SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing WP_012709542.1 NCBI__GCF_000018545.1:WP_012709542.1 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)

P13009 Methionine synthase; 5-methyltetrahydrofolate--homocysteine methyltransferase; Methionine synthase, vitamin-B12-dependent; MS; EC 2.1.1.13 from Escherichia coli (strain K12) (see 5 papers)
62% identity, 97% coverage: 29:1246/1256 of query aligns to 14:1224/1227 of P13009

query
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P13009

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C247 (= C261) binding Zn(2+)
C310 (= C324) binding Zn(2+); mutation C->A,S: Loss of zinc binding. Loss of catalytic activity.
C311 (= C325) binding Zn(2+); mutation C->A,S: Loss of zinc binding. Loss of catalytic activity.
E694 (= E707) binding methylcob(III)alamin
GDVHD 756:760 (= GDVHD 775:779) binding methylcob(III)alamin
D757 (= D776) mutation to E: Decreases activity by about 70%.; mutation to N: Decreases activity by about 45%.
H759 (= H778) binding axial binding residue; mutation to G: Loss of catalytic activity.
S804 (= S823) binding methylcob(III)alamin
T808 (= T827) binding methylcob(III)alamin
S810 (= S829) mutation to A: Decreases activity by about 40%.
A860 (= A880) binding methylcob(III)alamin
D946 (= D967) binding S-adenosyl-L-methionine
R1134 (= R1156) binding S-adenosyl-L-methionine
YY 1189:1190 (≠ YF 1211:1212) binding S-adenosyl-L-methionine

Sites not aligning to the query:

1 modified: Initiator methionine, Removed

Q99707 Methionine synthase; MS; 5-methyltetrahydrofolate--homocysteine methyltransferase; Cobalamin-dependent methionine synthase; Vitamin-B12 dependent methionine synthase; EC 2.1.1.13 from Homo sapiens (Human) (see 6 papers)
56% identity, 97% coverage: 23:1246/1256 of query aligns to 22:1262/1265 of Q99707

query
sites
Q99707

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R61 (≠ C62) natural variant: R -> K
C255 (≠ T256) to Y: in dbSNP:rs1140598
GSR 382:384 (≠ GSA 381:383) binding (6S)-5,6,7,8-tetrahydrofolate
D449 (= D448) binding (6S)-5,6,7,8-tetrahydrofolate
N470 (= N469) binding (6S)-5,6,7,8-tetrahydrofolate
D537 (= D536) binding (6S)-5,6,7,8-tetrahydrofolate
N579 (= N578) binding (6S)-5,6,7,8-tetrahydrofolate
R585 (= R584) binding (6S)-5,6,7,8-tetrahydrofolate
R591 (= R590) binding (6S)-5,6,7,8-tetrahydrofolate
D919 (≠ A913) to G: in dbSNP:rs1805087
D963 (≠ S956) mutation to E: Decreases binding to MTRR; when associated with N-1071.
K1071 (≠ R1057) mutation to N: Decreases binding to MTRR; when associated with E-963.

4cczA Crystal structure of human 5-methyltetrahydrofolate-homocysteine methyltransferase, the homocysteine and folate binding domains
57% identity, 50% coverage: 23:650/1256 of query aligns to 6:611/611 of 4cczA

query
sites
4cczA

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R

V

L

E

A

A

Y

Y

A

Q

E

E

Q

Q

V

A

R

K

G

G

L

L

I

L

D

D

G

G

A

V

D

D

I

I

I

L

L

L

I

I

E

E

T

T

I

I

F

F

D

D

T

T

L

A

N

N

A

A

K

K

A

A

I

L

F

F

A

A

T

L

Q

Q

E

N

V

L

F

F

A

E

E

E

K

K

K

Y

I

A

H

P

L

R

P

P

V

I

M

F

V

I

S

S

G

G

T

T

I

I

T

V

D

D

L

K

S

S

G

G

R

R

T

T

L

L

S

S

G

G

Q

Q

T

T

P

G

T

E

A

G

F

F

W

V

Y

I

S

S

V

V

R

S

H

H

A

G

A

E

P

P

F

L

T

C

I

I

G

G

L

L

N

N

C

C

A

A

L

L

G

G

A

A

D

A

A

E

M

M

R

R

A

P

H

F

I

I

D

E

E

I

L

I

S

G

T

K

V

C

A

T

D

T

T

A

L

Y

V

V

C

L

A

C

Y

Y

P

P

N

N

A

A

G

G

L

-

P

-

N

-

E

-

F

-

G

-

R

-

Y

-

D

-

E

-

S

-

P

-

E

-

T

-

M

-

A

-

Q

-

I

-

E

-

A

-

F

F

V

A

R

M

D

D

G

G

L

L

V

V

N

N

I

I

V

V

G

G

C

C

G

G

S

S

T

T

P

P

A

D

H

H

I

I

R

R

A

E

I

I

A

A

E

E

A

A

V

V

Q

K

K

N

Y

C

P

K

P

P

R

R

Q

V

V

P

P

P

E

A

-

T

-

A

I

F

E

E

R

G

R

H

M

M

R

L

L

L

S

S

G

G

L

L

E

E

P

P

F

F

T

R

L

I

T

G

D

P

E

Y

I

T

P

N

F

F

V

V

N

N

V

I

G

G

E
|
E

R

R

T

C

N

N

V

V

T

A

G
|
G

S

S

A
x
R

K

K

F

F

R

A

K

K

L

L

I

I

T

M

T

A

G

G

D

N

Y

Y

A

E

A

A

L

L

D

C

V

V

A

A

R

K

D

V

Q

Q

V

V

A

E

N

M

G

G

A

A

Q

Q

I

V

I

L

D

D

I

V

N

N

M

M

D

D

E

D

G

G

L

M

I

L

D

D

S

G

T

P

R

S

A

A

M

M

V

T

E

R

F

F

L

C

N

N

L

L

V

I

A

A

S

S

E

E

P

P

D

D

I

I

A

A

C

K

V

V

P

P

V

L

M

C

I

I

D

D

S

S

K

N

W

F

E

A

V

V

I

I

E

E

A

A

G

G

L

L

K

K

C

C

V

C

Q

Q

G

G

K

K

A

C

L

I

V

V

N
|
N

S

S

I

I

S

S

L

L

K

K

E

E

G

G

E

E

E

D

A

D

F

F

L

L

H

E

H

K

A

A

R

R

L

K

V

I

R

K

A

K

Y

Y

G

G

A

A

V

M

V

V

M
|
M

A

A

F

F

D

D

E

E

K

E

G

G

Q

Q

A

A

D

T

S

E

R

T

A

D

R

T

K

K

V

I

E

R

I

V

C

C

R

T

R

R

A

A

Y

Y

R

H

L

L

T

V

E

K

V

L

G

G

F

F

P

N

P

P

E

N

D

D

I

I

F

F

D
|
D

P

P

N

N

I

I

F

L

A

T

V

I

A

G

T

T

G

G

I

M

D

E

E

E

H

H

N

N

N

L

Y

Y

G

A

V

I

D

N

F

F

I

I

E

H

A

A

T

T

H

K

E

V

I

I

I

K

A

E

T

T

L

L

P

P

H

G

V

A

H

R

V

I

S

S

G

G

G
|
G

V

L

S
|
S

N
|
N

L

L

S

S

F
|
F

S

S

F

F

R
|
R

G

G

N

M

E

E

P

A

V

I

R
|
R

E

E

A

A

M

M

H

H

A

G

V

V

F

F

L

L

Y

Y

H

H

A

A

I

I

Q

K

A

S

G

G

M

M

D

D

M

M

G

G

I

I

V

V

N

N

A

A

G

G

Q

N

L

L

A

P

V

V

Y

Y

D

D

A

D

I

I

D

H

P

K

E

E

L

L

R

L

E

Q

A

L

C

C

E

E

D

D

V

L

V

I

L

W

N

N

R

K

R

D

P

P

D

E

A

A

T

T

E

E

R

K

L

L

E

R

I

Y

A

A

E

Q

binding (6s)-5,6,7,8-tetrahydrofolate: E336 (= E375), G342 (= G381), R344 (≠ A383), N430 (= N469), M458 (= M497), D497 (= D536), G536 (= G575), S538 (= S577), N539 (= N578), F542 (= F581), R545 (= R584), R551 (= R590)

