SitesBLAST

A22 (≠ S26) mutation to V: Defective replication fork reversal (RFR), UV light resistant, resistant to mitomycin C (MMC).
Y184 (= Y188) mutation to H: Defective RFR, UV light resistant, resistant to MMC.
P220 (= P224) mutation to S: Defective RFR, UV light resistant, variably resistant to MMC.
A250 (= A254) mutation to T: Defective RFR, UV light resistant, sensitive to MMC.

7x7pM Cryoem structure of dsdna-ruvb-ruva domain3 complex (see paper)
64% identity, 88% coverage: 26:337/354 of query aligns to 2:309/309 of 7x7pM

query
sites
7x7pM

S

A

L

I

R

R

P

P

L

L

C

K

L

L

A

A

D

D

F

Y

T

I

G

G

Q

Q

A

P

A

S

A

V

R

R

Q

E

N

Q

L

M

A

E

V

L

F

F

I

I

E

H

A

A

R

R

A

G

R

R

R

Q

E

E

A

A

L

L

D

D

H

H

V

T

L

L

F

I

V

F

G

G

P

P

G

G

L

L

G

G

K

K

T

T

L

L

A

A

Q

N

I

I

V

I

A

A

R

Q

E

E

L

M

G

G

V

V

N

S

F

I

R

K

S

S

T

T

S

S

G

G

P

P

V

V

I

L

A

E

K

R

A

P

G

G

D

D

L

L

A

A

Q

L

L

L

T

T

A

N

L

L

E

E

D

A

R

G

D

D

V

V

L

L

F

F

I

V

D

D

E

E

I

I

H

H

R

R

L

L

N

S

P

P

A

I

V

V

E

E

I

V

L

L

Y

Y

P

P

A

A

M

M

E

E

D

D

F

F

Q

Q

L

L

D

D

L

I

I

M

I

I

G

A

E

-

G

-

P

-

G

-

A

A

R

R

S

S

V

I

K

K

I

L

D

D

L

L

A

P

R

P

F

F

T

T

L

L

V

V

G

G

A

A

T

T

R

R

A

A

G

G

L

M

L

L

T

T

T

N

P

P

L

L

R

R

D

D

R

R

F

F

G

G

I

I

P

V

I

Q

R

R

L

L

D

E

F

F

Y

Y

T

N

V

V

E

E

E

D

L

L

E

A

K

T

I

I

V

V

T

S

R

R

G

S

A

A

R

G

V

I

H

L

G

G

L

L

A

E

I

I

E

E

A

P

E

Q

G

G

A

A

N

A

E

E

I

I

A

A

R

K

R

R

A

A

R

R

G

G

T

T

P

P

R

R

I

I

A

A

G

N

R

R

L

L

R

R

V

V

R

R

D

D

F

F

A

A

I

E

V

V

D

R

G

G

V

Q

E

G

R

D

V

I

T

T

R

R

A

V

L

I

A

A

D

D

K

K

A

A

L

L

R

N

L

L

D

D

V

V

D

D

P

E

I

R

G

G

L

F

D

D

Q

H

M

L

D

D

R

R

Y

L

L

L

D

L

V

T

I

M

A

I

L

D

S

K

F

F

G

D

G

G

P

P

V
|
V

G
|
G

I

I

E

D

T
x
N

I

L

A

A

L

L

S

S

E

E

P

E

R

R

D

H

A

T

I

I

E

E

D

D

I

V

I

L

E

E

P

P

Y

Y

L

L

I

I

Q

Q

G

G

F

Y

L

I

Q

M

R
|
R

T
|
T

P
|
P

R

R

G

G

R
|
R

L

V

T

T

A

R

N

H

A

A

F

Y

R

L

H

H

L

F

G

G

L

L

K

N

E

I

P

P

binding : V257 (= V285), G258 (= G286), N261 (≠ T289), R289 (= R317), T290 (= T318), P291 (= P319), R294 (= R322)

Q56313 Holliday junction branch migration complex subunit RuvB; EC 3.6.4.12 from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (see paper)
52% identity, 92% coverage: 12:337/354 of query aligns to 4:329/334 of Q56313

