SitesBLAST

129 C→S: Holoprotein exhibits no photochromic activity.
130 H→F: Chromophore ligating activity (in vitro) is 30-40% lower than wild-type.; H→Q: Chromophore ligating activity (in vitro) is about 10% more efficient than wild-type.

4rnhA Pamora tandem diguanylate cyclase - phosphodiesterase, c-di-gmp complex (see paper)
40% identity, 32% coverage: 494:736/762 of query aligns to 174:417/423 of 4rnhA

query
sites
4rnhA

S

E

L

L

A

E

N

S

D

D

L

L

A

R

A

A

L

L

A

E

R

L

N

-

G

G

E

E

V

F

F

V

L

L

E

H

Y

Y

Q
|
Q

P

P

Q

Q

I

F

R

T

M

G

D

D

G

G

R

R

A

R

-

L

H

T

G

G

A

A

E
|
E

A

A

L
|
L

R
|
R

W

W

H

Q

H

H

P

P

A

R

Y

R

G

G

R

L

I

V

A

P

P
|
P

P

S

I

E

T

F

V
x
I

A

P

L

V

A

L

E

E

D

E

T

I

G

G

I

L

I

V

D

A

R

Q

L

V

G

G

M

D

F

W

V
x
L

L

L

H

A

R

E

A

A

C

C

A

K

R

Q

R

L

V

R

A

S

W

W

T

H

G

K

E

A

V

K

P

V

D

R

G

V

F

P

V

K

M

V

S

S

V

V

N
|
N

V
x
L

A

S

P

A

R

R

Q

Q

L

F

Q

A

N

D

P

G

R

Q

F

L

D

G

R

E

D

R

V

I

L

A

A

A

V

I

L

L

A

Y

R

E

T

T

G

G

L

I

A

P

P

P

H

A

L

C

L

L

E

E

L

L

E
|
E

L

L

T

T

E

E

S

S

T

I

V

L

L

M

L

S

P

D

D

V

A

A

R

E

T

A

V

M

A

Q

A

I

L

L

R

S

R

G

L

L

R

K

A

R

A

L

G

G

V

L

R

A

V

I

A

A

I

V

D
|
D

D

D

F

F

G

G

M

T

G

G

H

Y

A

S

S

S

L

L

R

N

Y

Y

L

L

R

K

D

Q

F

F

P

P

V

I

D

D

T

V

V

L

K

K

I

I

D

D

R
|
R

S

S

L

F

T

V

E

D

A

G

-

L

S

P

H

H

G

G

D

E

V

Q

N

D

E

A

H

Q

I

I

V

A

R

R

S

A

I

I

V

I

E

A

L

M

A

A

R

H

S

S

L

L

D

N

I

L

T

M

T

V

L

I

V

A

E
|
E

G
|
G

V
|
V

E
|
E

R

S

R

Q

E

A

Q

Q

F

L

E

D

R

F

F

L

V

R

E

E

L

H

G

G

C

C

L

D

V

E

F

V

Q

Q

G
|
G

Y
|
Y

L

L

F

F

S

G

R

R

P

P

V

M

R

P

A

A

V

E

Q

Q

binding 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one): Q193 (= Q514), E207 (= E527), L209 (= L529), L210 (= L530), R211 (= R531), P222 (= P542), I226 (≠ V546), L242 (≠ V562), N266 (= N586), L267 (≠ V587), D328 (= D648), R352 (= R672), E385 (= E704), G386 (= G705), V387 (= V706), E388 (= E707), G406 (= G725), Y407 (= Y726)
binding magnesium ion: E207 (= E527), N266 (= N586), E298 (= E618), D328 (= D648)

8arvA Structure of the eal domain of bifa from pseudomonas aeruginosa
42% identity, 32% coverage: 494:734/762 of query aligns to 1:242/255 of 8arvA

query
sites
8arvA

S

E

L

L

A

E

N

K

D

D

L

L

A

R

A

D

A

A

L

L

A

Q

R

R

N

H

G

-

E

E

V

L

F

H

L

L

E

V

Y

Y

Q

Q

P

P

Q

Q

I

V

R

D

M

Y

-

R

D

D

G

H

R

R

A

V

H

V

G

G

A

V

E
|
E

A

A

L

L

R

R

W

W

H

Q

H

H

P

P

A

L

Y

H

G

G

R

F

I

V

A

P

P

P

P

D

I

L

T

F

V

I

A

P

L

L

A

A

E

E

D

Q

T

N

G

G

I

S

I

I

D

F

R

S

L

I

G

G

M

E

F

W

V

V

L

L

H

D

R

Q

A

A

C

C

A

R

R

Q

R

L

V

R

A

E

W

W

T

H

G

D

E

Q

V

G

P

F

D

D

G

D

F

L

V

R

M

M

S

A

V

V

N
|
N

V

L

A

S

P

T

R

V

Q

Q

L

L

Q

H

N

H

P

N

R

A

F

L

D

P

R

R

D

V

V

V

L

S

A

N

V

L

L

L

A

Q

R

V

T

Y

G

R

L

L

A

P

P

A

H

R

L

S

L

L

E

E

L

L

E
|
E

L

V

T

T

E

E

S

-

T

T

V

G

L

L

L

M

P

E

D

D

A

I

R

S

T

T

V

A

A

A

A

Q

-

H

L

L

R

L

R

S

L

L

R

R

A

R

A

A

G

G

V

A

R

L

V

I

A

A

I

I

D
|
D

D

D

F

F

G

G

M

T

G

G

H

Y

A

S

S

S

L

L

R

S

Y

Y

L

L

R

K

D

S

F

L

P

P

V

L

D

D

T

K

V

I

K

K

I

I

D

D

R

K

S

S

L

F

T

V

E

Q

A

D

S

L

H

L

G

Q

D

D

V

E

N

D

E

D

-

A

H

T

I

I

V

V

R

R

S

A

I

I

V

I

E

Q

L

L

A

G

R

K

S

S

L

L

D

G

I

M

T

Q

T

V

L

I

V

A

E

E

G

G

V

V

E

E

R

T

R

A

E

E

Q

Q

F

E

E

A

R

Y

F

I

V

I

E

A

L

E

G

G

C

C

L

N

V

E

F

G

Q

Q

G

G

Y

Y

L

L

F

Y

S

S

R

K

P

P

V

L

R

P

A

A

binding magnesium ion: E34 (= E527), N93 (= N586), E125 (= E618), D155 (= D648)