3bulA E. Coli i690c/g743c meth c-terminal fragment (649-1227) (see paper)
60% identity, 46% coverage: 667:1246/1256 of query aligns to 4:574/577 of 3bulA

query
sites
3bulA

W

W

R

R

Q

S

W

W

P

E

V

V

A

N

K

K

R

R

L

L

E

E

H

Y

A

S

L

L

V

V

N

K

G

G

I

I

T

T

E

E

F

F

I

I

E

E

A

Q

D

D

T

T

E

E

A

A

R

R

L

Q

A

Q

A

A

E

T

R

R

P

P

L

C

H

E

V

V

I

I

E

E

G

G

P

P

L

L

M

M

A

D

G

G

M

M

N

N

V

V

G

G

D

D

L

L

F

F

G

G

A

E

G

G

K

K

M

M

F

F

L

L

P

P

Q

Q

V

V

K

K

S

S

A

A

R

R

V

V

M

M

K

K

Q

Q

A

A

V

V

A

A

V

Y

L

L

L

E

P

P

Y

F

M

I

E

E

A

A

E

S

K

K

L

-

A

-

N

-

G

-

E

E

G

Q

T

C

R

K

A

T

S

N

A

-

G

G

K

K

I

M

L

V

M

I

A

A

T

T

V

V

K

K

G

G

D
|
D

V

V

H
|
H

D

D

I

I

G

G

K

K

N

N

I

I

V
|
V

G

G

V

V

L

L

A

Q

C

C

N

N

Y

Y

E

E

I

I

I

V

D

D

L

L

G

G

V

V

M

M

V

V

P

P

S

A

A

E

K

K

I

I

L

L

E

R

V

T

A

A

R

K

Q

E

E

V

K

N

V

A

D

D

A

L

I

I

G
|
G

L
|
L

S
|
S

G

G

L
|
L

I
|
I

T
|
T

P

P

S
|
S

L

L

D

D

E

E

M

M

V

V

H

N

V

V

A

A

S

K

E

E

L

M

E

E

R

R

E

Q

G

G

F

F

D

T

I

I

P

P

L

L

I

I

G
|
G

A

A

T

T

S

S

R

K

V

A

H

H

T

T

A

A

V

V

K

K

I

I

N

E

P

Q

R

N

Y

Y

G

S

L

-

G

G

Q

P

T

T

V

V

Y

Y

V

V

T
x
Q

D
x
N

A
|
A

S

S

R

R

A
x
T

V

V

G

G

V

V

S

A

L

L

S

S

P

D

E

T

A

Q

R

R

D

D

G

D

Y

F

K

V

E

A

T

R

V

T

R

R

A

K

E

E

Y

Y

L

E

K

T

V

V

A

R

D

I

A

Q

H

H

A

G

R

R

N

K

E

K

A

P

E

R

K

T

R

P

L

V

P

T

L

L

S

E

Q

A

A

A

R

R

A

D

N

N

A

D

S

F

K

A

L

F

D

D

W

W

D

Q

A

A

Y

Y

R

T

P

P

K

P

T

V

P

A

S

H

F

R

L

L

G

G

T

V

R

Q

V

E

F

V

E

E

S

A

W

-

D

S

L

I

A

E

E

T

L

L

A

R

R

N

Y

Y

I

I

D

D

W

W

T

T

P

P

F

F

Q
x
M

T

T

W

W

E

S

L

L

K

A

G

G

V

K

Y

Y

P

P

R

R

I

I

L

L

D

E

D

D

E

E

H

V

Q

V

G

G

P

V

A

E

A

A

R

Q

Q

R

L

L

F

F

A

K

D

D

A

A

Q

N

A

D

M

M

L

L

E

D

K

K

I

L

I

S

A

A

E

E

K

K

W

T

F

L

A

N

P

P

K

R

A

G

V

V

G

G

F

L

W

F

P

P

A

A

G

N

S

R

A

V

G

G

D

D

I

I

R

E

L

I

F

Y

T

R

D

D

E

E

R

T

R

R

E

T

R

H

E

V

L

I

A

N

T

V

F

S

F

H

T

H

L

L

R

R

Q

Q

L

-

A

T

K

E

R

K

D

T

G

G

R

F

P

A

N

N

V

Y

A

C

L

L

A

A

D

D

F

F

V

V

A

A

P

P

V

K

E

L

S

S

G

G

R

K

R

A

D

D

Y

Y

L

I

G

G

G

A

F

F

V

A

V

V

T

T

A

G

G

G

I

L

E

E

V

D

A

A

I

L

A

A

E

D

R

A

F

F

E

E

R

A

A

Q

N

H

D

D

Y

Y

S

N

S

K

I

I

L

M

V

V

K

K

A

A

L

L

A

A

D
|
D

R

R

F

L

A

A

E

E

A

A

F

F

A

A

E

E

R

Y

M

L

H

H

E

E

Y

R

V

V

R

R

K

K

E

V

L

Y

W

W

G

G

Y

Y

A

A

P

P

D

N

E

E

S

N

F

L

T

S

P

N

Q

E

E

E

L

L

I

I

A

R

E

E

P

N

Y

Y

T

Q

G

G

I

I

R

R

P

P

A
|
A

P
|
P

G
|
G

Y
|
Y

P

P

A

A

Q

C

P

P

D

E

H
|
H

T

T

E

E

K
|
K

E

A

T

T

L

I

F

W

R

E

L

L

D

E

A

V

E

E

A

K

A

H

I

T

G

G

V

M

R

K

L

L

T

T

E

E

N

S

Y

F

A

A

M
|
M

W

W

P

P

G
|
G

S

A

S

S

V
|
V

S
|
S

G

G

L

W

Y

Y

V

F

G

S

H

H

P

P

D

D

A

S

Y

K

Y

Y

F

Y

G

A

V

V

A

A

K

Q

I

I

E

Q

R

R

D

D

Q

Q

V

V

E

E

D

D

Y

Y

A

A

T

R

R

R

K

K

R

G

M

M

G

S

V

V

R

T

E

E

V

V

E

E

R

R

W

W

L

L

S

A

P

P

I

N

L

L

N

G

Y

Y

active site: D107 (= D776), H109 (= H778), S160 (= S829)
binding cobalamin: H109 (= H778), V116 (= V785), G152 (= G821), L153 (= L822), S154 (= S823), L156 (= L825), I157 (= I826), T158 (= T827), G183 (= G852), G184 (= G853), Q208 (≠ T878), N209 (≠ D879), A210 (= A880), T213 (≠ A883), M302 (≠ Q973), D443 (= D1115), A486 (= A1158), P487 (= P1159), G488 (= G1160), Y489 (= Y1161), H495 (= H1167), K498 (= K1170), M521 (= M1193), G524 (= G1196), V527 (= V1199), S528 (= S1200)

3ivaA Structure of the b12-dependent methionine synthase (meth) c-teminal half with adohcy bound (see paper)
60% identity, 46% coverage: 667:1246/1256 of query aligns to 4:574/576 of 3ivaA

