SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing WP_012673914.1 NCBI__GCF_000021545.1:WP_012673914.1 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)

P0A8N5 Lysine--tRNA ligase, heat inducible; Lysyl-tRNA synthetase; LysRS; EC 6.1.1.6 from Escherichia coli (strain K12) (see 2 papers)
50% identity, 76% coverage: 139:575/577 of query aligns to 67:504/505 of P0A8N5

query
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P0A8N5

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K114 (≠ D186) modified: N6-acetyllysine
K156 (= K228) modified: N6-acetyllysine

Sites not aligning to the query:

1 modified: Initiator methionine, Removed

3e9iA Lysyl-tRNA synthetase from bacillus stearothermophilus complexed with l-lysine hydroxamate-amp (see paper)
52% identity, 75% coverage: 139:573/577 of query aligns to 55:483/484 of 3e9iA

query
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active site: R245 (= R335), E247 (= E337), R252 (≠ T342), H253 (= H343), E403 (= E493), N406 (= N496), R462 (= R552)
binding 5'-O-{(R)-hydroxy[(L-lysylamino)oxy]phosphoryl}adenosine: G199 (= G289), E223 (= E313), R245 (= R335), H253 (= H343), N254 (= N344), F257 (= F347), M259 (= M349), E261 (= E351), Y263 (= Y353), E403 (= E493), H404 (≠ L494), N406 (= N496), F408 (≠ Y498), E410 (= E500), G459 (= G549)

3e9hA Lysyl-tRNA synthetase from bacillus stearothermophilus complexed with l-lysylsulfamoyl adenosine (see paper)
52% identity, 75% coverage: 139:573/577 of query aligns to 55:483/484 of 3e9hA

query
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E

M

Q

G

G

D

N

E

D

E

E

A

A

M

H

D

E

V

M

D

D

E

E

T

D

F

F

L

L

T

E

A

A

L

L

E

E

Y

Y

G

G

L

M

P

P

T

T

A

G

G
|
G

E

L

G

G

I

I

G
|
G

I

V

D

D

R
|
R

L

L

V

V

M

M

M

L

L

L

T

T

D

N

S

S

V

P

S

S

I

I

R

R

E

D

V

V

I

L

L

L

F

F

P

P

T

Q

L

M

R

R

active site: R245 (= R335), E247 (= E337), R252 (≠ T342), H253 (= H343), E403 (= E493), N406 (= N496), R462 (= R552)
binding 5'-o-[(l-lysylamino)sulfonyl]adenosine: E223 (= E313), R245 (= R335), H253 (= H343), N254 (= N344), F257 (= F347), M259 (= M349), E261 (= E351), Y263 (= Y353), E403 (= E493), H404 (≠ L494), N406 (= N496), F408 (≠ Y498), E410 (= E500), G455 (= G545), G459 (= G549), R462 (= R552)
binding magnesium ion: E396 (= E486), E403 (= E493), N406 (= N496)

3a74A Lysyl-tRNA synthetase from bacillus stearothermophilus complexed with diadenosine tetraphosphate (ap4a)
52% identity, 75% coverage: 139:573/577 of query aligns to 55:483/484 of 3a74A