5m3cB Structure of the hybrid domain (ggdef-eal) of pa0575 from pseudomonas aeruginosa pao1 at 2.8 ang. With gtp and ca2+ bound to the active site of the ggdef domain (see paper)
40% identity, 32% coverage: 494:734/762 of query aligns to 174:415/426 of 5m3cB

query
sites
5m3cB

S

A

L

L

A

E

N

T

D

E

L

L

A

R

A

A

L

L

A

E

R

R

N

D

G

-

E

E

V

L

F

Q

L

L

E

Y

Y

Y

Q

Q

P

P

Q

K

I

L

R

S

M

L

D

E

-

S

G

G

R

L

A

L

H

V

G

G

A

A

E
|
E

A

A

L

L

L

V

R

R

W

W

H

Y

H

H

P

P

A

L

Y

F

G

G

R

E

I

I

A

S

P

P

P

E

I

R

T

F

V

I

A

P

L

L

A

A

E

E

D

D

T

C

G

G

I

L

I

I

D

L

R

P

L

L

G

G

M

D

F

W

V

V

L

L

H

E

R

H

A

A

C

C

A

Q

R

Q

R

M

V

G

A

E

W

W

T

Q

G

K

-

L

E

H

V

A

P

P

D

F

G

G

F

-

V

P

M

L

S

S

V

V

N
|
N

V

L

A

A

P

G

R

A

Q

Q

L

L

Q

G

N

Q

P

P

R

Q

F

L

D

I

R

E

D

R

V

L

L

E

A

Q

V

L

L

L

A

E

R

Q

T

S

G

G

L

L

A

E

P

P

H

S

L

R

L

L

E

Q

L

L

E
|
E

L

I

T

T

E

E

S

S

T

F

V

I

L

M

L

N

P

Q

D

T

A

E

R

E

T

A

V

L

A

A

A

V

L

L

R

H

R

G

L

L

R

K

A

R

A

L

G

G

V

V

R

Q

V

L

A

A

I

I

D
|
D

D

D

F

F

G

G

M

T

G

G

H

Y

A

S

S

S

L

L

R

S

Y

Y

L

L

R

K

D

R

F

L

P

P

V

L

D

D

T

I

V

L

K

K

I

I

D

D

R

K

S

S

L

F

T

I

E

R

A

G

S

L

H

P

G

D

D

D

V

P

N

H

E

D

-

A

H

A

I

I

V

T

R

R

S

A

I

I

V

I

E

A

L

L

A

G

R

R

S

S

L

M

D

Q

I

L

T

T

T

V

L

I

V

A

E

E

G

G

V

V

E

E

R

T

R

E

E

G

Q

Q

F

Q

E

S

R

F

F

L

V

T

E

H

L

E

G

G

C

C

L

E

V

Q

F

I

Q

Q

G

G

Y

F

L

V

F

L

S

S

R

P

P

P

V

L

R

P

A

A

binding calcium ion: E207 (= E527), N266 (= N586), E298 (= E618), D328 (= D648)

Sites not aligning to the query:

binding calcium ion: 38, 39, 81
binding guanosine-5'-triphosphate: 38, 39, 40, 41, 42, 43, 46, 51, 54, 55, 58, 77, 80, 81, 151, 155

3n3tB Crystal structure of putative diguanylate cyclase/phosphodiesterase complex with cyclic di-gmp (see paper)
40% identity, 31% coverage: 494:731/762 of query aligns to 5:245/261 of 3n3tB