query
sites
3ivaA

W

W

R

R

Q

S

W

W

P

E

V

V

A

N

K

K

R

R

L

L

E

E

H

Y

A

S

L

L

V

V

N

K

G

G

I

I

T

T

E

E

F

F

I

I

E

E

A

Q

D

D

T

T

E

E

A

A

R

R

L

Q

A

Q

A

A

E

T

R

R

P

P

L

C

H

E

V

V

I

I

E

E

G

G

P

P

L

L

M

M

A

D

G

G

M

M

N

N

V

V

G

G

D

D

L

L

F

F

G

G

A

E

G

G

K

K

M

M

F

F

L

L

P

P

Q

Q

V

V

K

K

S

S

A

A

R

R

V

V

M

M

K

K

Q

Q

A

A

V

V

A

A

V

Y

L

L

L

E

P

P

Y

F

M

I

E

E

A

A

E

S

K

K

L

-

A

-

N

-

G

-

E

E

G

Q

T

C

R

K

A

T

S

N

A

-

G

G

K

K

I

M

L

V

M

I

A

A

T

T

V

V

K

K

G

G

D
|
D

V

V

H
|
H

D

D

I

I

G
|
G

K

K

N

N

I

I

V
|
V

G

G

V

V

L

L

A

Q

C

C

N

N

Y

Y

E

E

I

I

I

V

D

D

L

L

G

G

V

V

M

M

V

V

P

P

S

A

A

E

K

K

I

I

L

L

E

R

V

T

A

A

R

K

Q

E

E

V

K

N

V

A

D

D

A

L

I

I

G
|
G

L
|
L

S
|
S

G

G

L
|
L

I
|
I

T
|
T

P

P

S
|
S

L

L

D

D

E

E

M

M

V

V

H

N

V

V

A

A

S

K

E

E

L

M

E

E

R

R

E

Q

G

G

F

F

D

T

I

I

P

P

L

L

I

I

G
|
G

A

A

T

T

S

S

R

K

V

A

H

H

T

T

A

A

V

V

K

K

I

I

N

E

P

Q

R

N

Y

Y

G

S

L

-

G

G

Q

P

T

T

V

V

Y

Y

V

V

T
x
Q

D
x
N

A

A

S

S

R

R

A

T

V

V

G

G

V

V

S

A

L

L

S

S

P

D

E

T

A

Q

R

R

D

D

G

D

Y

F

K

V

E

A

T

R

V

T

R

R

A

K

E

E

Y

Y

L

E

K

T

V

V

A

R

D

I

A

Q

H

H

A

G

R

R

N

K

E

K

A

P

E

R

K

T

R

P

L

V

P

T

L

L

S

E

Q

A

A

A

R

R

A

D

N

N

A

D

S

F

K

A

L

F

D

D

W

W

D

Q

A

A

Y

Y

R

T

P

P

K

P

T

V

P

A

S

H

F

R

L

L

G

G

T

V

R

Q

V

E

F

V

E

E

S

A

W

-

D

S

L

I

A

E

E

T

L

L

A

R

R

N

Y

Y

I

I

D

D

W

W

T

T

P

P

F

F

Q

M

T
|
T

W

W

E

S

L

L

K

A

G

G

V

K

Y

Y

P

P

R

R

I

I

L

L

D

E

D

D

E

E

H

V

Q

V

G

G

P

V

A

E

A

A

R

Q

Q

R

L

L

F

F

A

K

D

D

A

A

Q

N

A

D

M

M

L

L

E

D

K

K

I

L

I

S

A

A

E

E

K

K

W

T

F

L

A

N

P

P

K

R

A

G

V

V

G

G

F

L

W

F

P

P

A

A

G

N

S

R

A

V

G

G

D

D

I

I

R

E

L

I

F

Y

T

R

D

D

E

E

R

T

R

R

E

T

R

H

E

V

L

I

A

N

T

V

F

S

F

H

T

H

L

L

R

R

Q

Q

L

-

A

T

K

E

R

K

D

T

G

G

R

F

P

A

N

N

V

Y

A

C

L

L

A

A

D

D

F

F

V

V

A

A

P

P

V

K

E

L

S

S

G

G

R

K

R

A

D

D

Y

Y

L

I

G

G

G

A

F

F

V

A

V

V

T

T

A

G

G

G

I

L

E

E

V

D

A

A

I

L

A

A

E

D

R

A

F

F

E

E

R

A

A

Q

N

H

D

D

Y

Y

S

N

S

K

I

I

L

M

V

V

K

K

A

A

L

L

A

A

D
|
D

R

R

F

L

A

A

E
|
E

A

A

F

F

A

A

E

E

R

Y

M

L

H

H

E

E

Y

R

V

V

R

R

K

K

E

V

L

Y

W

W

G

G

Y

Y

A

A

P

P

D

N

E

E

S

N

F

L

T

S

P

N

Q

E

E

E

L

L

I

I

A

R

E

E

P

N

Y

Y

T

Q

G

G

I

I

R
|
R

P
|
P

A
|
A

P

P

G
|
G

Y
|
Y

P

P

A
|
A

Q

C

P

P

D

E

H
|
H

T

T

E

E

K

K

E

A

T

T

L

I

F

W

R

E

L

L

D

E

A

V

E

E

A

K

A

H

I

T

G

G

V

M

R

K

L

L

T

T

E

E

N

S

Y

F

A
|
A

M
|
M

W

W

P

P

G
|
G

S

A

S

S

V
|
V

S
|
S

G

G

L

W

Y

Y

V

F

G

S

H

H

P

P

D

D

A

S

Y

K

Y
|
Y

F

Y

G

A

V

V

A

A

K

Q

I

I

E

Q

R

R

D

D

Q

Q

V

V

E

E

D

D

Y

Y

A

A

T

R

R

R

K

K

R

G

M

M

G

S

V

V

R

T

E

E

V

V

E

E

R

R

W

W

L

L

S

A

P

P

I

N

L

L

N

G

Y

Y

active site: D107 (= D776), H109 (= H778), S160 (= S829)
binding cobalamin: H109 (= H778), G112 (= G781), V116 (= V785), G152 (= G821), L153 (= L822), S154 (= S823), L156 (= L825), I157 (= I826), T158 (= T827), G183 (= G852), G184 (= G853), Q208 (≠ T878), N209 (≠ D879), T303 (= T974), D443 (= D1115), A486 (= A1158), G488 (= G1160), Y489 (= Y1161), H495 (= H1167), A520 (= A1192), M521 (= M1193), G524 (= G1196), V527 (= V1199), S528 (= S1200)
binding s-adenosyl-l-homocysteine: E447 (= E1119), R484 (= R1156), P485 (= P1157), Y489 (= Y1161), A491 (= A1163), Y539 (= Y1211)

8g3hA Structure of cobalamin-dependent methionine synthase (meth) in a resting state (see paper)
36% identity, 70% coverage: 20:897/1256 of query aligns to 6:839/841 of 8g3hA