query
sites
3a74A

E

E

V

V

A

A

V

V

A

A

G

G

R

R

L

I

V

M

A

T

L

K

R

R

D

G

Q

M

G

G

K

K

A

A

A

G

F

F

G

A

H

H

L

I

Q

Q

D

D

A

V

D

T

G

G

K

Q

L

I

Q

Q

I

I

Y

Y

F

V

N

R

A

Q

D

D

I

D

L

V

G

G

Q

E

E

Q

N

Q

Y

Y

Q

E

K

-

A

L

M

F

D

K

L

I

I

S

D

D

I

L

G

G

D

D

I

I

V

V

G

G

V

V

K

R

G

G

K

T

L

M

F

F

R

K

T

T

M

K

T

V

G

G

E

E

L

L

T

S

V

I

E

K

V

V

H

S

S

S

Y

Y

Q

E

I

F

L

L

S

T

K

K

S

A

L

L

R

R

P

P

L

L

P

P

E

E

K

K

W

-

H

-

G

-

L

-

R

-

D

D

V

I

E

E

E

Q

R

R

Y

Y

R

R

Y

Q

R

R

F

Y

L

L

D

D

L

L

I

I

A

M

N

N

Q

P

R

E

S

S

R

K

E

K

I

T

F

F

K

I

L

T

R

R

S

S

K

L

A

I

I

I

K

Q

S

S

L

M

R

R

E

R

F

Y

L

L

E

D

S

S

K

H

G

G

F

Y

I

L

E

E

V

V

E

E

T

T

P

P

I

M

L

M

Q

H

P

A

V

V

A

A

S

G

G
|
G

A

A

L

A

A

A

K

R

P

P

F

F

I

I

T

T

Y

H

H

H

N

N

A

A

L

L

D

D

M

M

N

T

L

L

Y

Y

L

M

R

R

I

I

A

A

P

I

E
|
E

L

L

Y

H

L

L

K

K

M

R

L

L

V

I

V

V

G

G

F

L

N

E

R

K

V

V

F

Y

E

E

I

I

G

G

R

R

N

V

F

F

R
|
R

N

N

E
|
E

G

G

I

I

D

S

T

T

T
x
R

H
|
H

N
|
N

P

P

E

E

F
|
F

T

T

M
|
M

V

L

E
|
E

F

L

Y
|
Y

A

E

A

A

Y

Y

L

A

D

D

Y

F

N

R

D

D

L

I

M

M

A

K

L

L

T

T

E

E

E

N

L

L

F

I

R

A

K

H

I

I

L

A

L

T

D

E

T

V

V

L

G

G

T

T

L

T

K

K

I

I

K

Q

W

Y

E

G

D

E

Q

H

E

L

I

V

D

D

F

L

E

T

K

P

P

E

F

W

R

R

L

L

P

H

F

M

F

V

E

D

A

A

L

I

K

K

Q

E

K

Y

T

V

G

G

K

V

D

D

K

F

E

W

F

R

F

Q

L

M

D

S

Y

D

E

E

K

E

A

A

K

R

N

E

F

L

A

A

K

K

E

E

V

H

G

G

I

V

P

E

K

V

A

A

D

P

T

H

L

M

T

T

H

F

M

G

K

H

I

I

L

V

D

N

K

E

L

F

F

F

E
|
E

H

Q

F

K

V

V

E
|
E

E

D

D

K

L

L

V

I

Q

Q

P

P

T

T

F

F

V

I

I

Y

D

G

F

H

P

P

K

V

I

E

L

I

S

S

P

P

L

L

A

A

K

K

T

K

H

N

R

P

N

D

D

D

P

P

D

R

L

F

V

T

E

D

R

R

F

F

E
|
E

L

L

I

F

I

I

N

V

K

G

Q

R

E
|
E

L

H

A

A

N
|
N

A

A

Y
x
F

T

T

E
|
E

L

L

N

N

D

D

P

P

F

I

D

D

Q

Q

R

R

E

Q

R

R

F

F

I

E

Q

E

Q

Q

I

L

R

K

E

E

K

R

E

E

M

Q

G

G

D

N

E

D

E

E

A

A

M

H

D

E

V

M

D

D

E

E

T

D

F

F

L

L

T

E

A

A

L

L

E

E

Y

Y

G

G

L

M

P

P

T

T

A

G

G

G

E

L

G

G

I

I

G
|
G

I

V

D

D

R
|
R

L

L

V

V

M

M

M

L

L

L

T

T

D

N

S

S

V

P

S

S

I

I

R

R

E

D

V

V

I

L

L

L

F

F

P

P

T

Q

L

M

R

R

active site: R245 (= R335), E247 (= E337), R252 (≠ T342), H253 (= H343), E403 (= E493), N406 (= N496), R462 (= R552)
binding bis(adenosine)-5'-tetraphosphate: R245 (= R335), E247 (= E337), R252 (≠ T342), H253 (= H343), N254 (= N344), F257 (= F347), M259 (= M349), E358 (= E448), E362 (= E452), E403 (= E493), N406 (= N496), G459 (= G549), R462 (= R552)
binding 2,6-diamino-hexanoic acid amide: G199 (= G289), E223 (= E313), M259 (= M349), E261 (= E351), Y263 (= Y353), N406 (= N496), F408 (≠ Y498), E410 (= E500)
binding magnesium ion: E396 (= E486), E396 (= E486), E403 (= E493), E403 (= E493)

1bbuA Lysyl-tRNA synthetase (lyss) complexed with lysine (see paper)
50% identity, 76% coverage: 139:574/577 of query aligns to 56:486/486 of 1bbuA