query
sites
Q56313

L
x
F

V
x
L

S
x
T

P
|
P

Q
x
E

S
x
R

R
x
T

A
x
V

E
x
Y

D
|
D

G
x
S

S
x
G

E
x
V

A
x
Q

S
x
F

L
|
L

R
|
R

P
|
P

L
x
K

C
x
S

L
|
L

A
x
D

D
x
E

F
|
F

T
x
I

G
|
G

Q
|
Q

A
x
E

A
x
N

A
x
V

R
x
K

Q
x
K

N
x
K

L
|
L

A
x
S

V
x
L

F
x
A

I
x
L

E
|
E

A
|
A

R
x
K

A
x
M

R
|
R

R
x
G

E
|
E

A
x
V

L
|
L

D
|
D

H
|
H

V
|
V

L
|
L

F
x
L

V
x
A

G
|
G

P
|
P

G
|
G

L
|
L

G
|
G

K
|
K

T
|
T

L
|
L

A
|
A

Q
x
H

I
|
I

V
x
I

A
|
A

R
x
S

E
|
E

L
|
L

G
x
Q

V
x
T

N
|
N

F
x
I

R
x
H

S
x
V

T
|
T

S
|
S

G
|
G

P
|
P

V
|
V

I
x
L

A
x
V

K
|
K

A
x
Q

G
|
G

D
|
D

L
x
M

A
|
A

Q
x
I

L
|
L

T
|
T

A
x
S

L
|
L

E
|
E

D
x
R

R
x
G

D
|
D

V
|
V

L
|
L

F
|
F

I
|
I

D
|
D

E
|
E

I
|
I

H
|
H

R
|
R

L
|
L

N
|
N

P
x
K

A
|
A

V
|
V

E
|
E

I
x
L

L
|
L

Y
|
Y

P
x
S

A
|
A

M
x
I

E
|
E

D
|
D

F
|
F

Q
|
Q

L
x
I

D
|
D

L
x
I

I
x
M

I
|
I

G
|
G

E
x
K

G
|
G

P
|
P

G
x
S

A
|
A

R
x
K

S
|
S

V
x
I

K
x
R

I
|
I

D
|
D

L
x
I

A
x
Q

R
x
P

F
|
F

T
|
T

L
|
L

V
|
V

G
|
G

A
|
A

T
|
T

R
|
R

A
x
S

G
|
G

L
|
L

T
x
S

P
|
P

L
|
L

R
|
R

D
x
S

R
|
R

F
|
F

G
|
G

I
|
I

P
x
I

I
x
L

R
x
E

L
|
L

D
|
D

F
|
F

Y
|
Y

T
|
T

V
|
V

E
x
K

E
|
E

L
|
L

E
x
K

K
x
E

I
|
I

V
x
I

T
x
K

R
|
R

G
x
A

A
|
A

R
x
S

V
x
L

H
x
M

G
x
D

L
x
V

A
x
E

I
|
I

E
|
E

A
x
D

E
x
A

G
x
A

A
|
A

N
x
E

E
x
M

I
|
I

A
|
A

R
x
K

R
|
R

A
x
S

R
|
R

G
|
G

T
|
T

P
|
P

R
|
R

I
|
I

A
|
A

G
x
I

R
|
R

L
|
L

L
x
T

R
x
K

R
|
R

V
|
V

R
|
R

D
|
D

F
x
M

A
x
L

I
x
T

V
|
V

D
x
V

G
x
K

V
x
A

E
x
D

R
|
R

V
x
I

T
x
N

R
x
T

A
x
D

L
x
I

A
x
V

D
x
L

K
|
K

A
x
T

L
x
M

R
x
E

L
x
V

L
|
L

D
x
N

V
x
I

D
|
D

P
x
D

I
x
E

G
|
G

L
|
L

D
|
D

Q
x
E

M
x
F

D
|
D

R
|
R

R
x
K

Y
x
I

L
|
L

D
x
K

V
x
T

I
|
I

A
x
I

L
x
E

S
x
I

F
x
Y

G
x
R

G
|
G

P
|
P

V
|
V

G
|
G

I
x
L

E
x
N

T
x
A

I
x
L

A
|
A

A
x
S

L
|
L

S
x
G

E
x
V

P
x
E

R
x
A

D
|
D

A
x
T

I
x
L

E
x
S

D
x
E

I
x
V

I
x
Y

E
|
E

P
|
P

Y
|
Y

L
|
L

I
x
L

Q
|
Q

Q
x
A

G
|
G

F
|
F

L
|
L

Q
x
A

R
|
R

T
|
T

P
|
P

R
|
R

G
|
G

R
|
R

L
x
I

L
x
V

T
|
T

A
x
E

N
x
K

A
|
A

F
x
Y

R
x
K

H
|
H

L
|
L

G
x
K

L
x
Y

K
x
E

E
x
V

P
|
P

F27 (= F35) binding ADP; binding ATP
I28 (≠ T36) binding ADP; binding ATP
L62 (= L70) binding ADP; binding ATP
K64 (= K72) binding ADP
T65 (= T73) binding ADP
A156 (= A164) mutation to C: 38% DNA-dependent ATPase activity.; mutation to S: 32% DNA-dependent ATPase activity, allows branch migration.
TT 157:158 (= TT 165:166) mutation to VV: 5% DNA-dependent ATPase activity, no branch migration.
T158 (= T166) mutation to V: 5% DNA-dependent ATPase activity.
R170 (= R178) mutation R->A,R: 3-4% DNA-dependent ATPase activity, nobranch migration.
Y180 (= Y188) binding ADP
182:255 (vs. 190:263, 41% identical) Small ATPAse domain (RuvB-S)
P216 (= P224) binding ADP; binding ATP; mutation to G: 11% DNA-dependent ATPase activity, allows branch migration.
R217 (= R225) binding ADP; mutation to A: 43% DNA-dependent ATPase activity, allows branch migration.; mutation to K: 5% DNA-dependent ATPase activity, no branch migration.