query
sites
8g3hA

F

L

R

R

A

A

L

L

N

S

Q

Q

A

-

E

-

R

R

I

V

L

L

I

V

M

F

D

D

G

G

A

A

M

M

G

G

T

T

E

E

I

L

Q

Q

Q

K

L

R

G

D

F

L

V

T

E

P

D

E

H

D

F

Y

R

G

G

E

E

E

R

A

F

Y

G

Y

G

G

C

C

A

P

C

-

H

-

Q

-

G

-

N

-

D

E

L

V

L

L

T

N

L

R

T

T

Q

R

P

P

K

D

A

V

I

V

E

R

E

E

I

I

H

H

Y

L

R

S

Y

Y

A

L

L

E

A

A

G

G

A

A

D

E

I

V

L

I

E

E

T

T

N

N

T

S

F

F

S

G

S

A

T

L

R

R

I

H

A

V

Q

L

A

A

D

E

Y

Y

G

G

M

L

E

G

D

E

M

E

V

A

Y

E

D

E

L

L

N

A

R

Y

D

R

G

A

A

A

R

R

L

I

A

A

R

K

R

E

A

A

K

E

R

P

A

Y

E

G

A

A

E

-

D

-

G

-

R

-

F

F

V

V

A

A

G

G

A

A

L

L

G

G

P

P

T

G

N

T

R

K

T

L

A

V

S

S

I

L

S

G

P

-

D

-

V

-

N

-

P

-

G

-

Y

-

R

-

A

Q

V

I

S

S

F

W

D

E

L

L

R

F

L

S

A

A

Y

Y

A

K

E

E

Q

A

V

V

R

R

G

G

L

L

I

V

D

R

G

G

A

V

D

D

I

L

I

I

L

L

I

L

E

E

T

T

I

A

F

Q

D

D

T

I

L

L

N

Q

A

V

K

R

A

C

A

A

I

V

F

L

A

A

T

A

Q

R

E

E

V

A

F

M

A

A

E

E

K

L

K

G

I

V

H

E

L

L

P

P

V

L

M

Q

V

V

S

Q

G

V

T

T

I

F

T

-

D

E

L

A

S

T

G

G

R

T

T

M

L

L

S

V

G

G

Q

T

T

D

P

E

T

Q

A

A

F

A

W

L

Y

A

S

A

V

L

R

E

H

S

A

L

A

P

P

I

F

D

T

V

I

V

G

G

L

M

N

N

C

C

A

A

L

T

G

G

A

P

D

D

A

L

M

M

R

D

A

A

H

K

I

I

D

R

E

Y

L

F

S

A

T

Q

V

E

A

S

D

T

T

R

L

F

V

V

C

A

A

C

Y

L

P

P

N

N

A

A

G

G

L

L

P

P

-

R

N

N

E

E

F

G

G

G

R

R

-

V

Y

Y

D

D

E

L

S

T

P

P

E

E

T

E

M

L

A

A

A

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Q

W

I

H

E

L

A

K

F

F

V

V

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T

D

E

G

Y

L

G

V

V

N

N

I

A

V

V

G

G

C

C

G

G

S

T

T

G

P

P

A

E

H

H

I

I

R

R

A

K

I

V

A

A

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E

A

A

V

V

Q

G

K

G

Y

R

P

P

-

S

-

P

-

V

-

H

-

K

-

T

-

A

-

F

P

P

R

P

Q

Q

V

V

P

A

E

S

I

L

E

-

R

-

M

-

R

-

L

-

S

-

G

-

L

Y

E

Q

P

A

F

V

T

P

L

L

T

R

D
x
Q

E

E

I
x
T

P
x
S

F

L

V

L

N

L

V

V

G

G

E

E

R

R

T

L

N

N

V

A

T

T

G

G

S

S

A

K

K

R

F

F

R

R

K

E

L

L

I

L

T

F

T

A

G

G

D

D

Y

L

A

E

A

G

A

I

L

L

D

A

V

L

A

A

R

Q

D

E

Q

Q

V

V

A

A

N

E

G

G

A

A

Q

H

I

V

I

L

D

D

I

L

N

S

M

V

D

A

E

W

G

T

L

G

I

R

D

D

S

E

T

L

R

E

A

D

M

M

V

K

E

R

F

V

L

L

N

S

L

K

V

L

A

A

S

T

E

G

P

-

D

-

I

-

A

V

C

T

V

V

P

P

V

F

M

M

I

V

D

D

S

S

S

T

K

S

W

P

E

E

V

V

I

M

E

E

A

E

G

A

L

L

K

K

C

R

V

L

Q

P

G

G

K

R

A

A

L

I

V

L

N

N

S

S

I

A

S

N

L

L

K

E

E

D

G

G

E

L

E

E

A

K

F

F

L

D

H

R

H

V

A

A

R

S

L

L

V

A

R

K

A

A

Y

H

G

G

A

A

V

L

V

V

V

A

M

L

A

A

F

I

D

D

E

E

K

E

G

G

Q

M

A

A

D

K

S

T

R

R

A

V

R

K

K

K

V

V

E

E

I

V

C

A

R

L

R

R

A

M

Y

Y

R

E

L

R

L

L

T

T

E

E

E

H

V

H

G

G

F

L

P

R

P

P

E

E

D

D

I

L

F

F

D

D

P

L

N

L

I

T

F

F

A

P

V

I

A

T

T

Q

G

G

I

D

D

E

E

E

H

T

N

R

N

P

Y

L

G

A

V

R

D

E

F

T

I

L

E

L

A

A

T

L

H

E

E

E

I

L

I

R

A

E

T

R

L

L

P

P

H

G

V

V

H

G

V

F

S

V

G

L

G

G

V

V

S

S

N

N

L

V

S

S

F

F

S

G

F

L

R

K

G

P

N

K

E

-

P

-

V

A

R

R

E

R

A

V

M

L

H

N

A

S

V

V

F

F

L

L

Y

D

H

E

A

A

I

R

Q

K

A

K

G

G

M

L

D

T

M

A

G

A

I

I

V

V

N

D

A

A

G

G

Q

K

L

I

A

L

V

P

Y

I

D

S

A

Q

I

I

D

P

P

E

E

E

L

A

R

Y

E

A

A

L

C

A

E

L

D

D

V

L

V

I

L

Y

N

D

R

R

P

-

D

E

A

G

T

Q

E

D

R

P

L

L

L

F

E

A

I

F

A

I

E

R

R

F

Y

F

R

E

G

E

Q

H

G

K

G

E

A

V

Q

L

G

A

K

E

E

D

K

K

D

E

L

-

A

A

W

F

R

Q

Q

A

W

L

P

P

V

V

A

E

K

E

R

R

L

L

E

R

H

R

A

R

L

V

V

L

N

E

G

G

I

K

T

R

E

V

F

G

I

L

E

E

A

E

D

D

T

L

E

A

E

E

A

A

R

-

L

L

A

G

A

R

E

M

R

R

P

P

L

L

H

E

V

I

I

I

E

N

G

G

P

P

L

L

M

L

A

E

G

A

M

M

N

K

V

E

V

V

G

G

D

E

L

L

F
|
F

G

G

A

A

G

G

K

K

M

M

F

Q

L

L

P

P

Q

F

V
|
V

V

L

K

Q

S

A

A

A

R

E

V

V

M

M

K
|
K

Q

Q

A

A

V

V

A

A

V

Y

L

L

L

E

P

P

Y

H

M

M

E

E

A

K

E

K

K

-

L

-

A

-

N

-

G

-

G

G

E

E

G

G

T

K

R

-

A

-

S

-

A

-

G

G

K

K

I

L

L

V

M

L

A

A

T

T

V

V

K

K

G
|
G

D

D

V
|
V

H
|
H

D
|
D

I
|
I

G
|
G

K

K

N

N

I

L

V
|
V

G

D

V

I

L

L

A

T

C

N

N

N

N

G

Y

Y

E

T

I

V

I

Y

D

N

L

L

G

G

V

I

M

K

V

V

P

P

S

I

A

E

K

E

I

M

L

L

E

K

V

A

A

V

R

D

Q

E

E

V

K

K

V

P

D

H

A

A

I

L

G

G

L
x
M

S
|
S

G

G

L
|
L

I

L

T
x
V

P

K

S

S

L

T

D

Q

E

V

M

M

V

K

H

E

V

N

A

L

S

E

E

Y

L

M

E

R

R

A

E

R

G

G

F

Y

D

T

I

L

P

P

L

V

L
x
I

I
x
L

G
|
G

A
|
A

T

A

T

L

S

T

R

R

-

A

-

Y

V

V

H

E

T

E

A

L

V

R

K

S

I

I

N

Y

P

P

R

-

Y

-

G

-

L

-

G

-

Q

E

T

V

V

Y

Y
|
Y

V
x
A

T
x
E

D
|
D

A

A

S

F

R

E

A

G

V

L

G

A

V

L

V

M

S

E

L

L

L

T

S

G

P

H

E

R

A

P

R

K

D

D

binding cobalamin: Q328 (≠ D366), T330 (≠ I368), S331 (≠ P369), F675 (= F721), V685 (= V731), K693 (= K739), G720 (= G775), V722 (= V777), H723 (= H778), D724 (= D779), I725 (= I780), G726 (= G781), V730 (= V785), M767 (≠ L822), S768 (= S823), L770 (= L825), V772 (≠ T827), I795 (≠ L850), L796 (≠ I851), G797 (= G852), G798 (= G853), A799 (= A854), Y818 (= Y876), A819 (≠ V877), E820 (≠ T878), D821 (= D879)

3k13C Structure of the pterin-binding domain metr of 5- methyltetrahydrofolate-homocysteine methyltransferase from bacteroides thetaiotaomicron
70% identity, 23% coverage: 367:650/1256 of query aligns to 1:283/287 of 3k13C