query
sites
3n3tB

S

T

L

L

A

D

N

T

D

R

L

L

A

R

A

Q

A

A

L

L

A

E

R

R

N

N

G

-

E

E

V

L

F

V

L

L

E

H

Y

Y

Q
|
Q

P

P

Q

I

I

V

R

E

M

L

-

A

D

S

G

G

R

R

A

I

H

V

G

G

A

G

E
|
E

A

A

L
|
L

L
x
V

R
|
R

W

W

H

E

H

D

P

P

A

E

Y

R

G

G

R

L

I

V

A

M

P
|
P

P

S

I

A

T

F

V
x
I

A

P

L

A

A

A

E

E

D

D

T

T

G

G

I

L

I
|
I

D

V

R

A

L

L

G

S

M

D

F

W

V
|
V

L

L

H

E

R

A

A

C

C

C

A

T

R

Q

R

L

V

R

A

A

W

W

T

Q

-

Q

G

G

E

R

V

A

P

A

D

D

G

D

F

L

V

T

M

L

S

S

V

V

N
|
N

V

I

A

S

P

T

R

R

Q

Q

L

F

Q

E

N

G

P

E

R

H

F

L

D

T

R

R

D

A

V

V

L

D

A

R

V

A

L

L

A

A

R

R

T

S

G

G

L

L

A

R

P

P

H

D

L

C

L

L

E

E

L

L

E
|
E

L

I

T

T

E

E

S

N

T

V

V

M

L

L

L

V

P

M

D

T

A

D

R

E

T

V

V

R

A

T

A

C

L

L

R

D

R

A

L

L

R

R

A

A

A

R

G

G

V

V

R

R

V

L

A

A

I

L

D
|
D

F

F

G

G

M

T

G

G

H

Y

A

S

S

S

L

L

R

S

Y

Y

L

L

R

S

D

Q

F

L

P

P

V

F

D

H

T

G

V

L

K

K

I

I

D

D

R
x
Q

S

S

L

F

T

V

E

R

A

K

S

I

H

P

G

A

D

H

V

P

N

S

E

E

-

T

H

Q

I

I

V

V

R

T

S

T

I

I

V

L

E

A

L

L

A

A

R

R

S

G

L

L

D

G

I

M

T

E

T

V

L

V

V

A

E
|
E

G
|
G

V
x
I

E
|
E

R

T

R

A

E

Q

Q

Q

F

Y

E

A

R

F

F

L

V

R

E

D

L

R

G

G

C

C

L

E

V

F

F

G

Q

Q

G
|
G

Y
x
N

L

L

F

M

S

S

R

T

P
|
P

binding 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one): Q24 (= Q514), E38 (= E527), L40 (= L529), V41 (≠ L530), R42 (= R531), P53 (= P542), I57 (≠ V546), I66 (= I555), V73 (= V562), N99 (= N586), D161 (= D648), D162 (= D649), Q185 (≠ R672), E218 (= E704), G219 (= G705), I220 (≠ V706), E221 (= E707), G239 (= G725), N240 (≠ Y726), P245 (= P731)
binding magnesium ion: E38 (= E527), N99 (= N586), E131 (= E618), D161 (= D648), D161 (= D648), D162 (= D649), E218 (= E704)

5m1tA Pamucr phosphodiesterase, c-di-gmp complex (see paper)
39% identity, 32% coverage: 494:738/762 of query aligns to 2:247/247 of 5m1tA

query
sites
5m1tA

S

Q

L

L

A

L

N

H

D

D

L

L

A

R

A

Q

A

A

L

L

A

E

R

R

N

R

G

-

E

Q

V

L

F

V

L

L

E

H

Y

Y

Q
|
Q

P

P

Q

K

I

V

R

L

M

A

-

P

D

N

G

G

R

P

A

M

H

I

G

G

A

V

E
|
E

A

A

L
|
L

R
|
R

W

W

H

E

H

H

P

P

A

Q

Y

H

G

G

R

L

I

I

A

T

P
|
P

P

G

I

Q

T

F

V
x
L

A

P

L

L

A

A

E

E

D

K

T

T

G

G

I

L

I

I

D

V

R

Q

L

I

G

G

M

E

F

W

V
|
V

L

L

H

D

R

E

A

A

C

C

A

R

R

Q

R

M

V

R

A

L

W

W

T

L

G

D

E

G

V

G

P

H

D

A

G

D

F

W

V

N

M

I

S

A

V

V

N
|
N

V
x
L

A
x
S

P

A

R

L

Q
|
Q

L

F

Q

A

N

H

P

A

R

G

F

L

D

V

R

D

D

S

V

V

L

R

A

N

V

A

L

L

A

L

R

R

T

H

G

S

L

L

A

E

P

P

H

S

L

H

L

L

E

I

L

L

E
|
E

L

V

T

T

E

E

S

S

T

T

V

A

L

M

L

R

P

D

D

A

A

D

R

A

T

S

V

L

A

V

A

I

L

L

R

E

R

Q

L

L

R

S

A

A

A

M

G

G

V

V

R

G

V

I

A

S

I

I

D
|
D

F

F

G

G

M

T

G

G

H

Y

A

S

S

S

L

L

R

L

Y

Y

L

L

R

K

D

R

F

L

P

P

V

A

D

S

T

E

V

L

K

K

I

I

D

D

R
|
R

S

G

-

F

L

I

T

N

E

E

A

L

S

A

H

H

G

D

D

S

V

D

N

D

E

A

H

A

I

I

V

V

R

S

S

A

I

I

V

V

E

A

L

L

A

G

R

R

S

T

L

L

D

N

I

L

T

K

T

I

L

V

V

A

E
|
E

G
|
G

V
|
V

E
|
E

R

T

R

E

E

A

Q

Q

F

Q

E

E

R

F

F

L

V

T

E

R

L

L

G

G

C

C

L

N

V

S

F

L

Q

Q

G
|
G

Y
x
F

L

L

F

L

S

G

R

R

P

P

V

M

R

P

A

A

V

E

Q

Q

C

L

L

L

binding 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one): Q21 (= Q514), E35 (= E527), L37 (= L529), L38 (= L530), R39 (= R531), P50 (= P542), L54 (≠ V546), V70 (= V562), N94 (= N586), L95 (≠ V587), S96 (≠ A588), Q99 (= Q591), D156 (= D648), D157 (= D649), R180 (= R672), E213 (= E704), G214 (= G705), V215 (= V706), E216 (= E707), G234 (= G725), F235 (≠ Y726)
binding magnesium ion: E35 (= E527), N94 (= N586), E126 (= E618), D156 (= D648), D156 (= D648), D157 (= D649), E213 (= E704)

3qnqD Crystal structure of the transporter chbc, the iic component from the n,n'-diacetylchitobiose-specific phosphotransferase system (see paper)
27% identity, 54% coverage: 46:454/762 of query aligns to 10:424/436 of 3qnqD