Sites not aligning to the query:

1:181 Large ATPase domain (RuvB-L)
256:334 Head domain (RuvB-H)

8efyA Structure of double homo-hexameric aaa+ atpase ruvb motors
58% identity, 88% coverage: 26:337/354 of query aligns to 1:313/313 of 8efyA

query
sites
8efyA

S

A

L

L

R

R

P

P

L

K

C

T

L

L

A

D

D

E

F
x
Y

T
x
I

G

G

Q

Q

A

E

A

R

A

L

R

K

Q

Q

N

K

L

L

A

R

V

V

F

Y

I

L

E

E

A

A

R

K

A

A

R

R

R

K

E

E

A

P

L

L

D

E

H

H

V

L

L

L

F

L

V

F

G

G

P

P

G
|
G

L
|
L

G
|
G

K

K

T

T

T
|
T

L

L

A

A

Q

H

I

V

V

I

A

A

R

H

E

E

L

L

G

G

V

V

N

N

F

L

R

R

S

V

T

T

S

S

G

G

P

P

V

A

I

I

A

E

K

K

A

P

G

G

D

D

L

L

A

A

Q

I

L

L

-

A

T

N

A

S

L

L

E

E

D

E

R

G

D

D

V

I

L

L

F

F

I

I

D
|
D

E
|
E

I

I

H

H

R

R

L

L

N

S

P

R

A

Q

V

A

E

E

I

H

L

L

Y

Y

P

P

A

A

M

M

E
|
E

D

D

F

F

Q

V

L

M

D

D

L

I

I

V

I

I

G

G

E

Q

G

G

P

P

G

A

A

A

R

R

S

T

V

I

K

R

I

L

D

E

L

L

A

P

R

R

F

F

T

T

L

L

V

I

G

G

A

A

T

T

R

R

A

P

G

G

L

L

L

I

T

T

T

A

P

P

L

L

R

L

D

S

R
|
R

F

F

G

G

I

I

P

V

I

E

R

H

L

L

D

E

F

Y

Y

Y

T

T

V

P

E

E

L

L

E

A

K

Q

I

G

V

V

T

M

R

R

G

D

A

A

R

R

V

L

H

L

G

G

L

V

A

R

I

I

E

T

A

E

E

E

G

A

A

A

N

L

E

E

I

I

A

G

R

R

A

S

R

R

G

G

T

T

P
x
M

R

R

I

V

A

A

G

K

R

R

L

L

L

F

R

R

V

V

R

R

D

D

F

F

A

A

I

Q

V

V

D

A

G

G

V

E

E

E

R

V

V

I

T

T

R

R

A

E

L

R

A

A

D

L

K

E

A

A

L

L

R

A

L

A

L

L

D

G

V

L

D

D

P

E

I

L

G

G

L

L

D

E

Q

K

M

R

D

D

R

R

R

E

Y

I

L

L

D

E

V

V

I

L

A

I

L

L

S

R

F

F

G

G

P

P

V

V

G

G

I

L

E

A

T
|
T

I

L

A

A

A

T

A

A

L

L

S

S

E

E

P

D

R

P

D

G

A

T

I

L

E

E

D

E

I

V

I

H

E

E

P

P

Y

Y

L

L

I

I

Q

R

Q

Q

G

G

F

L

L

L

Q

K

R

R

T

T

P
|
P

R
|
R

G

G

R
|
R

L

V

L

A

T

T

A

E

N

L

A

A

F

Y

R

R

H

H

L

L

G

G

L

Y

K

P

E

P

P

P

binding adenosine-5'-diphosphate: Y10 (≠ F35), I11 (≠ T36), G44 (= G69), L45 (= L70), G46 (= G71), T49 (= T74), M200 (≠ P224)
binding phosphothiophosphoric acid-adenylate ester: E111 (= E135), R154 (= R178)
binding magnesium ion: D93 (= D117), E94 (= E118)
binding : T265 (= T289), P295 (= P319), R296 (= R320), R298 (= R322)