query
sites
3k13C

E

E

I

I

P

N

F

F

V

V

N

N

V

I

G

G

E
|
E

R

R

T

C

N

N

V

V

T

A

G
|
G

S

S

A
x
R

K

K

F

F

R

L

K

R

L

L

I

V

T

N

T

E

G

K

D

K

Y

Y

A

D

A

E

A

A

L

L

D

S

V

I

A

A

R

R

D

Q

Q

Q

V

V

A

E

N

D

G

G

A

A

Q

L

I

V

I

I

D

D

I

V

N

N

M

M

D

D

E

D

G

G

L

L

I

L

D

D

S

A

T

R

R

T

A

E

M

M

V

T

E

T

F

F

L

L

N

N

L

L

V

I

A

M

S

S

E

E

P

P

D

E

I

I

A

A

C

R

V

V

P

P

V

V

M

M

I

I

D

D

S

S

K

K

W

W

E

E

V

V

I

I

E

E

A

A

G

G

L

L

K

K

C

C

V

L

Q

Q

G

G

K

K

A

S

L

I

V

V

N
|
N

S

S

I

I

S

S

L

L

K

K

E

E

G

G

E

E

A

V

F

F

L

L

H

E

H

H

A

A

R

R

L

I

V

I

R

K

A

Q

Y

Y

G

G

A

A

V

T

V

V

M

M

A

A

F

F

D

D

E

E

K

K

G

G

Q

Q

A

A

D

D

S

T

R

A

A

A

R

R

K

K

V

I

E

E

I

V

C

C

R

E

R

R

A

A

Y

Y

R

R

L

L

T

V

E

D

E

K

V

V

G

G

F

F

P

N

P

P

E

H

D

D

I

I

F

F

D
|
D

P

P

N

N

I

V

F

L

A

A

V

V

A

A

T

T

G

G

I

I

D

E

E

E

H

H

N

N

Y

Y

G

A

V

V

D

D

F

F

I

I

E

E

A

A

T

T

H

G

E

W

I

I

I

R

A

K

T

N

L

L

P

P

H

G

V

A

H

H

V

V

S

S

G

G

G
|
G

V

V

S
|
S

N
|
N

L

L

S

S

F

F

S

S

F

F

R
|
R

G

G

N

N

E

N

P

Y

V

I

R
|
R

E

E

A

A

M

M

H

H

A

A

V

V

F

F

L

L

Y

Y

H

H

A

A

I

I

Q

Q

A

Q

G

G

M

M

D

D

M

M

G

G

I
|
I

V

V

N

N

A

P

G

G

Q

S

L

V

A

-

V

L

Y

Y

D

S

A

D

I

I

D

P

P

A

E

D

L

T

R

L

E

E

A

K

C

I

E

E

D

D

V

V

L

L

N

N

R

R

P

P

D

D

A

A

T

A

E

E

R

R

L

L

L

I

E

E

I

L

A

A

E

E

binding n-[4-({[(6s)-2-amino-4-hydroxy-5-methyl-5,6,7,8-tetrahydropteridin-6-yl]methyl}amino)benzoyl]-l-glutamic acid: E9 (= E375), G15 (= G381), R17 (≠ A383), N103 (= N469), D170 (= D536), G209 (= G575), S211 (= S577), N212 (= N578), R218 (= R584), R224 (= R590), I244 (= I610)

1mskA Methionine synthase (activation domain) (see paper)
56% identity, 26% coverage: 926:1246/1256 of query aligns to 6:324/327 of 1mskA

query
sites
1mskA

L

L

S

E

Q

A

A

A

R

R

A

D

N

N

A

D

S

F

K

A

L

F

D

D

W

W

D

Q

A

A

Y

Y

R

T

P

P

K

P

T

V

P

A

S

H

F

R

L

L

G

G

T

V

R

Q

V

E

F

V

E

E

S

A

W

-

D

S

L

I

A

E

E

T

L

L

A

R

R

N

Y

Y

I

I

D
|
D

W

W

T

T

P

P

F

F

Q

M

T

T

W

W

E

S

L

L

K

A

G

G

V

K

Y

Y

P

P

R

R

I

I

L

L

D

E

D

D

E

E

H

V

Q

V

G

G

P

V

A

E

A

A

R

Q

Q

R

L

L

F

F

A

K

D

D

A

A

Q

N

A

D

M

M

L

L

E

D

K

K

I

L

I

S

A

A

E

E

K

K

W

T

F

L

A

N

P

P

K

R

A

G

V

V

G

G

F

L

W

F

P

P

A

A

G

N

S

R

A

V

G

G

D

D

I

I

R

E

L

I

F

Y

T

R

D

D

E

E

R

T

R

R

E

T

R

H

E

V

L

I

A

N

T

V

F

S

F

H

T

H

L

L

R

R

Q

Q

L

T

A

E

K

K

R

T

D

-

G

G

R

F

P

A

N

N

V

Y

A

C

L

L

A

A

D

D

F

F

V

V

A

A

P

P

V

K

E

L

S

S

G

G

R

K

R

A

D

D

Y

Y

L

I

G

G

G

A

F

F

V

A

V

V

T

T

A

G

G

G

I

L

E

E

V

D

A

A

I

L

A

A

E

D

R

A

F

F

E

E

R

A

A

Q

N

H

D

D

Y

Y

S

N

S

K

I

I

L

M

V

V

K

K

A

A

L

L

A

A

D

D

R

R

F

L

A

A

E

E

A

A

F

F

A

A

E

E

R

Y

M

L

H

H

E

E

Y

R

V

V

R

R

K

K

E

V

L

Y

W

W

G

G

Y

Y

A

A

P

P

D

N

E

E

S

N

F

L

T

S

P

N

Q

E

E

E

L

L

I

I

A

R

E

E

P

N

Y

Y

T

Q

G

G

I

I

R
|
R

P
|
P

A

A

P

P

G

G

Y
|
Y

P

P

A
|
A

Q

C

P

P

D

E

H

H

T

T

E

E

K

K

E

A

T

T

L

I

F

W

R

E

L

L

D

E

A

V

E

E

A

K

A

H

I

T

G

G

V

M

R

K

L

L

T

T

E

E

N

S

Y

F

A

A

M

M

W

W

P

P

G

G

S

A

S

S

V

V

S

S

G

G

L

W

Y

Y

V

F

G

S

H

H

P

P

D

D

A

S

Y

K

Y
|
Y

F

Y

G

A

V

V

A

A

K

Q

I

I

E

Q

R

R

D

D

Q

Q

V

V

E

E

D

D

Y

Y

A

A

T

R

R

R

K

K

R

G

M

M

G

S

V

V

R

T

E

E

V

V

E

E

R

R

W

W

L

L

S

A

P

P

I

N

L

L

N

G

Y

Y

binding s-adenosylmethionine: D46 (= D967), R234 (= R1156), P235 (= P1157), Y239 (= Y1161), A241 (= A1163), Y289 (= Y1211)

6bdyA Crystal structure of the meth reactivation domain bound to sinefungin (see paper)
56% identity, 26% coverage: 926:1246/1256 of query aligns to 6:324/326 of 6bdyA

query
sites
6bdyA

L

L

S

E

Q

A

A

A

R

R

A

D

N

N

A

D

S

F

K

A

L

F

D

D

W

W

D

Q

A

A

Y

Y

R

T

P

P

K

P

T

V

P

A

S

H

F

R

L

L

G

G

T

V

R

Q

V

E

F

V

E

E

S

A

W

-

D

S

L

I

A

E

E

T

L

L

A

R

R

N

Y

Y

I

I

D
|
D

W

W

T

T

P

P

F

F

Q

M

T

T

W

W

E

S

L

L

K

A

G

G

V

K

Y

Y

P

P

R

R

I

I

L

L

D

E

D

D

E

E

H

V

Q

V

G

G

P

V

A

E

A

A

R

Q

Q

R

L

L

F

F

A

K

D

D

A

A

Q

N

A

D

M

M

L

L

E

D

K

K

I

L

I

S

A

A

E

E

K

K

W

T

F

L

A

N

P

P

K

R

A

G

V

V

G

G

F

L

W

F

P

P

A

A

G

N

S

R

A

V

G

G

D

D

I

I

R

E

L

I

F

Y

T

R

D

D

E

E

R

T

R

R

E

T

R

H

E

V

L

I

A

N

T

V

F

S

F

H

T

H

L

L

R

R

Q

Q

L

T

A

E

K

K

R

T

D

-

G

G

R

F

P

A

N

N

V

Y

A

C

L

L

A

A

D

D

F

F

V

V

A

A

P

P

V

K

E

L

S

S

G

G

R

K

R

A

D

D

Y

Y

L

I

G

G

G

A

F

F

V

A

V

V

T

T

A

G

G

G

I

L

E

E

V

D

A

A

I

L

A

A

E

D

R

A

F

F

E

E

R

A

A

Q

N

H

D

D

Y

Y

S

N

S

K

I

I

L

M

V

V

K

K

A

A

L

L

A

A

D

D

R

R

F

L

A

A

E

E

A

A

F

F

A

A

E

E

R

Y

M

L

H

H

E

E

Y

R

V

V

R

R

K

K

E

V

L

Y

W

W

G

G

Y

Y

A

A

P

P

D

N

E

E

S

N

F

L

T

S

P

N

Q

E

E

E

L

L

I

I

A

R

E

E

P

N

Y

Y

T

Q

G

G

I

I

R
|
R

P
|
P

A
|
A

P

P

G

G

Y
|
Y

P
|
P

A
|
A

Q

C

P

P

D

E

H

H

T

T

E

E

K

K

E

A

T

T

L

I

F

W

R

E

L

L

D

E

A

V

E

E

A

K

A

H

I

T

G

G

V

M

R

K

L

L

T

T

E

E

N

S

Y

F

A

A

M

M

W

W

P

P

G

G

S

A

S

S

V

V

S

S

G

G

L

W

Y

Y

V

F

G

S

H

H

P

P

D

D

A

S

Y

K

Y
|
Y

F

Y

G

A

V

V

A

A

K

Q

I

I

E

Q

R

R

D

D

Q

Q

V

V

E

E

D

D

Y

Y

A

A

T

R

R

R

K

K

R

G

M

M

G

S

V

V

R

T

E

E

V

V

E

E

R

R

W

W

L

L

S

A

P

P

I

N

L

L

N

G

Y

Y

binding sinefungin: D46 (= D967), R234 (= R1156), P235 (= P1157), A236 (= A1158), Y239 (= Y1161), P240 (= P1162), A241 (= A1163), Y289 (= Y1211)