query
sites
3qnqD

V

V

T

A

E

G

R

K

V

V

A

A

D

E

Q

Q

P

R

V

H

V

L

I

L

A

A

V

I

Q

R

R
x
D

A

G

L

L

A
x
V

L
|
L

V

T

L

M

P
|
P

L
x
F

V

L

T

I

V

I

G

G

A

S

F

I

A

F

L

L

M

I

V

I

R

S

H

T

T

L

P

P

F

I

P

P

L

G

L

Y

R

S

A

E

A

F

L

M

D

A

A

S

L

L

F

F

G

G

P

K

A

N

W

W

I

N

T

V

M

A

G

L

D

G

A

Y

L

P

V

V

S

S

G

A

T

T

F

F

G

N

I

I

A

M

S

A

L

L

A

I

V

A

L

V

C

F

A

G

F

I

S

A

G

Y

T
x
R

M

L

A

G

M
x
E

V

Y

Y

Y

N

K

Q

-

R

-

G

-

Q

-

F

-

V

V

S

D

P

A

V

L

M
x
A

S

S

A

G

I

A

V

L

V

S

L

L

A

V

C

T

F

F

F

L

V

L

V

A

T

T

-

P

-

F

N

Q

P

V

A

A

S

Y

D

I

M

M

P

P

-

G

W

T

R

K

D

E

M

S

F

I

S

L

M

V

D

D

-

G

-

V

-

I

-

P

-

A

-

L

-

M

-

G

-

S

R

Q

G

G

L

L

L

F

L

V

A

A

F

M

M

I

V

I

S

A

V

I

G

I

G

S

A

T

W

E

L

I

F

Y

L

-

R

R

L

F

S

L

D

V

V

Q

K

K

R

K

L

M

Q

I

L

I

P

K

L

M

E

P

A

E

V

T

G

V

H

P

D
x
P

P
x
A

V

V

V

T

R
|
R

D

S

I

F

L

A

T
x
A

V

L

M

I

P

P

A

-

G

G

M

F

L

I

T

V

I

V

V

T

A

V

F

V

G

W

L

I

R

R

V

L

G

I

L

F

V

E

D

H

S

T

G

T

I

F

P

G

D

S

L

I

H

H

G

N

A

V

L

V

R

G

S

K

G

L

M

L

T

Q

R

E

P

P

F

L

I

S

E

I

G

L

G

G

N

A

T

S

L

L

G

W

L

G

G

A

L

V

L

I

Y

A

T

V

G

I

L

L

S

V

Q

H

V

V

L

L

W

W

F

A

F

C

G

G

A

I

H

H

G

G

P

A

N

T

L

I

L

V

F

G

P

G

I

V

E

M

D

S

A

P

I

I

F

W

A

L

P

S

A

L

G

M

A

D

A

Q

N

N

A

R

A

I

A

A

L

F

A

Q

T

A

G

G

Q

Q

V

D

P

V

P

P

F

N

V

T

L

I

T

T

K

A

T

Q

F

F

D

D

V

L

F

W

T

I

R

Y

M

M

G

G

S

S

G

G

S

A

T

T

L

L

C

A

L

L

I

V

A

V

A

G

I

M

L

L

Y

L

A

F

S

A

R

R

D

S

S

Q

G

Q

T

L

R

K

R

S

L

L

A

G

L

R

V

L

A

S

L

I

L

A

P

P

A

G

L

I

C

F

N

N

V

I

N

N

E

E

P

M

L

V

L

T

F

F

G

G

L

M

P

P

L

I

V

V

M

M

N

N

P

P

V

L

Y

L

L

L

I

I

P

P

F

F

L

I

L

V

V

V

P

P

L

V

A

V

Q

L

T

T

A

I

A

V

A

S

H

Y

A

F

A

A

T

M

L

E

L

W

H

G

L

L

V

V

P

A

Y

R

-

P

T

S

L

G

P

A

D

A

V

V

V

T

W

W

T

T

P

P

P

I

L

L

L

F

N

S

G

G

Y

Y

A

L

A

G

T

S

-

G

G

G

S

K

V

I

A

S

G

G

S

V

L

I

M

L

Q

Q

A

L

L

V

N

N

L

F

G

A

L

L

G

A

V

F

A

V

L

I

Y

Y

L

L

P

P

F

F

V

L

R

K

A

I

S

W

D

D

A

K

L

Q

R

K

binding nonyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside: D25 (≠ R61), V28 (≠ A64), L29 (= L65), P32 (= P68), F33 (≠ L69), R89 (≠ T125), E92 (≠ M128), A100 (≠ M143), P176 (≠ D207), A177 (≠ P208), R180 (= R211), A184 (≠ T215)

P76129 Oxygen sensor protein DosP; Direct oxygen-sensing phosphodiesterase; Direct oxygen sensor protein; Ec DOS; Heme-regulated cyclic di-GMP phosphodiesterase; EC 3.1.4.52 from Escherichia coli (strain K12) (see 6 papers)
34% identity, 32% coverage: 499:744/762 of query aligns to 544:790/799 of P76129

query
sites
P76129

L

L

A

G

A

A

L

L

A

K

R

E

-

A

-

I

-

S

N

N

G

N

E

Q

V

L

F

K

L

L

E

V

Y

Y

Q

Q

P

P

Q

Q

I

I

R

F

M

A

D

E

-

T

G

G

R

E

A

L

H

Y

G

G

A

I

E

E

A

A

L

L

L

A

R

R

W

W

H
|
H

H

D

P

P

A

L

Y
x
H

G

G

R

H

I

V

A

P

P

P

P

S

I

R

T

F

V

I

A

P

L

L

A

A

E

E

D

E

T

I

G

G

I

E

I

I

D

E

R

N

L

I

G

G

M

R

F

W

V

V

L

I

H

A

R

E

A

A

C

C

A

R

R

Q

R

L

V

A

A

E

W

W

T

R

G

S

E

Q

V

N

P

I

D

H

G

I

F

P

V

A

M

L

S

S

V

V

N

N

V

L

A

S

P

A

R

L

Q

H

L

F

Q

R

N

S

P

N

R

Q

F

L

D

P

R

N

D

Q

V

V

L

S

A

D

V

A

L

M

A

H

R

A

T

W

G

G

L

I

A

D

P

G

H

H

L

Q

L

L

E

T

L

V

E

E

L

I

T

T

E

E

S

S

T

M

V

M

L

M

L

E

P

H

D

D

A

T

R

E

T

I

V

F

A

K

A

R

L

I

R

Q

R

I

L

L

R

R

A

D

A

M

G

G

V

V

R

G

V

L

A

S

I

V

D

D

F

F

G

G

M

T

G

G

H

F

A

S

S

G

L

L

R

S

Y

R

L

L

R

V

D

S

F

L

P

P

V

V

D

T

T

E

V

I

K

K

I

I

D

D

R

K

S

S

L

F

T

V

E

D

A

R

S

C

H

-

G

-

D

-

V

L

N

T

E

E

H

K

-

R

-

I

-

L

-

A

I

L

V

L

R

E

S

A

I

I

V

T

E

S

L

I

A

G

R

Q

S

S

L

L

D

N

I

L

T

T

T

V

L

V

V

A

E

E

G

G

V

V

E

E

R

T

R

K

E

E

Q

Q

F

F

E

E

R

M

F

L

V

R

E

K

L

I

G

H

C

C

L

R

V

V

F

I

Q

Q

G

G

Y

Y

L

F

F

F

S

S

R

R

P

P

V

L

R

P

A

A

V

-

Q

-

C

-

L

-

E

E

V

E

V

I

S

P

G

G

W

W

H582 (= H533) mutation to A: Loss of cAMP PDE activity.
H586 (≠ Y537) mutation to A: Loss of cAMP PDE activity.