query
sites
1bbuA

E

E

V

V

A

A

V

V

A

A

G

G

R

R

L

M

V

M

A

T

L

R

R

R

D

I

Q

M

G

G

K

K

A

A

A

S

F

F

G

V

H

T

L

L

Q

Q

D

D

A

V

D

G

G

G

K

R

L

I

Q

Q

I

L

Y

Y

F

V

N

A

A

R

D

D

I

D

L

L

G

P

Q

E

E

G

N

V

Y

Y

Q

N

K

E

A

Q

M

F

D

K

L

K

I

W

D

D

I

L

G

G

D

D

I

I

V

L

G

G

V

A

K

K

G

G

K

K

L

L

F

F

R

K

T

T

M

K

T

T

G

G

E

E

L

L

T

S

V

I

E

H

V

C

H

T

S

E

Y

L

Q

R

I

L

L

L

S

T

K

K

S

A

L

L

R

R

P

P

L

L

P

P

E

D

K

-

W

-

H

-

G

-

L

-

R

-

D

D

V

Q

E

E

E

A

R

R

Y

Y

R

R

Y

Q

R

R

F

Y

L

L

D

D

L

L

I

I

A

S

N

N

Q

D

R

E

S

S

R

R

E

N

I

T

F

F

K

K

L

V

R

R

S

S

K

Q

A

I

I

L

K

S

S

G

L

I

R

R

E

Q

F

F

L

M

E

V

S

N

K

R

G

G

F

F

I

M

E

E

V

V

E

E

T

T

P

P

I

M

L

M

Q

Q

P

V

V

I

A

P

S

G

G
|
G

A

A

L

A

A

A

K

R

P

P

F

F

I

I

T

T

Y

H

H

H

N

N

A

A

L

L

D

D

M

L

N

D

L

M

Y

Y

L

L

R

R

I

I

A

A

P

P

E
|
E

L

L

Y

Y

L

L

K

K

M

R

L

L

V

V

G

G

F

F

N

E

R

R

V

V

F

F

E

E

I

I

G

N

R

R

N

N

F

F

R
|
R

N

N

E
|
E

G

G

I

I

D

S

T

V

T
x
R

H
|
H

N

N

P

P

E

E

F

F

T

T

M

M

V

M

E
|
E

F

L

Y
|
Y

A

M

A

A

Y

Y

L

A

D

D

Y

Y

N

K

D

D

L

L

M

I

A

E

L

L

T

T

E

E

E

S

L

L

F

F

R

R

K

T

I

L

L

A

L

Q

D

D

T

I

V

L

G

G

T

K

L

T

K

E

I

V

K

T

W

Y

E

G

D

D

Q

V

E

T

I

L

D

D

F

F

E

G

K

K

P

P

F

F

R

E

R

K

L

L

P

T

F

M

F

R

E

E

A

A

L

I

K

K

Q

K

-

Y

K

R

T

P

G

E

K

T

D

D

K

M

E

A

F

D

F

L

L

D

D

N

Y

F

E

D

K

S

A

A

K

K

N

A

F

I

A

A

K

E

E

S

V

I

G

G

I

I

P

H

K

V

A

E

D

K

T

S

L

W

T

G

H

L

M

G

K

R

I

I

L

V

D

T

K

E

L

I

F

F

E

E

H

E

F

V

V

A

E

E

E

A

D

H

L

L

V

I

Q

Q

P

P

T

T

F

F

V

I

I

T

D

E

F

Y

P

P

K

A

I

E

L

V

S

S

P

P

L

L

A

A

K

R

T

R

H

N

R

D

N

V

D

N

P

P

D

E

L

I

V

T

E

D

R

R

F

F

E

E

L

F

I

F

I

I

N

G

K

G

Q

R

E
|
E

L

I

A

G

N
|
N

A

G

Y
x
F

T

S

E
|
E

L

L

N

N

D

D

P

A

F

E

D

D

Q

Q

R

A

E

Q

R

R

F

F

I

L

Q

D

Q

Q

I

V

R

A

E

A

K

K

E

D

M

A

G

G

D

D

E

D

E

E

A

A

M

M

D

F

V

Y

D

D

E

E

T

D

F

Y

L

V

T

T

A

A

L

L

E

E

Y

H

G

G

L

L

P

P

T

T

A

A

G
|
G

E

L

G
|
G

I

I

G

G

I

I

D

D

R
|
R

L

M

V

V

M

M

M

L

L

F

T

T

D

N

S

S

V

H

S

T

I

I

R

R

E

D

V

V

I

I

L

L

F

F

P

P

T

A

L

M

R

R

P

P

active site: R246 (= R335), E248 (= E337), R253 (≠ T342), H254 (= H343), E405 (= E493), N408 (= N496), R464 (= R552)
binding lysine: G200 (= G289), E224 (= E313), E262 (= E351), Y264 (= Y353), F410 (≠ Y498), E412 (= E500), G457 (= G545), G459 (= G547)

1e24A Lysyl-tRNA synthetase (lysu) hexagonal form complexed with lysine and atp and mn2+ (see paper)
50% identity, 76% coverage: 139:574/577 of query aligns to 56:485/485 of 1e24A