8efvA Structure of single homo-hexameric holliday junction atp-dependent DNA helicase ruvb motor
58% identity, 88% coverage: 26:337/354 of query aligns to 1:313/313 of 8efvA

query
sites
8efvA

S

A

L

L

R
|
R

P
|
P

L

K

C

T

L

L

A

D

D

E

F
x
Y

T
x
I

G

G

Q

Q

A

E

A

R

A

L

R

K

Q

Q

N

K

L

L

A

R

V

V

F

Y

I

L

E

E

A

A

R

K

A

A

R

R

R

K

E

E

A

P

L

L

D

E

H

H

V

L

L

L

F

L

V

F

G

G

P

P

G
|
G

L
|
L

G
|
G

K

K

T

T

T
|
T

L

L

A

A

Q

H

I

V

V

I

A

A

R

H

E

E

L

L

G

G

V

V

N

N

F

L

R

R

S

V

T

T

S

S

G

G

P

P

V

A

I

I

A

E

K

K

A

P

G

G

D

D

L

L

A

A

Q

I

L

L

-

A

T

N

A

S

L

L

E

E

D

E

R

G

D

D

V

I

L

L

F

F

I

I

D

D

E

E

I

I

H

H

R

R

L

L

N

S

P
x
R

A

Q

V

A

E

E

I

H

L

L

Y

Y

P

P

A

A

M

M

E
|
E

D

D

F

F

Q

V

L

M

D

D

L

I

I

V

I

I

G

G

E

Q

G

G

P

P

G

A

A

A

R

R

S

T

V

I

K

R

I

L

D

E

L

L

A

P

R

R

F

F

T

T

L

L

V

I

G

G

A

A

T

T

R

R

A

P

G

G

L

L

L

I

T

T

T

A

P

P

L

L

R

L

D

S

R
|
R

F

F

G

G

I

I

P

V

I

E

R

H

L

L

D

E

F

Y

Y

Y

T

T

V

P

E

E

L

L

E

A

K

Q

I

G

V

V

T

M

R

R

G

D

A

A

R

R

V

L

H

L

G

G

L

V

A

R

I

I

E

T

A

E

E

E

G

A

A

A

N

L

E

E

I

I

A

G

R

R

A

S

R

R

G

G

T

T

P

M

R
|
R

I

V

A

A

G

K

R

R

L

L

L

F

R

R

V

V

R

R

D

D

F

F

A

A

I

Q

V

V

D

A

G

G

V

E

E

E

R

V

V

I

T

T

R

R

A

E

L

R

A

A

D

L

K

E

A

A

L

L

R

A

L

A

L

L

D

G

V

L

D

D

P

E

I

L

G

G

L

L

D

E

Q

K

M

R

D

D

R

R

R

E

Y

I

L

L

D

E

V

V

I

L

A

I

L

L

S

R

F

F

G

G

P

P

V
|
V

G

G

I
x
L

E

A

T
|
T

I

L

A

A

A

T

A

A

L

L

S

S

E

E

P

D

R

P

D

G

A

T

I

L

E

E

D

E

I

V

I

H

E

E

P

P

Y

Y

L

L

I

I

Q

R

Q

Q

G

G

F

L

L

L

Q

K

R

R

T

T

P
|
P

R
|
R

G

G

R
|
R

L

V

L

A

T

T

A

E

N

L

A

A

F

Y

R

R

H

H

L

L

G

G

L

Y

K

P

E

P

P

P

binding adenosine-5'-diphosphate: R3 (= R28), P4 (= P29), Y10 (≠ F35), I11 (≠ T36), G44 (= G69), L45 (= L70), G46 (= G71), T49 (= T74), R201 (= R225)
binding phosphothiophosphoric acid-adenylate ester: E111 (= E135), R154 (= R178)
binding : R100 (≠ P124), V261 (= V285), L263 (≠ I287), T265 (= T289), P295 (= P319), R296 (= R320), R298 (= R322)

Q5SL87 Holliday junction branch migration complex subunit RuvB; EC 3.6.4.12 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) (see 2 papers)
58% identity, 88% coverage: 26:337/354 of query aligns to 5:317/324 of Q5SL87