Sites not aligning to the query:

69 mutation H->A,G: Loss of heme binding.
75 mutation H->A,G: No loss of heme binding.
87 mutation M->A,I: Ferrous heme iron changes from an exclusively hexacoordinate low-spin form to an exclusively pentacoordinate high-spin form. Ferric heme iron remains hexacoordinate but becomes a mixture of high and low spin. Increases c-di-GMP PDE activity 7-fold in absence of O(2), CO or NO, no additional increase upon addition of gases (M-A only).; M→H: No change in heme coordination; increases c-di-GMP PDE activity 2-fold in absence of O(2), CO or NO, and 2-fold more upon addition of gases.
89 mutation R->A,E,I: The Fe(2+)-O(2) form loses c-di-GMP PDE activity, due to reduced O(2) affinity and/or increased auto-oxidation. NO and CO forms are less affected.
91 L→F: Alters O(2) binding, increases auto-oxidation.; L→T: Increases auto-oxidation.
107 L→F: Significantly reduces heme-binding affinity; increases auto-oxidation.; L→T: Increases auto-oxidation.

3sy8B Crystal structure of the response regulator rocr (see paper)
35% identity, 31% coverage: 506:743/762 of query aligns to 153:391/392 of 3sy8B

query
sites
3sy8B

N

N

G

G

E

E

V

F

F

E

L

A

E

Y

Y

Y

Q

Q

P

P

Q

K

I

V

R

A

M

L

D

D

G

G

R

G

A

G

H

L

-

I

G

G

A

A

E
|
E

A

V

L

L

L

A

R

R

W

W

H

N

H

H

P

P

A

H

Y

L

G

G

R

V

I

L

A

P

P

P

P

S

I

H

T

F

V

L

A

Y

L

V

A

M

E

E

D

T

T

Y

G

N

I

L

I

V

D

D

R

K

L

L

-

F

-

W

G

Q

M

L

F

F

V

S

L

Q

H

G

R

L

A

A

C

T

A

R

R

R

R

K

V

L

A

A

W

Q

T

L

G

G

E

Q

V

P

P

I

D

N

G

-

F

-

V

-

M

L

S

A

V

F

N
|
N

V

V

A

H

P

P

R

S

Q

Q

L

L

Q

G

N

S

P

R

R

A

F

L

D

A

R

E

D

N

V

I

L

S

A

A

V

L

L

L

A

T

R

E

T

F

G

H

L

L

A

P

P

P

H

S

L

S

L

V

E

M

L

F

E
|
E

L

I

T

T

E

E

S

T

T

G

V

L

L

I

L

S

P

A

D

P

A

A

R

S

T

S

V

L

A

E

A

N

L

L

R

V

R

R

L

L

R

W

A

I

A

M

G

G

V

C

R

G

V

L

A

A

I

M

D
|
D

D

D

F

F

G

G

M

A

G

G

H

Y

A

S

S

S

L

L

R

D

Y

R

L

L

R

C

D

E

F

F

P

P

V

F

D

S

T

Q

V

I

K

K

I

L

D

D

R

R

S

T

L

F

T

V

E

Q

A

K

S

M

H

K

G

T

D

Q

V

P

N

R

E

S

-

C

H

A

I

V

V

I

R

S

S

S

I

V

V

V

E

A

L

L

A

A

R

Q

S

A

L

L

D

G

I

I

T

S

T

L

L

V

V

V

E

E

G

G

V

V

E

E

R

S

R

D

E

E

Q

Q

F

R

E

V

R

R

F

L

V

I

E

E

L

L

G

G

C

C

L

S

V

I

F

A

Q

Q

G

G

Y

Y

L

L

F

F

S

A

R

R

P

P

V

M

R

P

A

E

V

Q

Q

H

C

F

L

L

E

D

V

Y

V

C

S

S

G

G

binding magnesium ion: E175 (= E527), N233 (= N586), E265 (= E618), D295 (= D648)

3sy8D Crystal structure of the response regulator rocr (see paper)
35% identity, 32% coverage: 506:747/762 of query aligns to 126:368/371 of 3sy8D