query
sites
1e24A

E

E

V

V

A

S

V

V

A

A

G

G

R

R

L

M

V

M

A

T

L

R

R

R

D

I

Q

M

G

G

K

K

A

A

A

S

F

F

G

V

H

T

L

L

Q

Q

D

D

A

V

D

G

G

G

K

R

L

I

Q

Q

I

L

Y

Y

F

V

N

A

A

R

D

D

I

S

L

L

G

P

Q

E

E

G

N

V

Y

Y

Q

N

K

D

A

Q

M

F

D

K

L

K

I

W

D

D

I

L

G

G

D

D

I

I

V

I

G

G

V

A

K

R

G

G

K

T

L

L

F

F

R

K

T

T

M

Q

T

T

G

G

E

E

L

L

T

S

V

I

E

H

V

C

H

T

S

E

Y

L

Q

R

I

L

L

L

S

T

K

K

S

A

L

L

R

R

P

P

L

L

P

P

E

-

K

-

W

-

H

-

G

-

L

-

R

-

D

D

V

Q

E

E

E

V

R

R

Y

Y

R

R

Y

Q

R

R

F

Y

L

L

D

D

L

L

I

I

A

A

N

N

Q

D

R

K

S

S

R

R

E

Q

I

T

F

F

K

V

L

V

R

R

S

S

K

K

A

I

I

L

K

A

S

A

L

I

R

R

E

Q

F

F

L

M

E

V

S

A

K

R

G

G

F

F

I

M

E

E

V

V

E

E

T

T

P

P

I

M

L

M

Q

Q

P

V

V

I

A

P

S

G

G
|
G

A

A

L

S

A

A

K

R

P

P

F

F

I

I

T

T

Y

H

H

H

N

N

A

A

L

L

D

D

M

L

N

D

L

M

Y

Y

L

L

R

R

I

I

A

A

P

P

E
|
E

L

L

Y

Y

L

L

K

K

M

R

L

L

V

V

G

G

F

F

N

E

R

R

V

V

F

F

E

E

I

I

G

N

R

R

N

N

F

F

R
|
R

N

N

E
|
E

G

G

I

I

D

S

T

V

T
x
R

H
|
H

N
|
N

P

P

E

E

F
|
F

T

T

M
|
M

V

M

E
|
E

F

L

Y
|
Y

A

M

A

A

Y

Y

L

A

D

D

Y

Y

N

H

D

D

L

L

M

I

A

E

L

L

T

T

E

E

E

S

L

L

F

F

R

R

K

T

I

L

L

A

L

Q

D

E

T

V

V

L

G

G

T

T

L

T

K

K

I

V

K

T

W

Y

E

G

D

E

Q

H

E

V

I

F

D

D

F

F

E

G

K

K

P

P

F

F

R

E

R

K

L

L

P

T

F

M

F

R

E

E

A

A

L

I

K

K

Q

K

-

Y

K

R

T

P

G

E

K

T

D

D

K

M

E

A

F

D

F

L

L

D

D

N

Y

F

E

D

K

A

A

A

K

K

N

A

F

L

A

A

K

E

E

S

V

I

G

G

I

I

P

T

K

V

A

E

D

K

T

S

L

W

T

G

H

L

M

G

K

R

I

I

L

V

D

T

K

E

L

I

F

F

E

D

H

E

F

V

V

A

E

E

E

A

D

H

L

L

V

I

Q

Q

P

P

T

T

F

F

V

I

I

T

D

E

F

Y

P

P

K

A

I

E

L

V

S

S

P

P

L

L

A

A

K

R

T

R

H

N

R

D

N

V

D

N

P

P

D

E

L

I

V

T

E

D

R

R

F

F

E
|
E

L

F

I

F

I

I

N

G

K

G

Q

R

E
|
E

L
x
I

A

G

N
|
N

A

G

Y
x
F

T

S

E
|
E

L

L

N

N

D

D

P

A

F

E

D

D

Q

Q

R

A

E

E

R

R

F

F

I

Q

Q

E

Q

Q

I

V

R

N

E

A

K

K

E

A

M

A

G

G

D

D

E

D

E

E

A

A

M

M

D

F

V

Y

D

D

E

E

T

D

F

Y

L

V

T

T

A

A

L

L

E

E

Y

Y

G

G

L

L

P

P

T

T

A

A

G
|
G

E

L

G
|
G

I

I

G
|
G

I

I

D

D

R
|
R

L

M

V

I

M

M

M

L

L

F

T

T

D

N

S

S

V

H

S

T

I

I

R

R

E

D

V

V

I

I

L

L

F

F

P

P

T

A

L

M

R

R

P

P

active site: R245 (= R335), E247 (= E337), R252 (≠ T342), H253 (= H343), E404 (= E493), N407 (= N496), R463 (= R552)
binding adenosine-5'-triphosphate: R245 (= R335), R252 (≠ T342), H253 (= H343), N254 (= N344), F257 (= F347), M259 (= M349), E404 (= E493), I405 (≠ L494), G460 (= G549), R463 (= R552)
binding lysine: G199 (= G289), E223 (= E313), E261 (= E351), Y263 (= Y353), N407 (= N496), F409 (≠ Y498), E411 (= E500), G456 (= G545), G458 (= G547)
binding manganese (ii) ion: E397 (= E486), E404 (= E493)

1e22A Lysyl-tRNA synthetase (lysu) hexagonal form complexed with lysine and the non-hydrolysable atp analogue amp-pcp (see paper)
50% identity, 76% coverage: 139:574/577 of query aligns to 56:485/485 of 1e22A