query
sites
Q5SL87

S
x
A

L
|
L

R
|
R

P
|
P

L
x
K

C
x
T

L
|
L

A
x
D

D
x
E

F
x
Y

T
x
I

G
|
G

Q
|
Q

A
x
E

A
x
R

A
x
L

R
x
K

Q
|
Q

N
x
K

L
|
L

A
x
R

V
|
V

F
x
Y

I
x
L

E
|
E

A
|
A

R
x
K

A
|
A

R
|
R

R
x
K

E
|
E

A
x
P

L
|
L

D
x
E

H
|
H

V
x
L

L
|
L

F
x
L

V
x
F

G
|
G

P
|
P

G
|
G

L
|
L

G
|
G

K
|
K

T
|
T

L
|
L

A
|
A

Q
x
H

I
x
V

V
x
I

A
|
A

R
x
H

E
|
E

L
|
L

G
|
G

V
|
V

N
|
N

F
x
L

R
|
R

S
x
V

T
|
T

S
|
S

G
|
G

P
|
P

V
x
A

I
|
I

A
x
E

K
|
K

A
x
P

G
|
G

D
|
D

L
|
L

A
|
A

Q
x
I

L
|
L

-
x
A

T
x
N

A
x
S

L
|
L

E
|
E

D
x
E

R
x
G

D
|
D

V
x
I

L
|
L

F
|
F

I
|
I

D
|
D

E
|
E

I
|
I

H
|
H

R
|
R

L
|
L

N
x
S

P
x
R

A
x
Q

V
x
A

E
|
E

I
x
H

L
|
L

Y
|
Y

P
|
P

A
|
A

M
|
M

E
|
E

D
|
D

F
|
F

Q
x
V

L
x
M

D
|
D

L
x
I

I
x
V

I
|
I

G
|
G

E
x
Q

G
|
G

P
|
P

G
x
A

A
|
A

R
|
R

S
x
T

V
x
I

K
x
R

I
x
L

D
x
E

L
|
L

A
x
P

R
|
R

F
|
F

T
|
T

L
|
L

V
x
I

G
|
G

A
|
A

T
|
T

R
|
R

A
x
P

G
|
G

L
|
L

L
x
I

T
|
T

T
x
A

P
|
P

L
|
L

R
x
L

D
x
S

R
|
R

F
|
F

G
|
G

I
|
I

P
x
V

I
x
E

R
x
H

L
|
L

D
x
E

F
x
Y

Y
|
Y

T
|
T

V
x
P

E
|
E

L
|
L

E
x
A

K
x
Q

I
x
G

V
|
V

T
x
M

R
|
R

G
x
D

A
|
A

R
|
R

V
x
L

H
x
L

G
|
G

L
x
V

A
x
R

I
|
I

E
x
T

A
x
E

E
|
E

G
x
A

A
|
A

N
x
L

E
|
E

I
|
I

A
x
G

R
|
R

A
x
S

R
|
R

G
|
G

T
|
T

P
x
M

R
|
R

I
x
V

A
|
A

G
x
K

R
|
R

L
|
L

L
x
F

R
|
R

V
|
V

R
|
R

D
|
D

F
|
F

A
|
A

I
x
Q

V
|
V

D
x
A

G
|
G

V
x
E

E
|
E

R
x
V

V
x
I

T
|
T

R
|
R

A
x
E

L
x
R

A
|
A

D
x
L

K
x
E

A
|
A

L
|
L

R
x
A

L
x
A

L
|
L

D
x
G

V

L

D

D

P
x
E

I
x
L

G
|
G

L
|
L

D
x
E

Q
x
K

M
x
R

D
|
D

R
|
R

R
x
E

Y
x
I

L
|
L

D
x
E

V
|
V

I
x
L

A
x
I

L
|
L

S
x
R

F
|
F

G
|
G

P
|
P

V
|
V

G
|
G

I
x
L

E
x
A

T
|
T

I
x
L

A
|
A

A
x
T

A
|
A

L
|
L

S
|
S

E
|
E

P
x
D

R
x
P

D
x
G

A
x
T

I
x
L

E
|
E

D
x
E

I
x
V

I
x
H

E
|
E

P
|
P

Y
|
Y

L
|
L

I
|
I

Q
x
R

Q
|
Q

G
|
G

F
x
L

L
|
L

Q
x
K

R
|
R

T
|
T

P
|
P

R
|
R

G
|
G

R
|
R

L
x
V

L
x
A

T
|
T

A
x
E

N
x
L

A
|
A

F
x
Y

R
|
R

H
|
H

L
|
L

G
|
G

L
x
Y

K
x
P

E
x
P

P
|
P

Y14 (≠ F35) binding ATP
I15 (≠ T36) binding ATP
G48 (= G69) binding ATP
K51 (= K72) binding ATP
T52 (= T73) binding ATP
T53 (= T74) binding ATP
Y168 (= Y188) binding ATP
169:239 (vs. 189:259, 55% identical) Small ATPAse domain (RuvB-S)
Y309 (≠ F329) mutation to R: Suitable for crystallization.