1bmtA How a protein binds b12: a 3.O angstrom x-ray structure of the b12- binding domains of methionine synthase (see paper)
68% identity, 20% coverage: 667:916/1256 of query aligns to 4:246/246 of 1bmtA

query
sites
1bmtA

W

W

R

R

Q

S

W

W

P

E

V

V

A

N

K

K

R

R

L

L

E

E

H

Y

A

S

L

L

V

V

N

K

G

G

I

I

T

T

E

E

F

F

I

I

E

E

A

Q

D

D

T

T

E

E

A

A

R

R

L

Q

A

Q

A

A

E

T

R

R

P

P

L

I

H

E

V

V

I

I

E
|
E

G

G

P

P

L

L

M
|
M

A

D

G

G

M
|
M

N

N

V

V

G
|
G

D

D

L

L

F

F

G

G

A

E

G

G

K

K

M

M

F

F

L
|
L

P

P

Q

Q

V
|
V

V

V

K

K

S

S

A

A

R

R

V

V

M

M

K

K

Q

Q

A

A

V

V

A

A

V

Y

L

L

L

E

P

P

Y

F

M

I

E

E

A

A

E

S

K

K

L

E

A

Q

N

G

G

-

E

-

G

-

T

-

R

-

A

K

S

T

A

N

G

G

K

K

I

M

L

V

M

I

A

A

T

T

V

V

K

K

G

G

D
|
D

V
|
V

H
|
H

D
|
D

I
|
I

G

G

K

K

N

N

I
|
I

V

V

G

G

V

V

L

L

A

Q

C

C

N

N

Y

Y

E

E

I

I

I

V

D

D

L

L

G

G

V

V

M

M

V

V

P

P

S

A

A

E

K

K

I

I

L

L

E

R

V

T

A

A

R

K

Q

E

E

V

K

N

V

A

D

D

A

L

I

I

G
|
G

L
|
L

S
|
S

G

G

L
|
L

I
|
I

T
|
T

P

P

S
|
S

L

L

D

D

E

E

M

M

V

V

H

N

V

V

A

A

S

K

E

E

L

M

E

E

R

R

E

Q

G

G

F

F

D

T

I

I

P

P

L

L

I

I

G
|
G

A
|
A

T

T

S

S

R

K

V

A

H

H

T

T

A

A

V

V

K

K

I

I

N

E

P

Q

R

N

Y

Y

G

S

L

-

G

G

Q

P

T

T

V

V

Y

Y

V
|
V

T

Q

D
x
N

A
|
A

S

S

R

R

A

T

V

V

G

G

V

V

S

A

L

L

S

S

P

D

E

T

A

Q

R

R

D

D

G

D

Y

F

K

V

E

A

T

R

V

T

R

R

A

K

E

E

Y

Y

L

E

K

T

V

V

A

R

D

I

A

Q

H

H

A

G

R

R

active site: D107 (= D776), H109 (= H778), S160 (= S829)
binding co-methylcobalamin: E44 (= E707), M48 (= M711), M51 (= M714), G55 (= G718), L65 (= L728), V68 (= V731), D107 (= D776), V108 (= V777), H109 (= H778), D110 (= D779), I111 (= I780), I115 (= I784), G152 (= G821), L153 (= L822), S154 (= S823), L156 (= L825), I157 (= I826), T158 (= T827), G183 (= G852), G184 (= G853), A185 (= A854), V207 (= V877), N209 (≠ D879), A210 (= A880)

8sseA Methionine synthase, c-terminal fragment, cobalamin and reactivation domains from thermus thermophilus hb8 (see paper)
34% identity, 43% coverage: 671:1214/1256 of query aligns to 1:506/507 of 8sseA

query
sites
8sseA

P

P

V

L

A

L

K

E

R

R

L

L

E

K

H

R

A

R

L

V

V

V

N

E

G

G

I

R

T

K

E

Q

F

G

I

L

E

E

A

A

D

D

T

L

E

E

A

A

R

L

L

K

A

A

A

G

E

H

R

K

P

P

L

L

H

D

V

L

I

I

E

N

G

G

P

P

L

L

M

L

A

A

G

G

M

M

N

K

V

E

V

V

G

G

D

D

L

L

F

F

G

G

A

A

G

G

K

K

M

M

F

Q

L

L

P

P

Q

F

V

V

V

L

K

Q

S

A

A

A

R

E

V

V

M

M

K

K

Q

R

A

A

V

V

A

A

V

Y

L

L

L

E

P

P

Y

H

M

M

E

E

A

K

E

E

K

-

L

-

A

-

N

-

G

-

G

G

E

K

G

G

T

T

R

-

A

-

S

-

A

-

G

-

K

-

I

L

L

V

M

L

A

A

T

T

V

V

K

K

G

G

D

D

V

V

H
|
H

D

D

I

I

G
|
G

K

K

N

N

I

L

V
|
V

G

D

V

I

L

L

A

S

C

N

N

N

N

G

Y

Y

E

R

I

V

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|
G

Y
|
Y

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P

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V

G

H

H

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F

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binding cobalamin: H97 (= H778), G100 (= G781), V104 (= V785), S142 (= S823), L145 (≠ I826), V146 (≠ T827), I169 (≠ L850), G171 (= G852), G172 (= G853), A173 (= A854), H405 (≠ K1111), V409 (≠ D1115), S451 (≠ A1158), F452 (≠ P1159), G453 (= G1160), Y454 (= Y1161), Q463 (≠ K1170), L485 (≠ M1193), E488 (≠ G1196), A490 (≠ S1198), S492 (= S1200)

3bofA Cobalamin-dependent methionine synthase (1-566) from thermotoga maritima complexed with zn2+ and homocysteine (see paper)
28% identity, 47% coverage: 21:612/1256 of query aligns to 5:538/560 of 3bofA

query
sites
3bofA

R

R

A

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L

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N

N

binding zinc ion: C207 (= C261), C272 (= C324)

1q8jA Cobalamin-dependent methionine synthase (1-566) from thermotoga maritima (cd2+, hcy, methyltetrahydrofolate complex) (see paper)
28% identity, 47% coverage: 21:612/1256 of query aligns to 5:538/559 of 1q8jA

