V

A

D

D

A

A

I

V

L

F

A

A

D

D

K

R

Y

-

V

-

N

-

Y

-

D

D

W

Y

L

L

-

V

-

P

-

I

K

V

T

A

E

E

A

S

G

G

R

G

A

E

Y

L

E

M

F

F

K

V

G

G

D

D

P

D

V

V

V

P

E

L

G

G

D

G

K

G

I

V

A

G

I

M

A

G

V

L

R

R

K

E

G

S

N

D

D

G

E

E

L

L

R

R

N

G

K

K

L

F

N

D

A

A

L

I

K

T

E

S

I

M

L

K

A

E

D

D

G

G

T

T

Y

L

K

N

K

T

I

M

N

I

D

K

K

K

Y

W

F

F

binding lysine: E7 (= E32), Y10 (= Y35), W48 (= W73), G66 (≠ S91), M67 (≠ L92), S68 (= S93), R73 (= R98), Q107 (= Q138), T110 (= T141), I111 (≠ L142), Q112 (≠ A143)

Query Sequence

>Pf6N2E2_3856 Lysine-arginine-ornithine-binding periplasmic protein precursor (TC 3.A.1.3.1)
MQTYRKFLLAAAVSLVFSTSAMAVEKLKMGIEAAYPPFNNKDASGQVVGFDKDIGDALCA
KMKVECEVVTSNWDGIIPALMAKKFDFLISSLSVNDERKQAVDFTDPYYSNKLQFIAPKN
VDFKVDKESLKGKVIGAQRSTLAGTWLEDELGSDITAKLYDTQENAYLDLTSGRVDAILA
DKYVNYDWLKTEAGRAYEFKGDPVVEGDKIAIAVRKGNDELRNKLNAALKEILADGTYKK
INDKYFPFSIY

Or try a new SitesBLAST search

SitesBLAST's Database

SitesBLAST's database includes (1) SwissProt entries with experimentally-supported functional features; and (2) protein structures with bound ligands, from the BioLip database.

by Morgan Price, Arkin group
Lawrence Berkeley National Laboratory