query
sites
1e22A

E

E

V

V

A

S

V

V

A

A

G

G

R

R

L

M

V

M

A

T

L

R

R

R

D

I

Q

M

G

G

K

K

A

A

A

S

F

F

G

V

H

T

L

L

Q

Q

D

D

A

V

D

G

G

G

K

R

L

I

Q

Q

I

L

Y

Y

F

V

N

A

A

R

D

D

I

S

L

L

G

P

Q

E

E

G

N

V

Y

Y

Q

N

K

D

A

Q

M

F

D

K

L

K

I

W

D

D

I

L

G

G

D

D

I

I

V

I

G

G

V

A

K

R

G

G

K

T

L

L

F

F

R

K

T

T

M

Q

T

T

G

G

E

E

L

L

T

S

V

I

E

H

V

C

H

T

S

E

Y

L

Q

R

I

L

L

L

S

T

K

K

S

A

L

L

R

R

P

P

L

L

P

P

E

-

K

-

W

-

H

-

G

-

L

-

R

-

D

D

V

Q

E

E

E

V

R

R

Y

Y

R

R

Y

Q

R

R

F

Y

L

L

D

D

L

L

I

I

A

A

N

N

Q

D

R

K

S

S

R

R

E

Q

I

T

F

F

K

V

L

V

R

R

S

S

K

K

A

I

I

L

K

A

S

A

L

I

R

R

E

Q

F

F

L

M

E

V

S

A

K

R

G

G

F

F

I

M

E

E

V

V

E

E

T

T

P

P

I

M

L

M

Q

Q

P

V

V

I

A

P

S

G

G
|
G

A

A

L

S

A

A

K

R

P

P

F

F

I

I

T

T

Y

H

H

H

N

N

A

A

L

L

D

D

M

L

N

D

L

M

Y

Y

L

L

R

R

I

I

A

A

P

P

E
|
E

L

L

Y

Y

L

L

K

K

M

R

L

L

V

V

G

G

F

F

N

E

R

R

V

V

F

F

E

E

I

I

G

N

R

R

N

N

F

F

R
|
R

N

N

E
|
E

G

G

I

I

D

S

T

V

T
x
R

H
|
H

N
|
N

P

P

E

E

F
|
F

T

T

M
|
M

V

M

E
|
E

F

L

Y
|
Y

A

M

A

A

Y

Y

L

A

D

D

Y

Y

N

H

D

D

L

L

M

I

A

E

L

L

T

T

E

E

E

S

L

L

F

F

R

R

K

T

I

L

L

A

L

Q

D

E

T

V

V

L

G

G

T

T

L

T

K

K

I

V

K

T

W

Y

E

G

D

E

Q

H

E

V

I

F

D

D

F

F

E

G

K

K

P

P

F

F

R

E

R

K

L

L

P

T

F

M

F

R

E

E

A

A

L

I

K

K

Q

K

-

Y

K

R

T

P

G

E

K

T

D

D

K

M

E

A

F

D

F

L

L

D

D

N

Y

F

E

D

K

A

A

A

K

K

N

A

F

L

A

A

K

E

E

S

V

I

G

G

I

I

P

T

K

V

A

E

D

K

T

S

L

W

T

G

H

L

M

G

K

R

I

I

L

V

D

T

K

E

L

I

F

F

E

D

H

E

F

V

V

A

E

E

E

A

D

H

L

L

V

I

Q

Q

P

P

T

T

F

F

V

I

I

T

D

E

F

Y

P

P

K

A

I

E

L

V

S

S

P

P

L

L

A

A

K

R

T

R

H

N

R

D

N

V

D

N

P

P

D

E

L

I

V

T

E

D

R

R

F

F

E
|
E

L

F

I

F

I

I

N

G

K

G

Q

R

E
|
E

L
x
I

A

G

N
|
N

A

G

Y
x
F

T

S

E
|
E

L

L

N

N

D

D

P

A

F

E

D

D

Q

Q

R

A

E

E

R

R

F

F

I

Q

Q

E

Q

Q

I

V

R

N

E

A

K

K

E

A

M

A

G

G

D

D

E

D

E

E

A

A

M

M

D

F

V

Y

D

D

E

E

T

D

F

Y

L

V

T

T

A

A

L

L

E

E

Y

Y

G

G

L

L

P

P

T

T

A

A

G
|
G

E

L

G
|
G

I

I

G
|
G

I

I

D

D

R
|
R

L

M

V

I

M

M

M

L

L

F

T

T

D

N

S

S

V

H

S

T

I

I

R

R

E

D

V

V

I

I

L

L

F

F

P

P

T

A

L

M

R

R

P

P

active site: R245 (= R335), E247 (= E337), R252 (≠ T342), H253 (= H343), E404 (= E493), N407 (= N496), R463 (= R552)
binding phosphomethylphosphonic acid adenylate ester: R245 (= R335), R252 (≠ T342), H253 (= H343), N254 (= N344), F257 (= F347), E404 (= E493), I405 (≠ L494), G460 (= G549), R463 (= R552)
binding lysine: G199 (= G289), E223 (= E313), M259 (= M349), E261 (= E351), Y263 (= Y353), N407 (= N496), F409 (≠ Y498), E411 (= E500), G456 (= G545), G458 (= G547)
binding magnesium ion: E397 (= E486), E404 (= E493)