query
sites
3sy8D

N

N

G

G

E

E

V

F

F

E

L

A

E

Y

Y

Y

Q

Q

P

P

Q

K

I

V

R

A

M

L

D

D

G

G

R

G

A

G

H

L

-

I

G

G

A

A

E
|
E

A

V

L

L

L

A

R

R

W

W

H

N

H

H

P

P

A

H

Y

L

G

G

R

V

I

L

A

P

P

P

P

S

I

H

T

F

V

L

A

Y

L

V

A

M

E

E

D

T

T

Y

G

N

I

L

I

V

D

D

R

K

L

L

-

F

-

W

G

Q

M

L

F

F

V

S

L

Q

H

G

R

L

A

A

C

T

A

R

R

R

R

K

V

L

A

A

W

Q

T

L

G

G

E

Q

V

P

P

I

D

N

G

-

F

-

V

-

M

L

S

A

V

F

N
|
N

V

V

A

H

P

P

R

S

Q

Q

L

L

Q

G

N

S

P

R

R

A

F

L

D

A

R

E

D

N

V

I

L

S

A

A

V

L

L

L

A

T

R

E

T

F

G

H

L

L

A

P

P

P

H

S

L

S

L

V

E

M

L

F

E
|
E

L

I

T

T

E

E

S

T

T

G

V

L

L

I

L

S

P

A

D

P

A

A

R

S

T

S

V

L

A

E

A

N

L

L

R

V

R

R

L

L

R

W

A

I

A

M

G

G

V

C

R

G

V

L

A

A

I

M

D
|
D

D

D

F

F

G

G

M

A

G

G

H

Y

A

S

S

S

L

L

R

D

Y

R

L

L

R

C

D

E

F

F

P

P

V

F

D

S

T

Q

V

I

K

K

I

L

D

D

R

R

S

T

L

F

T

V

E

Q

A

K

S

M

H

K

G

T

D

Q

V

P

N

R

E

S

-

C

H

A

I

V

V

I

R

S

S

S

I

V

V

V

E

A

L

L

A

A

R

Q

S

A

L

L

D

G

I

I

T

S

T

L

L

V

V

V

E

E

G

G

V

V

E

E

R

S

R

D

E

E

Q

Q

F

R

E

V

R

R

F

L

V

I

E

E

L

L

G

G

C

C

L

S

V

I

F

A

Q

Q

G

G

Y

Y

L

L

F

F

S

A

R

R

P

P

V

M

R

P

A

E

V

Q

Q

H

C

F

L

L

E

D

V

Y

V

C

S

S

G

G

W

S

G

L

G

E

H

H

binding magnesium ion: E148 (= E527), N206 (= N586), E238 (= E618), D268 (= D648)

6hq7A Structure of eal enzyme bd1971 - cgmp bound form (see paper)
32% identity, 33% coverage: 480:732/762 of query aligns to 102:366/377 of 6hq7A

query
sites
6hq7A

K

K

C
x
R

I
x
L

D

R

R
|
R

P

P

G

G

E

-

Q

G

G

S

R

R

I

I

A

S

S

S

S

A

L

L

-

D

-

Q

-

I

-

K

-

L

A

E

N

N

D

Q

L

I

A

F

A

Q

A

A

L

F

A

-

R

Q

N

N

G

K

E

E

V

F

F

E

L

L

E

F

Y

Y

Q

Q

P

P

Q

I

I

V

R

N

M

L

D

K

G

N

R

K

A

T

-

I

H

T

G

G

A

C

E
|
E

A

A

L

L

R

R

W

W

H

N

H

S

P

P

A

Q

Y

H

G

G

R

L

I

V

A

S

P

P

P

N

I

L

T

F

V

I

A

D

L

I

A

I

E

E

D

N

T

S

G

S

I

M

I

V

D

I

R

P

L

I

G

G

M

H

F

W

V

I

L

I

H

N

R

Q

A

A

C

L

A

K

R

D

-

L

-

R

-

T

-

I

-

Q

-

D

-

Q

-

L

R

R

V

L

A

N

W

K

T

K

G

E

E

R

V

M

P

A

D

D

G

D

F

F

V

M

M

M

S

S

V

I

N

N

V

I

A

S

P

G

R

R

Q

Q

L

F

Q

T

N

H

P

S

R

D

F

F

D

V

R

N

D

N

V

L

L

E

A

D

V

L

L

R

A

E

R

K

T

H

G

D

L

L

A

H

P

T

H

Q

L

N

L

I

E

K

L

L

E
|
E

L

M

T

T

E

E

S

R

T

-

V

I

L

M

P

D

D

G

A

A

R

I

T

A

V

I

A

D

A

A

L

L

R

N

R

Q

L

C

R

R

A

S

A

L

G

G

V

Y

R

A

V

I

A

S

I

I

D
|
D

D

D

F

F

G

G

M

T

G

G

H

F

A

S

S

G

L

L

R

Q

Y

Y

L

L

R

T

D

Q

F

M

P

P

V

I

D

S

T

F

V

L

K

K

I

I

D

D

R

R

S

S

L

F

T

V

E

M

A

K

S

I

H

L

G

S

D

D

-

P

V

K

N

S

E

K

H

A

I

V

V

V

R

S

S

S

I

I

V

I

E

H

L

L

A

A

R

H

S

A

L

M

D

D

I

I

T

E

T

V

L

I

V

A

E

E

G

G

V

I

E

E

R

H

E

E

Q

E

F

A

E

L

R

V

F

L

V

E

E

T

L

L

G

G

C

A

L

R

V

F

F

G

Q

Q

G

G

Y

Y

L

L

F

F

S

S

R

K

P

P

V

V

binding magnesium ion: E153 (= E527), E252 (= E618), D281 (= D648)
binding cyclic guanosine monophosphate: R103 (≠ C481), L104 (≠ I482), R106 (= R484)

Sites not aligning to the query:

binding cyclic guanosine monophosphate: 12, 31, 42, 43, 51, 52, 53, 54, 55, 62, 63, 64

4hjfA Eal domain of phosphodiesterase pdea in complex with c-di-gmp and ca++
35% identity, 32% coverage: 494:740/762 of query aligns to 6:254/263 of 4hjfA