Sites not aligning to the query:

1:168 Large ATPase domain (RuvB-L)
242:324 Head domain (RuvB-H)

1ixsB Structure of ruvb complexed with ruva domain iii (see paper)
58% identity, 88% coverage: 26:337/354 of query aligns to 2:314/315 of 1ixsB

query
sites
1ixsB

S

A

L

L

R

R

P

P

L

K

C

T

L

L

A

D

D

E

F
x
Y

T
x
I

G

G

Q

Q

A

E

A

R

A

L

R

K

Q

Q

N

K

L

L

A

R

V

V

F

Y

I

L

E

E

A

A

R

K

A

A

R

R

R

K

E

E

A

P

L

L

D

E

H

H

V

L

L

L

F

L

V

F

G

G

P

P

G

G

L

L

G
|
G

K
|
K

T
|
T

L

L

A

A

Q

H

I

V

V

I

A

A

R

H

E

E

L

L

G

G

V

V

N

N

F

L

R

R

S

V

T

T

S

S

G

G

P

P

V

A

I

I

A

E

K

K

A

P

G

G

D

D

L

L

A

A

Q

I

L

L

-

A

T

N

A

S

L

L

E

E

D

E

R

G

D

D

V

I

L

L

F

F

I

I

D
|
D

E

E

I

I

H

H

R

R

L

L

N

S

P

R

A

Q

V

A

E

E

I

H

L

L

Y

Y

P

P

A

A

M

M

E

E

D

D

F

F

Q

V

L

M

D

D

L

I

I

V

I

I

G

G

E

Q

G

G

P

P

G

A

A

A

R

R

S

T

V

I

K

R

I

L

D

E

L

L

A

P

R

R

F

F

T

T

L

L

V

I

G

G

A

A

T

T

T
|
T

R

R

A

P

G

G

L

L

L

I

T

T

T

A

P

P

L

L

R

L

D

S

R

R

F

F

G

G

I

I

P

V

I

E

R

H

L

L

D

E

F

Y

Y

Y

T

T

V

P

E

E

L

L

E

A

K

Q

I

G

V

V

T

M

R

R

G

D

A

A

R

R

V

L

H

L

G

G

L

V

A

R

I

I

E

T

A

E

E

E

G

A

A

A

N

L

E

E

I

I

A

G

R

R

A

S

R

R

G

G

T

T

P
x
M

R
|
R

I

V

A

A

G

K

R

R

L

L

L

F

R

R

V

V

R

R

D

D

F

F

A

A

I

Q

V

V

D

A

G

G

V

E

E

E

R

V

V

I

T

T

R

R

A

E

L

R

A

A

D

L

K

E

A

A

L

L

R

A

L

A

L

L

D

G

V

L

D

D

P

E

I

L

G

G

L

L

D

E

Q

K

M

R

D

D

R

R

R

E

Y

I

L

L

D

E

V

V

I

L

A

I

L

L

S

R

F

F

G

G

P

P

V

V

G

G

I

L

E

A

T

T

I

L

A

A

A

T

A

A

L

L

S

S

E

E

P

D

R

P

D

G

A

T

I

L

E

E

D

E

I

V

I

H

E

E

P

P

Y

Y

L

L

I

I

Q

R

Q

Q

G

G

F

L

L

L

Q

K

R

R

T

T

P

P

R

R

G

G

R

R

L

V

L

A

T

T

A

E

N

L

A

A

F

Y

R

R

H

H

L

L

G

G

L

Y

K

P

E

P

P

P

active site: K48 (= K72), T49 (= T73), D94 (= D117), T143 (= T166), R202 (= R225)
binding phosphoaminophosphonic acid-adenylate ester: Y11 (≠ F35), I12 (≠ T36), G47 (= G71), K48 (= K72), T49 (= T73), T50 (= T74), M201 (≠ P224), R202 (= R225)

1hqcA Structure of ruvb from thermus thermophilus hb8 (see paper)
58% identity, 88% coverage: 26:337/354 of query aligns to 1:313/314 of 1hqcA