1e1tA Lysyl-tRNA synthetase (lysu) hexagonal form complexed with the lysyl_adenylate intermediate (see paper)
50% identity, 76% coverage: 139:574/577 of query aligns to 56:485/485 of 1e1tA

query
sites
1e1tA

E

E

V

V

A

S

V

V

A

A

G

G

R

R

L

M

V

M

A

T

L

R

R

R

D

I

Q

M

G

G

K

K

A

A

A

S

F

F

G

V

H

T

L

L

Q

Q

D

D

A

V

D

G

G

G

K

R

L

I

Q

Q

I

L

Y

Y

F

V

N

A

A

R

D

D

I

S

L

L

G

P

Q

E

E

G

N

V

Y

Y

Q

N

K

D

A

Q

M

F

D

K

L

K

I

W

D

D

I

L

G

G

D

D

I

I

V

I

G

G

V

A

K

R

G

G

K

T

L

L

F

F

R

K

T

T

M

Q

T

T

G

G

E

E

L

L

T

S

V

I

E

H

V

C

H

T

S

E

Y

L

Q

R

I

L

L

L

S

T

K

K

S

A

L

L

R

R

P

P

L

L

P

P

E

-

K

-

W

-

H

-

G

-

L

-

R

-

D

D

V

Q

E

E

E

V

R

R

Y

Y

R

R

Y

Q

R

R

F

Y

L

L

D

D

L

L

I

I

A

A

N

N

Q

D

R

K

S

S

R

R

E

Q

I

T

F

F

K

V

L

V

R

R

S

S

K

K

A

I

I

L

K

A

S

A

L

I

R

R

E

Q

F

F

L

M

E

V

S

A

K

R

G

G

F

F

I

M

E

E

V

V

E

E

T

T

P

P

I

M

L

M

Q

Q

P

V

V

I

A

P

S

G

G
|
G

A

A

L

S

A

A

K

R

P

P

F

F

I

I

T

T

Y

H

H

H

N

N

A

A

L

L

D

D

M

L

N

D

L

M

Y

Y

L

L

R

R

I

I

A

A

P

P

E
|
E

L

L

Y

Y

L

L

K

K

M

R

L

L

V

V

G

G

F

F

N

E

R

R

V

V

F

F

E

E

I

I

G

N

R

R

N

N

F

F

R
|
R

N

N

E
|
E

G

G

I

I

D

S

T

V

T
x
R

H
|
H

N
|
N

P

P

E

E

F
|
F

T

T

M
|
M

V

M

E
|
E

F

L

Y
|
Y

A

M

A

A

Y

Y

L

A

D

D

Y

Y

N

H

D

D

L

L

M

I

A

E

L

L

T

T

E

E

E

S

L

L

F

F

R

R

K

T

I

L

L

A

L

Q

D

E

T

V

V

L

G

G

T

T

L

T

K

K

I

V

K

T

W

Y

E

G

D

E

Q

H

E

V

I

F

D

D

F

F

E

G

K

K

P

P

F

F

R

E

R

K

L

L

P

T

F

M

F

R

E

E

A

A

L

I

K

K

Q

K

-

Y

K

R

T

P

G

E

K

T

D

D

K

M

E

A

F

D

F

L

L

D

D

N

Y

F

E

D

K

A

A

A

K

K

N

A

F

L

A

A

K

E

E

S

V

I

G

G

I

I

P

T

K

V

A

E

D

K

T

S

L

W

T

G

H

L

M

G

K

R

I

I

L

V

D

T

K

E

L

I

F

F

E

D

H

E

F

V

V

A

E

E

E

A

D

H

L

L

V

I

Q

Q

P

P

T

T

F

F

V

I

I

T

D

E

F

Y

P

P

K

A

I

E

L

V

S

S

P

P

L

L

A

A

K

R

T

R

H

N

R

D

N

V

D

N

P

P

D

E

L

I

V

T

E

D

R

R

F

F

E
|
E

L

F

I

F

I

I

N

G

K

G

Q

R

E
|
E

L
x
I

A

G

N
|
N

A

G

Y
x
F

T

S

E
|
E

L

L

N

N

D

D

P

A

F

E

D

D

Q

Q

R

A

E

E

R

R

F

F

I

Q

Q

E

Q

Q

I

V

R

N

E

A

K

K

E

A

M

A

G

G

D

D

E

D

E

E

A

A

M

M

D

F

V

Y

D

D

E

E

T

D

F

Y

L

V

T

T

A

A

L

L

E

E

Y

Y

G

G

L

L

P

P

T

T

A

A

G
|
G

E

L

G
|
G

I

I

G
|
G

I

I

D

D

R
|
R

L

M

V

I

M

M

M

L

L

F

T

T

D

N

S

S

V

H

S

T

I

I

R

R

E

D

V

V

I

I

L

L

F

F

P

P

T

A

L

M

R

R

P

P

active site: R245 (= R335), E247 (= E337), R252 (≠ T342), H253 (= H343), E404 (= E493), N407 (= N496), R463 (= R552)
binding adenosine-5'-[lysyl-phosphate]: G199 (= G289), E223 (= E313), R245 (= R335), R252 (≠ T342), H253 (= H343), N254 (= N344), F257 (= F347), M259 (= M349), E261 (= E351), Y263 (= Y353), E404 (= E493), I405 (≠ L494), N407 (= N496), F409 (≠ Y498), E411 (= E500), G456 (= G545), G458 (= G547), G460 (= G549)
binding magnesium ion: E397 (= E486), E404 (= E493)
binding pyrophosphate 2-: H253 (= H343), E404 (= E493), R463 (= R552)