query
sites
4hjfA

S

A

L

L

A

E

N

A

D

D

L

L

A

R

A

G

A

A

L

I

A

G

R

R

N

-

G

G

E

E

V

I

F

T

L

P

E

Y

Y

F

Q
|
Q

P

P

Q

I

I

V

R

R

M

L

D

S

-

T

G

G

R

A

A

L

H

S

G

G

A

F

E
|
E

A

A

L
|
L

L
x
A

R
|
R

W

W

H

I

H

H

P

P

A

R

Y

R

G

G

R

M

I

L

A

P

P
|
P

P
x
D

I

E

T

F

V
x
L

A

P

L

L

A

I

E

E

D

E

T

M

G

G

I

L

I

M

D

S

R

E

L

L

G

G

M

A

F

H

V
x
M

L

M

H

H

R

A

A

A

C

A

A

Q

R

Q

R

L

V

S

A

T

W

W

T

R

G

A

E

A

V

H

P

P

-

A

-

M

D

G

G

N

F

L

V

T

M

V

S

S

V

V

N
|
N

V
x
L

A
x
S

P

T

R

G

Q

E

L

I

Q

D

N

R

P

P

R

G

F

L

D

V

R

A

D

D

V

V

L

A

A

E

V

T

L

L

A

R

R

V

T

N

G

R

L

L

A

P

P

R

H

G

L

A

L

L

E

K

L

L

E
|
E

L

V

T

T

E

E

S

S

T

D

V

I

L

M

L

R

P

D

D

P

A

E

R

R

T

A

V

A

A

V

A

I

L

L

R

K

R

T

L

L

R

R

A

D

A

A

G

G

V

A

R

G

V

L

A

A

I

L

D
|
D

F

F

G

G

M

T

G

G

H

F

A

S

S

S

L

L

R

S

Y

Y

L

L

R

T

D

R

F

L

P

P

V

F

D

D

T

T

V

L

K

K

I

I

D

D

R
|
R

S

Y

L

F

T

V

E

R

A

T

S

M

H

G

G

N

D

N

V

A

N

G

E

S

-

A

H

K

I

I

V

V

R

R

S

S

I

V

V

V

E

K

L

L

A

G

R

Q

S

D

L

L

D

D

I

L

T

E

T

V

L

V

V

A

E
|
E

G
|
G

V
|
V

E
|
E

R

N

R

A

E

E

Q

M

F

A

E

H

R

A

F

L

V

Q

E

S

L

L

G

G

C

C

L

D

V

Y

F

G

Q

Q

G
|
G

Y
x
F

L

G

F

Y

S

A

R

-

P

P

V

A

R

L

A

S

V

P

Q

Q

C

E

L

A

E

E

V

V

binding 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one): Q25 (= Q514), E39 (= E527), L41 (= L529), A42 (≠ L530), R43 (= R531), P54 (= P542), D55 (≠ P543), L58 (≠ V546), M74 (≠ V562), N100 (= N586), L101 (≠ V587), S102 (≠ A588), D162 (= D648), R186 (= R672), E219 (= E704), G220 (= G705), V221 (= V706), E222 (= E707), G240 (= G725), F241 (≠ Y726)
binding calcium ion: E39 (= E527), N100 (= N586), E132 (= E618), D162 (= D648), D162 (= D648), D163 (= D649), E219 (= E704)

3u2eA Eal domain of phosphodiesterase pdea in complex with 5'-pgpg and mg++
35% identity, 32% coverage: 494:740/762 of query aligns to 4:252/260 of 3u2eA

query
sites
3u2eA

S

A

L

L

A

E

N

A

D

D

L

L

A

R

A

G

A

A

L

I

A

G

R

R

N

-

G

G

E

E

V

I

F

T

L

P

E

Y

Y

F

Q
|
Q

P

P

Q

I

I

V

R

R

M

L

D

S

-

T

G

G

R

A

A

L

H

S

G

G

A

F

E
|
E

A

A

L
|
L

L
x
A

R
|
R

W

W

H

I

H

H

P

P

A

R

Y

R

G

G

R

M

I

L

A

P

P
|
P

P
x
D

I

E

T

F

V
x
L

A

P

L

L

A

I

E

E

D

E

T

M

G

G

I

L

I

M

D

S

R

E

L

L

G

G

M

A

F

H

V
x
M

L

M

H

H

R

A

A

A

C

A

A

Q

R

Q

R

L

V

S

A

T

W

W

T

R

G

A

E

A

V

H

P

P

-

A

-

M

D

G

G

N

F

L

V

T

M

V

S

S

V

V

N
|
N

V

L

A
x
S

P

T

R

G

Q

E

L

I

Q

D

N

R

P

P

R

G

F

L

D

V

R

A

D

D

V

V

L

A

A

E

V

T

L

L

A

R

R

V

T

N

G

R

L

L

A

P

P

R

H

G

L

A

L

L

E

K

L

L

E
|
E

L

V

T

T

E

E

S

S

T

D

V

I

L

M

L

R

P

D

D

P

A

E

R

R

T

A

V

A

A

V

A

I

L

L

R

K

R

T

L

L

R

R

A

D

A

A

G

G

V

A

R

G

V

L

A

A

I

L

D
|
D

F

F

G

G

M

T

G

G

H

F

A

S

S

S

L

L

R

S

Y

Y

L

L

R

T

D

R

F

L

P

P

V

F

D

D

T

T

V

L

K

K

I

I

D

D

R
|
R

S

Y

L

F

T

V

E

R

A

T

S

M

H

G

G

N

D

N

V

A

N

G

E

S

-

A

H

K

I

I

V

V

R

R

S

S

I

V

V

V

E

K

L

L

A

G

R

Q

S

D

L

L

D

D

I

L

T

E

T

V

L

V

V

A

E
|
E

G
|
G

V

V

E
|
E

R

N

R

A

E

E

Q

M

F

A

E

H

R

A

F

L

V

Q

E

S

L

L

G

G

C

C

L

D

V

Y

F

G

Q

Q

G
|
G

Y
x
F

L

G

F

Y

S

A

R

-

P

P

V

A

R

L

A

S

V

P

Q

Q

C

E

L

A

E

E

V

V

binding magnesium ion: E37 (= E527), N98 (= N586), E130 (= E618), D160 (= D648), D160 (= D648), D161 (= D649), E217 (= E704)
binding : Q23 (= Q514), E37 (= E527), L39 (= L529), A40 (≠ L530), R41 (= R531), P52 (= P542), D53 (≠ P543), L56 (≠ V546), M72 (≠ V562), N98 (= N586), S100 (≠ A588), D160 (= D648), D161 (= D649), R184 (= R672), E217 (= E704), G218 (= G705), E220 (= E707), G238 (= G725), F239 (≠ Y726)