query
sites
1hqcA

S

A

L

L

R

R

P

P

L

K

C

T

L

L

A

D

D

E

F
x
Y

T
x
I

G

G

Q

Q

A

E

A

R

A

L

R

K

Q

Q

N

K

L

L

A

R

V

V

F

Y

I

L

E

E

A

A

R

K

A

A

R

R

R

K

E

E

A

P

L

L

D

E

H

H

V

L

L

L

F

L

V

F

G

G

P

P

G

G

L

L

G

G

K
|
K

T
|
T

T

T

L

L

A

A

Q

H

I

V

V

I

A

A

R

H

E

E

L

L

G

G

V

V

N

N

F

L

R

R

S

V

T

T

S

S

G

G

P

P

V

A

I

I

A

E

K

K

A

P

G

G

D

D

L

L

A

A

Q

I

L

L

-

A

T

N

A

S

L

L

E

E

D

E

R

G

D

D

V

I

L

L

F

F

I

I

D
|
D

E

E

I

I

H

H

R

R

L

L

N

S

P

R

A

Q

V

A

E

E

I

H

L

L

Y

Y

P

P

A

A

M

M

E

E

D

D

F

F

Q

V

L

M

D

D

L

I

I

V

I

I

G

G

E

Q

G

G

P

P

G

A

A

A

R

R

S

T

V

I

K

R

I

L

D

E

L

L

A

P

R

R

F

F

T

T

L

L

V

I

G

G

A

A

T

T

T
|
T

R

R

A

P

G

G

L

L

L

I

T

T

T

A

P

P

L

L

R

L

D

S

R

R

F

F

G

G

I

I

P

V

I

E

R

H

L

L

D

E

F

Y

Y

Y

T

T

V

P

E

E

L

L

E

A

K

Q

I

G

V

V

T

M

R

R

G

D

A

A

R

R

V

L

H

L

G

G

L

V

A

R

I

I

E

T

A

E

E

E

G

A

A

A

N

L

E

E

I

I

A

G

R

R

A

S

R

R

G

G

T

T

P

M

R
|
R

I

V

A

A

G

K

R

R

L

L

L

F

R

R

V

V

R

R

D

D

F

F

A

A

I

Q

V

V

D

A

G

G

V

E

E

E

R

V

V

I

T

T

R

R

A

E

L

R

A

A

D

L

K

E

A

A

L

L

R

A

L

A

L

L

D

G

V

L

D

D

P

E

I

L

G

G

L

L

D

E

Q

K

M

R

D

D

R

R

R

E

Y

I

L

L

D

E

V

V

I

L

A

I

L

L

S

R

F

F

G

G

P

P

V

V

G

G

I

L

E

A

T

T

I

L

A

A

A

T

A

A

L

L

S

S

E

E

P

D

R

P

D

G

A

T

I

L

E

E

D

E

I

V

I

H

E

E

P

P

Y

Y

L

L

I

I

Q

R

Q

Q

G

G

F

L

L

L

Q

K

R

R

T

T

P

P

R

R

G

G

R

R

L

V

L

P

T

T

A

E

N

L

A

A

F

Y

R

R

H

H

L

L

G

G

L

Y

K

P

E

P

P

P

active site: K47 (= K72), T48 (= T73), D93 (= D117), T142 (= T166), R201 (= R225)
binding adenine: Y10 (≠ F35), I11 (≠ T36)

Q5M2B1 Holliday junction branch migration complex subunit RuvB; EC 3.6.4.12 from Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311) (see paper)
53% identity, 89% coverage: 20:333/354 of query aligns to 13:326/333 of Q5M2B1