query
sites
1q8jA

R

R

A

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L

V

N

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D

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E

L

S

K

P

P

E

H

T

D

M

F

A

A

A

V

Q

H

I

I

E

D

A

S

F

Y

V

Y

R

E

D

L

G

G

L

-

V

V

N

N

I

I

V

F

G

G

C

C

G

G

S

T

T

T

P

P

A

E

H

H

I

V

R

K

A

L

I

F

A

R

E

K

A

V

V

L

Q

G

K

N

Y

R

P

K

P

P

R

L

Q

Q

V

-

P

-

E

-

I

-

E

R

R

K

M

K

R

R

L

I

S

F

G

A

L

V

-

S

E

S

P

P

F

S

T

K

L

L

T

V

D

T

E

F

I

D

P

H

F

F

V

V

N

V

V

I

G

G

E
|
E

R

R

T

I

N

N

V

P

T

A

G

G

S

R

A

K

K

K

F

L

R

W

K

A

L

E

I

M

T

Q

T

K

G

G

D

N

Y

E

A

E

A

I

A

V

L

I

D

K

V

E

A

A

R

K

D

T

Q

Q

V

V

A

E

N

K

G

G

A

A

Q

E

I

V

I

L

D

D

I

V

N

N

M

F

D

G

E

-

G

-

L

-

I

I

D

E

S

S

T

Q

R

I

A

D

M

V

V

R

E

Y

F

V

L

E

N

K

L

I

V

V

A

Q

S

T

E

L

P

P

D

Y

I

V

A

S

C

N

V

V

P

P

V

L

M

S

I

L

D
|
D

S

I

S

Q

K

N

W

V

E

D

V

L

I

T

E

E

A

R

G

A

L

L

K

R

C

A

V

Y

Q

P

G

G

K

R

A

S

L

L

V

F

N
|
N

S

S

I

A

S

-

L

-

K

K

E

V

G

D

E

E

A

E

F

L

L

E

H

M

H

K

A

I

R

N

L

L

V

L

R

K

A

K

Y

Y

G

G

A

G

A

T

V

L

V

I

V

V

M

L

A

L

F

M

D

G

E

K

K

D

G

V

Q

P

A

K

D

S

S

F

R

E

A

E

R

R

K

K

V

-

E

E

I

Y

C

F

R

E

R

K

A

A

Y

L

R

K

L

I

L

L

T

-

E

E

E

R

V

H

G

D

F

F

P

-

P

S

E

D

D

R

I

V

I

I

F

F

D
|
D

P

P

N

G

I

V

F

L

A

P

V

L

-

G

A

A

T

E

G

G

I

K

D

P

E

V

H

E

N

V

N

L

Y

K

G

T

V

I

D

E

F

F

I

I

E

S

A

S

T

K

H

-

E

-

I

-

A

-

T

-

L

-

P

-

H

G

V

F

H

N

V

T

S

T

G

V

G
|
G

V

L

S

S

N
|
N

L

L

S

S

F
|
F

S

G

F

L

R

-

G

-

N

-

E

-

P

P

V

D

R
|
R

E

S

A

Y

M

Y

H

N

A

T

V

A

F

F

L

L

Y

V

H

L

A

G

I

I

Q

S

A

K

G

G

M

L

D

S

M

S

G

A

I
|
I

V

M

N

N

binding 5-methyl-5,6,7,8-tetrahydrofolic acid: E320 (= E375), D390 (= D448), N411 (= N469), D473 (= D536), G505 (= G575), N508 (= N578), F511 (= F581), R516 (= R590), I536 (= I610)

5vooA Methionine synthase folate-binding domain with methyltetrahydrofolate from thermus thermophilus hb8 (see paper)
36% identity, 22% coverage: 373:646/1256 of query aligns to 5:273/282 of 5vooA

query
sites
5vooA

V

V

G

G

E
|
E

R
|
R

T

L

N

N

V

A

T

T

G
|
G

S
|
S

A
x
K

K

R

F

F

R

R

K

E

L

M

I

L

T

F

T

A

G

R

D

D

Y

L

A

E

A

G

A

I

L

L

D

A

V

L

A

A

R

R

D

E

Q

Q

V

V

A

E

N

E

G

G

A

A

Q

H

I

A

I

L

D

D

I

L

N

S

M

V

D

A

E

W

G

T

L

G

I

R

D

D

S

E

T

L

R

E

A

D

M

L

V

R

E

W

F

L

L

L

N

P

L

H

V

L

A

A

S

T

E

A

P

-

D

-

I

-

A

L

C

T

V

V

P

P

V

V

M

M

I

V

D
|
D

S

S

S

T

K

S

W

P

E

E

V

A

I

M

E

E

A

L

G

A

L

L

K

K

C

Y

V

L

Q

P

G

G

K

R

A

V

L

L

V

L

N
|
N

S

S

I

A

S

N

L

L

K

E

E

D

G

G

E

L

E

E

A

R

F

F

L

D

H

R

H

V

A

A

R

S

L

L

V

A

R

K

A

A

Y

H

G

G

A

A

V

L

V

V

M

L

A

A

F

I

D

D

E

E

K

K

G

G

Q

M

A

A

D

K

S

T

R

R

A

E

R

E

K

K

V

V

E

R

I

V

C

A

R

L

R

R

A

M

Y

Y

R

E

L

R

L

L

T

T

E

E

E

H

V

H

G

G

F

L

P

R

P

P

E

E

D

D

I

L

F

F

D
|
D

P

L

N

L

I

T

F

F

A

P

V

I

A

T

T

Q

G

G

I

D

D

E

E

E

H

S

N

R

N

P

Y

L

G

A

V

K

D

E

F

T

I

L

E

L

A

A

T

M

H

E

E

E

I

L

I

R

A

E

T

R

L

L

P

P

H

G

V

V

H

G

V

F

S

V

G

L

G
|
G

V

V

S

S

N
|
N

L

V

S

S

F
|
F

S

G

F

L

R

K

G

P

N

R

E

-

P

-

V

A

R
|
R

E

R

A

V

M

L

H

N

A

S

V

V

F

F

L

L

Y

D

H

E

A

A

I

R

Q

K

A

R

G

G

M

L

D

T

M

A

G

A

I
|
I

V

V

N

D

A

A

G

G

Q

K

L

I

A

L

V

P

Y

I

D

S

A

Q

I

I

D

P

P

E

E

E

L

A

R

Y

E

A

A

L

C

A

E

L

D

D

V

L

V

I

L

Y

N

D

R

R

P

K

D

E

A

G

T

F

E

D

R

P

L

L

binding 5-methyl-5,6,7,8-tetrahydrofolic acid: E7 (= E375), R8 (= R376), G13 (= G381), S14 (= S382), K15 (≠ A383), D77 (= D448), N98 (= N469), D165 (= D536), G204 (= G575), N207 (= N578), F210 (= F581), R217 (= R590), I237 (= I610)

7xcnP Crystal structure of the mttb-mttc complex at 2.7 a resolution (see paper)
31% identity, 16% coverage: 686:892/1256 of query aligns to 20:215/215 of 7xcnP

query
sites
7xcnP

E

E

F

L

I

A

E

E

A

E

D

V

T

A

E

N

E

E

A

A

R

L

L

A

A

A

A

G

E

I

R

D

P

P

L

V

H

E

V

L

I

I

E

E

G

K

P

G

L

F

M

T

A

A

G

G

M

M

N

E

V

E

V

V

G

G

D

E

L

K

F

F

G

G

A

Q

G

G

K

E

M

L

F

F

L

L

P

P

Q

H

V

V

V

L

K

A

S

A

A

A

R

E

V

A

M

M

K

N

Q

S

A

G

V

I

A

K

V

V

L

I

L

T

P

P

Y

E

M

M

E

E

A

K

E

R

K

K

L

-

A

-

N

-

G

-

E

-

G

S

T

Q

R

T

A

K

S

S

A

L

G

G

K

T

I

V

L

A

M

I

A

G

T

T

V

I

K

E

G

G

D
|
D

V
x
I

H
|
H

D

S

I
|
I

G
|
G

K

K

N

D

I

I

V
|
V

G

A

V

S

V

M

L

L

A

N

C

I

N

A

N

G

Y

F

E

K

I

V

D

D

L

L

G

G

V

R

M

D

V

V

P

P

S

I

A

N

K

T

I

F

L

V

E

E

V

K

A

V

R

K

Q

E

E

L

K

K

V

P

D

Q

A

V

I

V

G

A

L
x
S

S
|
S

G

A

L
|
L

I
x
M

T
|
T

P

T

S

T

L

M

D

V

E

N

M

Q

V

I

H

Q

V

I

A

E

S

E

E

Q

L

L

E

K

R

E

E

A

G

G

F

V

-

R

-

D

D

Q

I

V

P

K

L

T

L
x
M

I

V

G
|
G

A

A

T

P

T

V

S

T

R

Q

V

-

H

D

T

W

A

A

V

D

K

K

I

I

N

-

P

-

R

-

Y

-

G

-

L

-

G

G

Q

A

T

D

V

I

Y

Y

V
x
G

T

E

D
x
S

A
|
A

S

N

R

D

A

A

V

V

G

A

V

K

V

V

S

K

S

A

L

A

L

L

S

N

binding 5-hydroxybenzimidazolylcobamide: D104 (= D776), I105 (≠ V777), H106 (= H778), I108 (= I780), G109 (= G781), V113 (= V785), S150 (≠ L822), S151 (= S823), L153 (= L825), M154 (≠ I826), T155 (= T827), M180 (≠ L850), G182 (= G852), G183 (= G853), G200 (≠ V877), S202 (≠ D879), A203 (= A880)