5yzxA Crystal structure of e.Coli lysu t146d mutant
50% identity, 76% coverage: 139:574/577 of query aligns to 55:484/484 of 5yzxA

query
sites
5yzxA

E

E

V

V

A

S

V

V

A

A

G

G

R

R

L

M

V

M

A

T

L

R

R

R

D

I

Q

M

G

G

K

K

A

A

A

S

F

F

G

V

H

T

L

L

Q

Q

D

D

A

V

D

G

G

G

K

R

L

I

Q

Q

I

L

Y

Y

F

V

N

A

A

R

D

D

I

S

L

L

G

P

Q

E

E

G

N

V

Y

Y

Q

N

K

D

A

Q

M

F

D

K

L

K

I

W

D

D

I

L

G

G

D

D

I

I

V

I

G

G

V

A

K

R

G

G

K

T

L

L

F

F

R

K

T

T

M

Q

T

T

G

G

E

E

L

L

T

S

V

I

E

H

V

C

H

T

S

E

Y

L

Q

R

I

L

L

L

S

D

K

K

S

A

L

L

R

R

P

P

L

L

P

P

E

-

K

-

W

-

H

-

G

-

L

-

R

-

D

D

V

Q

E

E

E

V

R

R

Y

Y

R

R

Y

Q

R

R

F

Y

L

L

D

D

L

L

I

I

A

A

N

N

Q

D

R

K

S

S

R

R

E

Q

I

T

F

F

K

V

L

V

R

R

S

S

K

K

A

I

I

L

K

A

S

A

L

I

R

R

E

Q

F

F

L

M

E

V

S

A

K

R

G

G

F

F

I

M

E

E

V

V

E

E

T

T

P

P

I

M

L

M

Q

Q

P

V

V

I

A

P

S

G

G

G

A

A

L

S

A

A

K

R

P

P

F

F

I

I

T

T

Y

H

H

H

N

N

A

A

L

L

D

D

M

L

N

D

L

M

Y

Y

L

L

R

R

I

I

A

A

P

P

E

E

L

L

Y

Y

L

L

K

K

M

R

L

L

V

V

G

G

F

F

N

E

R

R

V

V

F

F

E

E

I

I

G

N

R

R

N

N

F

F

R
|
R

N

N

E
|
E

G

G

I

I

D

S

T

V

T

R

H
|
H

N
|
N

P

P

E

E

F
|
F

T

T

M
|
M

V

M

E

E

F

L

Y

Y

A

M

A

A

Y

Y

L

A

D

D

Y

Y

N

H

D

D

L

L

M

I

A

E

L

L

T

T

E

E

E

S

L

L

F

F

R

R

K

T

I

L

L

A

L

Q

D

E

T

V

V

L

G

G

T

T

L

T

K

K

I

V

K

T

W

Y

E

G

D

E

Q

H

E

V

I

F

D

D

F

F

E

G

K

K

P

P

F

F

R

E

R

K

L

L

P

T

F

M

F

R

E

E

A

A

L

I

K

K

Q

K

-

Y

K

R

T

P

G

E

K

T

D

D

K

M

E

A

F

D

F

L

L

D

D

N

Y

F

E

D

K

A

A

A

K

K

N

A

F

L

A

A

K

E

E

S

V

I

G

G

I

I

P

T

K

V

A

E

D

K

T

S

L

W

T

G

H

L

M

G

K

R

I

I

L

V

D

T

K

E

L

I

F

F

E
x
D

H

E

F

V

V

A

E

E

E

A

D

H

L

L

V

I

Q

Q

P

P

T

T

F

F

V

I

I

T

D

E

F

Y

P

P

K

A

I

E

L

V

S

S

P

P

L

L

A

A

K

R

T

R

H

N

R

D

N

V

D

N

P

P

D

E

L

I

V

T

E

D

R

R

F

F

E
|
E

L

F

I

F

I

I

N

G

K

G

Q

R

E
|
E

L
x
I

A

G

N
|
N

A

G

Y

F

T

S

E

E

L

L

N

N

D

D

P

A

F

E

D

D

Q

Q

R

A

E

E

R

R

F

F

I

Q

Q

E

Q

Q

I

V

R

N

E

A

K

K

E

A

M

A

G

G

D

D

E

D

E

E

A

A

M

M

D

F

V

Y

D

D

E

E

T

D

F

Y

L

V

T

T

A

A

L

L

E

E

Y

Y

G

G

L

L

P

P

T

T

A

A

G

G

E

L

G

G

I

I

G
|
G

I

I

D

D

R
|
R

L

M

V

I

M

M

M

L

L

F

T

T

D

N

S

S

V

H

S

T

I

I

R

R

E

D

V

V

I

I

L

L

F

F

P

P

T

A

L

M

R

R

P

P

binding bis(adenosine)-5'-tetraphosphate: R244 (= R335), E246 (= E337), H252 (= H343), N253 (= N344), F256 (= F347), M258 (= M349), D358 (≠ E448), E403 (= E493), I404 (≠ L494), G459 (= G549), R462 (= R552)
binding calcium ion: D358 (≠ E448), E396 (= E486), E396 (= E486), E403 (= E493), N406 (= N496)