query
sites
Q5M2B1

E
|
E

D
x
E

G
x
Y

S
x
V

E
|
E

A
x
R

S
x
T

L
|
L

R
|
R

P
|
P

L
x
Q

C
x
Y

L
x
F

A
x
K

D
x
E

F
x
Y

T
x
I

G
|
G

Q
|
Q

A
x
D

A
x
K

A
x
V

R
x
K

Q
x
D

N
x
Q

L
|
L

A
x
K

V
x
I

F
|
F

I
|
I

E
|
E

A
|
A

R
x
K

A
x
L

R
|
R

R
x
D

E
|
E

A
|
A

L
|
L

D
|
D

H
|
H

V
x
T

L
|
L

F
x
L

V
x
F

G
|
G

P
|
P

G
|
G

L
|
L

G
|
G

K
|
K

T
|
T

L
x
M

A
|
A

Q
x
F

I
x
V

V
x
I

A
|
A

R
x
N

E
|
E

L
x
M

G
|
G

V
|
V

N
|
N

F
x
L

R
x
K

S
x
Q

T
|
T

S
|
S

G
|
G

P
|
P

V
x
A

I
|
I

A
x
E

K
|
K

A
|
A

G
|
G

D
|
D

L
|
L

A
x
V

A
|
A

Q
x
I

L
|
L

T
x
N

A
x
D

L
|
L

E
|
E

D
x
P

R
x
G

D
|
D

V
x
I

L
|
L

F
|
F

I
|
I

D
|
D

E
|
E

I
|
I

H
|
H

R
|
R

L
x
M

N
x
P

P
x
M

A
|
A

V
|
V

E
|
E

I
x
V

L
|
L

Y
|
Y

P
x
S

A
|
A

M
|
M

E
|
E

D
|
D

F
x
Y

Q
x
Y

L
x
I

D
|
D

L
x
I

I
x
M

I
|
I

G
|
G

E
x
A

G
|
G

P
x
E

G
x
T

A
x
S

R
|
R

S
|
S

V
|
V

K
x
H

I
x
L

D
|
D

L
|
L

A
x
P

R
x
P

F
|
F

T
|
T

L
|
L

V
|
V

G
|
G

A
|
A

T
|
T

R
|
R

A
|
A

G
|
G

L
x
M

L
|
L

T
x
S

T
x
N

P
|
P

L
|
L

R
|
R

D
x
A

R
|
R

F
|
F

G
|
G

I
|
I

P
x
N

I
x
G

R
x
H

L
x
M

D
x
E

F
x
Y

Y
|
Y

T
x
E

V
x
L

E
x
P

E
x
D

L
|
L

E
x
T

K
x
E

I
|
I

V
|
V

T
x
E

R
|
R

G
x
T

A
x
S

R
x
E

V
x
I

H
x
F

G
x
E

L
x
M

A
x
T

I
|
I

E
x
T

A
x
P

E
|
E

G
x
A

A
|
A

N
x
L

E
|
E

I
x
L

A
|
A

R
|
R

A
x
S

R
|
R

G
|
G

T
|
T

P
|
P

R
|
R

I
|
I

A
|
A

G
x
N

R
|
R

L
|
L

R
x
K

R
|
R

V
|
V

R
|
R

D
|
D

F
x
Y

A
|
A

I
x
Q

V
x
I

D
x
M

G
|
G

V
x
D

E
x
G

R
x
V

V
x
I

T
x
D

R
x
D

A
x
K

L
x
I

A
|
A

D
|
D

K
x
Q

A
|
A

L
|
L

R
x
T

L
x
M

L
|
L

D
|
D

V

V

D

D

P
x
H

I
x
E

G
|
G

L
|
L

D
|
D

Q
x
Y

M
x
V

D
|
D

R
x
Q

R
x
K

Y
x
I

L
|
L

D
x
R

V
x
T

I
x
M

A
x
I

L
x
E

S
x
M

F
x
Y

G
|
G

P
|
P

V
|
V

G
|
G

I
x
L

E
x
G

T
|
T

I
x
L

A
x
S

A
x
V

A
x
N

L
x
I

S
x
A

E
|
E

P
x
E

R
|
R

D
x
E

A
x
T

I
x
V

E
|
E

D
|
D

I
x
M

I
x
Y

E
|
E

P
|
P

Y
|
Y

L
|
L

I
|
I

Q
|
Q

Q
x
K

G
|
G

F
|
F

L
x
I

Q
x
M

R
|
R

T
|
T

P
x
R

R
x
T

G
|
G

R
|
R

L
x
V

L
x
A

T
|
T

A
|
A

N
x
K

A
|
A

F
x
Y

R
x
E

H
|
H

L
x
M

G
|
G

L20 (= L27) binding ATP
R21 (= R28) binding ATP
G62 (= G69) binding ATP
K65 (= K72) binding ATP
T66 (= T73) binding ATP; binding Mg(2+)
T67 (= T74) binding ATP
EDY 128:130 (≠ EDF 135:137) binding ATP
130:148 (vs. 137:155, 42% identical) Presensor-1 beta-hairpin
R171 (= R178) binding ATP
Y181 (= Y188) binding ATP
182:252 (vs. 189:259, 46% identical) Small ATPAse domain (RuvB-S)
R218 (= R225) binding ATP
R291 (= R298) binding DNA
R310 (= R317) binding DNA
R312 (≠ P319) binding DNA
R315 (= R322) binding DNA

Sites not aligning to the query:

1:181 Large ATPase domain (RuvB-L)
255:333 Head domain (RuvB-H)

7pblB Ruvab branch migration motor complexed to the holliday junction - ruvb aaa+ state s1 [t2 dataset] (see paper)
53% identity, 87% coverage: 26:333/354 of query aligns to 1:308/312 of 7pblB

query
sites
7pblB

S

T

L
|
L

R
|
R

P
|
P

L

Q

C

Y

L

F

A

K

D

E

F
x
Y

T

I

G

G

Q

Q

A

D

A

K

A

V

R

K

Q

D

N

Q

L

L

A

K

V

I

F

F

I

I

E

E

A

A

R

K

A

L

R

R

R

D

E

E

A

A

L

L

D

D

H

H

V

T

L

L

F

L

V

F

G

G

P

P

G
|
G

L

L

G
|
G

K
|
K

T
|
T

L

M

A

A

Q

F

I

V

V

I

A

A

R

N

E

E

L

M

G

G

V

V

N

N

F

L

R

K

S

Q

T

T

S

S

G

G

P

P

V

A

I

I

A

E

K

K

A

A

G

G

D

D

L

L

A

V

A

A

Q

I

L

L

T

N

A

D

L

L

E

E

D

P

R

G

D

D

V

I

L

L

F

F

I

I

D

D

E

E

I

I

H

H

R

R

L

M

N

P

P

M

A

A

V

V

E

E

I

V

L

L

Y

Y

P

S

A

A

M

M

E

E

D

D

F

Y

Q

Y

L

I

D

D

L

I

I

M

I

I

G

G

E

A

G

G

P

E

G

T

A

S

R

R

S

S

V

V

K

H

I

L

D

D

L

L

A

P

R

P

F

F

T

T

L

L

V

V

G

G

A

A

T

T

R

R

A

A

G

G

L

M

L

L

T

S

T

N

P

P

L

L

R

R

D

A

R

R

F

F

G

G

I

I

P

N

I

G

R

H

L

M

D

E