6hq5A Structure of eal enzyme bd1971 - camp and cyclic-di-gmp bound form (see paper)
31% identity, 31% coverage: 494:732/762 of query aligns to 119:365/376 of 6hq5A

query
sites
6hq5A

S

K

L

L

A

E

N

N

D

Q

L

I

A

F

A

Q

A

A

L

F

A

-

R

Q

N

N

G

K

E

E

V

F

F

E

L

L

E

F

Y

Y

Q
|
Q

P

P

Q

I

I

V

R

N

M

L

D

K

G

N

R

K

A

T

-

I

H

T

G

G

A

C

E
|
E

A

A

L
|
L

R
|
R

W

W

H

N

H

S

P

P

A

Q

Y

H

G

G

R

L

I

V

A

S

P

P

P

N

I

L

T

F

V
x
I

A

D

L

I

A

I

E
|
E

D

N

T

S

G

S

I

M

I

V

D

I

R

P

L

I

G

G

M

H

F

W

V
x
I

L

I

H

N

R

Q

A

A

C

L

A

K

R

D

-

L

-

R

-

T

-

I

-

Q

-

D

-

Q

-

L

R

R

V

L

A

N

W

K

T

K

G

E

E

R

V

M

P

A

D

D

G

D

F

F

V

M

M

M

S

S

V

I

N
|
N

V

I

A
x
S

P

G

R

R

Q

Q

L

F

Q

T

N

H

P

S

R

D

F

F

D

V

R

N

D

N

V

L

L

E

A

D

V

L

L

R

A

E

R

K

T

H

G

D

L

L

A

H

P

T

H

Q

L

N

L

I

E

K

L

L

E
|
E

L

M

T

T

E

E

S

R

T

-

V

I

L

M

P

D

D

G

A

A

R

I

T

A

V

I

A

D

A

A

L

L

R

N

R

Q

L

C

R

R

A

S

A

L

G

G

V

Y

R

A

V

I

A

S

I

I

D
|
D

F

F

G

G

M

T

G

G

H

F

A

S

S

G

L

L

R

Q

Y

Y

L

L

R

T

D

Q

F

M

P

P

V

I

D

S

T

F

V

L

K

K

I

I

D
|
D

R
|
R

S

S

L

F

T

V

E

M

A

K

S

I

H

L

G

S

D

D

-

P

V

K

N

S

E

K

H

A

I

V

V

V

R

S

S

S

I

I

V

I

E

H

L

L

A

A

R

H

S

A

L

M

D

D

I

I

T

E

T

V

L

I

V

A

E
|
E

G
|
G

V
x
I

E
|
E

R

H

E

E

Q

E

F

A

E

L

R

V

F

L

V

E

E

T

L

L

G

G

C

A

L

R

V

F

F

G

Q

Q

G
|
G

Y
|
Y

L

L

F

F

S

S

R

K

P

P

V

V

binding 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one): Q138 (= Q514), E152 (= E527), L154 (= L529), L155 (= L530), R156 (= R531), I171 (≠ V546), E175 (= E550), I187 (≠ V562), N219 (= N586), S221 (≠ A588), D280 (= D648), D281 (= D649), R304 (= R672), E337 (= E704), G338 (= G705), I339 (≠ V706), E340 (= E707), G358 (= G725), Y359 (= Y726)
binding calcium ion: E152 (= E527), N219 (= N586), E251 (= E618), D280 (= D648), D280 (= D648), D281 (= D649), D303 (= D671), E337 (= E704)

Sites not aligning to the query:

binding adenosine-3',5'-cyclic-monophosphate: 13, 32, 43, 44, 52, 53, 54, 55, 56, 63, 64, 65

4lj3A Crystal structure of the eal domain of c-di-gmp specific phosphodiesterase yaha in complex with substratE C-di-gmp and ca++ (see paper)
35% identity, 29% coverage: 512:732/762 of query aligns to 18:244/256 of 4lj3A

query
sites
4lj3A

E

E

Y

F

Q

K

P

P

Q

W

I

I

R
x
Q

-

P

-
x
V

-

F

-

C

-

A

M

Q

D

T

G

G

R

V

A

L

H
x
T

G
|
G

A
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binding 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one): Q24 (≠ R518), E38 (= E527), L40 (= L529), V41 (≠ L530), R42 (= R531), P53 (= P542), D54 (≠ P543), I57 (≠ V546), I66 (= I555), N97 (= N586), S99 (≠ A588), D159 (= D648), D160 (= D649), K183 (≠ R672), E216 (= E704), G217 (= G705), V218 (= V706), E219 (= E707), G237 (= G725), Y238 (= Y726), P243 (= P731)
binding calcium ion: E38 (= E527), N97 (= N586), E129 (= E618), D159 (= D648), D160 (= D649), E216 (= E704)
binding trans-4-(hydroxymethyl)cyclohexanol: V26 (vs. gap), T35 (≠ H524), G36 (= G525), C37 (≠ A526), H93 (≠ V582), G95 (≠ S584), V127 (≠ E616), E129 (= E618), F178 (≠ T667), K180 (= K669), V214 (≠ L702), F234 (≠ V722)

P21514 Cyclic di-GMP phosphodiesterase PdeL; EC 3.1.4.52 from Escherichia coli (strain K12) (see 2 papers)
35% identity, 29% coverage: 512:732/762 of query aligns to 121:347/362 of P21514

query
sites
P21514

E

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Q127 (≠ R518) binding
E141 (= E527) binding
VR 144:145 (≠ LR 530:531) binding
N200 (= N586) binding ; binding
F206 (≠ L592) mutation to S: Increases catalytic activity.
E232 (= E618) binding
F249 (≠ L635) mutation to L: Increases catalytic activity.
D262 (= D648) binding ; binding
D263 (= D649) mutation to N: Loss of activity.
K286 (≠ R672) binding
S298 (≠ N683) mutation to W: Slow monomer-dimer exchange. Equilibrium largely on the monomeric side, in particular in the presence of substrate. Strong decrease in activity.
G299 (≠ E684) mutation to S: Increases catalytic activity.
EGVE 319:322 (= EGVE 704:707) binding
Y341 (= Y726) binding

Sites not aligning to the query:

60 K→A: Does not bind to the PdeL box.

4lykA Crystal structure of the eal domain of c-di-gmp specific phosphodiesterase yaha in complex with activating cofactor mg++ (