1e1oA Lysyl-tRNA synthetase (lysu) hexagonal form, complexed with lysine (see paper)
50% identity, 76% coverage: 139:574/577 of query aligns to 56:484/484 of 1e1oA

query
sites
1e1oA

E

E

V

V

A

S

V

V

A

A

G

G

R

R

L

M

V

M

A

T

L

R

R

R

D

I

Q

M

G

G

K

K

A

A

A

S

F

F

G

V

H

T

L

L

Q

Q

D

D

A

V

D

G

G

G

K

R

L

I

Q

Q

I

L

Y

Y

F

V

N

A

A

R

D

D

I

S

L

L

G

P

Q

E

E

G

N

V

Y

Y

Q

N

K

D

A

Q

M

F

D

K

L

K

I

W

D

D

I

L

G

G

D

D

I

I

V

I

G

G

V

A

K

R

G

G

K

T

L

L

F

F

R

K

T

T

M

Q

T

T

G

G

E

E

L

L

T

S

V

I

E

H

V

C

H

T

S

E

Y

L

Q

R

I

L

L

L

S

T

K

K

S

A

L

L

R

R

P

P

L

L

P

P

E

-

K

-

W

-

H

-

G

-

L

-

R

-

D

D

V

Q

E

E

E

V

R

R

Y

Y

R

R

Y

Q

R

R

F

Y

L

L

D

D

L

L

I

I

A

A

N

N

Q

D

R

K

S

S

R

R

E

Q

I

T

F

F

K

V

L

V

R

R

S

S

K

K

A

I

I

L

K

A

S

A

L

I

R

R

E

Q

F

F

L

M

E

V

S

A

K

R

G

G

F

F

I

M

E

E

V

V

E

E

T

T

P

P

I

M

L

M

Q

Q

P

V

V

I

A

P

S

G

G
|
G

A

A

L

S

A

A

K

R

P

P

F

F

I

I

T

T

Y

H

H

H

N

N

A

A

L

L

D

D

M

L

N

D

L

M

Y

Y

L

L

R

R

I

I

A

A

P

P

E
|
E

L

L

Y

Y

L

L

K

K

M

R

L

L

V

V

G

G

F

F

N

E

R

R

V

V

F

F

E

E

I

I

G

N

R

R

N

N

F

F

R
|
R

N

N

E
|
E

G

G

I

I

D

-

T

S

T

V

H
|
H

N

N

P

P

E

E

F

F

T

T

M

M

V

M

E
|
E

F

L

Y
|
Y

A

M

A

A

Y

Y

L

A

D

D

Y

Y

N

H

D

D

L

L

M

I

A

E

L

L

T

T

E

E

E

S

L

L

F

F

R

R

K

T

I

L

L

A

L

Q

D

E

T

V

V

L

G

G

T

T

L

T

K

K

I

V

K

T

W

Y

E

G

D

E

Q

H

E

V

I

F

D

D

F

F

E

G

K

K

P

P

F

F

R

E

R

K

L

L

P

T

F

M

F

R

E

E

A

A

L

I

K

K

Q

K

-

Y

K

R

T

P

G

E

K

T

D

D

K

M

E

A

F

D

F

L

L

D

D

N

Y

F

E

D

K

A

A

A

K

K

N

A

F

L

A

A

K

E

E

S

V

I

G

G

I

I

P

T

K

V

A

E

D

K

T

S

L

W

T

G

H

L

M

G

K

R

I

I

L

V

D

T

K

E

L

I

F

F

E

D

H

E

F

V

V

A

E

E

E

A

D

H

L

L

V

I

Q

Q

P

P

T

T

F

F

V

I

I

T

D

E

F

Y

P

P

K

A

I

E

L

V

S

S

P

P

L

L

A

A

K

R

T

R

H

N

R

D

N

V

D

N

P

P

D

E

L

I

V

T

E

D

R

R

F

F

E

E

L

F

I

F

I

I

N

G

K

G

Q

R

E
|
E

L

I

A

G

N
|
N

A

G

Y
x
F

T

S

E
|
E

L

L

N

N

D

D

P

A

F

E

D

D

Q

Q

R

A

E

E

R

R

F

F

I

Q

Q

E

Q

Q

I

V

R

N

E

A

K

K

E

A

M

A

G

G

D

D

E

D

E

E

A

A

M

M

D

F

V

Y

D

D

E

E

T

D

F

Y

L

V

T

T

A

A

L

L

E

E

Y

Y

G

G

L

L

P

P

T

T

A

A

G
|
G

E

L

G
|
G

I

I

G

G

I

I

D

D

R
|
R

L

M

V

I

M

M

M

L

L

F

T

T

D

N

S

S

V

H

S

T

I

I

R

R

E

D

V

V