2i2xB Crystal structure of methanol:cobalamin methyltransferase complex mtabc from methanosarcina barkeri (see paper)
29% identity, 18% coverage: 670:892/1256 of query aligns to 41:243/258 of 2i2xB

query
sites
2i2xB

W

Y

P

P

V

I

A

A

K

K

R

A

L

I

E

F

H

E

A

G

L

E

V

E

N

D

G

D

I

V

T

V

E

E

F

G

I

L

E

Q

A

A

D

A

T

I

E

E

E

-

A

-

R

-

L

-

A

A

A

G

E

K

R

D

P

P

L

I

H

D

V

L

I

I

E

D

G

D

P

A

L

L

M

M

A

V

G

G

M

M

N

G

V

V

G

I

D

R

L

L

F

Y

G

D

A

E

G

G

K

V

M

I

F

F

L

L

P

P

Q

N

V

V

V

M

K

M

S

S

A

A

R

D

V

A

M

M

K

L

Q

E

A

G

V

I

A

-

V

-

L

-

P

-

Y

-

M

-

E

-

A

-

E

E

K

Y

L

C

A

K

N

E

G

N

G

S

E

G

G

A

T

T

R

P

A

K

S

T

A

K

G

G

K

T

I

V

L

V

M

C

A

H

T

V

V

A

K

E

G
|
G

D
|
D

V
|
V

H
|
H

D
|
D

I
|
I

G
|
G

K

K

N

N

I

I

V
|
V

G

T

V

A

V

L

L

L

A

R

C

A

N

N

N

G

Y

Y

E

N

I

V

D

D

L

L

G

G

V

R

M

D

V

V

P

P

S

A

A

E

K

E

I

V

L

L

E

A

V

A

A

V

R

Q

Q

K

E

E

K

K

V

P

D

I

A

M

I

L

G
x
T

L

G

S
x
T

G

A

L
|
L

I
x
M

T
|
T

P

T

S
x
T

L

M

D

Y

E

A

M

F

V

K

H

E

V

V

A

N

S

D

E

M

L

L

E

L

R

E

E

N

G

G

F

I

D

K

I

I

P

P

L

F

L
x
A

I

C

G
|
G

A
x
G

T

A

T

V

S

N

R

Q

V

D

H

F

T

V

A

S

V

-

K

-

I

-

N

-

P

-

R

Q

Y

F

G

A

L

L

G

G

Q

-

T

-

V

V

Y

Y

V
x
G

T
x
E

D
x
E

A
|
A

S

A

R

D

A

A

V

P

G

K

V

I

V

A

S

D

S

A

L

I

S

A

active site: D134 (= D776), H136 (= H778), T187 (≠ S829)
binding 5-hydroxybenzimidazolylcob(iii)amide: G133 (= G775), D134 (= D776), V135 (= V777), H136 (= H778), D137 (= D779), I138 (= I780), G139 (= G781), V143 (= V785), T179 (≠ G821), T181 (≠ S823), L183 (= L825), M184 (≠ I826), T185 (= T827), A208 (≠ L850), G210 (= G852), G211 (= G853), G212 (≠ A854), G228 (≠ V877), E229 (≠ T878), E230 (≠ D879), A231 (= A880)

Q46EH4 Methanol--corrinoid protein; Methanol:corrinoid methyltransferase 1 subunit of 27 kDa; MT1 subunit 27 kDa from Methanosarcina barkeri (strain Fusaro / DSM 804) (see paper)
29% identity, 18% coverage: 670:892/1256 of query aligns to 41:243/258 of Q46EH4

query
sites
Q46EH4

W

Y

P

P

V

I

A

A

K

K

R

A

L

I

E

F

H

E

A

G

L

E

V

E

N

D

G

D

I

V

T

V

E

E

F

G

I

L

E

Q

A

A

D

A

T

I

E

E

E

-

A

-

R

-

L

-

A

A

A

G

E

K

R

D

P

P

L

I

H

D

V

L

I

I

E

D

G

D

P

A

L

L

M

M

A

V

G

G

M

M

N

G

V

V

G

I

D

R

L

L

F

Y

G

D

A

E

G

G

K

V

M

I

F

F

L

L

P

P

Q

N

V

V

V

M

K

M

S

S

A

A

R

D

V

A

M

M

K

L

Q

E

A

G

V

I

A

-

V

-

L

-

P

-

Y

-

M

-

E

-

A

-

E

E

K

Y

L

C

A

K

N

E

G

N

G

S

E

G

G

A

T

T

R

P

A

K

S

T

A

K

G

G

K

T

I

V

L

V

M

C

A
x
H

T

V

V

A

K

E

G

G

D

D

V

V

H
|
H

D

D

I

I

G

G

K

K

N

N

I

I

V

V

G

T

V

A

V

L

L

L

A

R

C

A

N

N

N

G

Y

Y

E

N

I

V

D

D

L

L

G

G

V

R

M

D

V

V

P

P

S

A

A

E

K

E

I

V

L

L

E

A

V

A

A

V

R

Q

Q

K

E

E

K

K

V

P

D

I

A

M

I

L

G

T

L

G

S

T

G

A

L

L

I

M

T

T

P

T

S

T

L

M

D

Y

E

A

M

F

V

K

H

E

V

V

A

N

S

D

E

M

L

L

E

L

R

E

E

N

G

G

F

I

D

K

I

I

P

P

L

F

L

A

I

C

G

G

A

G

T

A

T

V

S

N

R

Q

V

D

H

F

T

V

A

S

V

-

K

-

I

-

N

-

P

-

R

Q

Y

F

G

A

L

L

G

G

Q

-

T

-

V

V

Y

Y

V

G

T

E

D

E

A

A

S

A

R

D

A

A

V

P

G

K

V

I

V

A

S

D

S

A

L

I

S

A

H129 (≠ A771) mutation to K: Does not affect cobalamin-binding.
H136 (= H778) mutation H->G,K: Abolishes cobalamin-binding.

Sites not aligning to the query:

256:258 HKH→KKK: Does not affect cobalamin-binding.

3ezxA Structure of methanosarcina barkeri monomethylamine corrinoid protein
32% identity, 15% coverage: 675:857/1256 of query aligns to 8:185/212 of 3ezxA

query
sites
3ezxA

R

K

L

L

E

R

H

D

A

A

L

I

V

V

N

N

G

Q

I

N

T

V

E

A

F

G

I

T

E

P

A

E

D

L

T

C

E

K

E

E

A

A

R

L

L

A

A

A

A

G

E

V

R

P

P

A

L

L

H

D

V

I

I

I

E

T

G

K

P

G

L

L

M

S

A

V

G

G

M
|
M

N

K

V

I

V

V

G

G

D

D

L

K

F
|
F

G

E

A

A

G

A

K

E

M

I

F

F

L

L

P

P

Q

Q

V

I

V

M

K

M

S

S

A

G

R

K

V

A

M

M

K

S

Q

N

A

A

V

M

A

E

V

V

L

L

L

T

P

P

Y

E

M

L

E

E

A

K

E

N

K

K

L

-

A

-

N

-

G

-

E

-

G

-

T

-

R

-

A

K

S

E

A

A

G

G

K

L

I

A

L

I

M

T

A

F

T

V

V

A

K

E

G

G

D
|
D

V
x
I

H
|
H

D
|
D

I
|
I

G

G

K

H

N

R

I

L

V
|
V

G

T

V

T

V

M

L

L

A

G

C

A

N

N

N

G

Y

F

E

Q

I

I

I

V

D

D

L

L

G

G

V

V

M

D

V

V

P

L

S

N

A

E

K

N

I

V

L

V

E

E

V

E

A

A

R

A

Q

K

E

H

K

K

V

G

D

E

A

K

I

V

G

L

L

L

-
x
V

-

G

S
|
S

G

A

L
|
L

I
x
M

T
|
T

P

T

S
|
S

L

M

D

L

E

G

M

Q

V

K

H

D

V

L

A

M

S

D

E

R

L

L

E

N

R

E

E

E

G

K

F

L

-

R

-

D

D

S

I

V

P

K

L

C

L
x
M

I

F

G
|
G

A

A

T

P

T

V

S

S

active site: D100 (= D776), H102 (= H778), S155 (= S829)
binding 5-hydroxybenzimidazolylcobamide: M47 (= M714), F54 (= F721), D100 (= D776), I101 (≠ V777), H102 (= H778), D103 (= D779), I104 (= I780), V109 (= V785), V147 (vs. gap), S149 (= S823), L151 (= L825), M152 (≠ I826), T153 (= T827), M178 (≠ L850), G180 (= G852), G181 (= G853)

Sites not aligning to the query:

binding 5-hydroxybenzimidazolylcobamide: 198, 200

4jgiB 1.5 angstrom crystal structure of a novel cobalamin-binding protein from desulfitobacterium hafniense dcb-2 (see paper)
34% identity, 11% coverage: 713:853/1256 of query aligns to 45:174/206 of 4jgiB

query
sites
4jgiB

G

G

M

M

N

T

V

K

V

V

G

G

D

E

L

R

F

F

G

D

A

S

G

G

K

E

M

Y

F

F

L

I

P

G

Q

D

V
x
L

V

I

K

F

S

A

A

G

R

E

V

I

M

L

K

Q

Q

A

A

A

V

M

A

D

V

K

L

L

L

K

P

P

Y

A

M

L

E

E

A

-

E

-

K

-

L

-

A

-

N

-

G

-

E

-

G

-

T

K

R

R

A

A

S

-

A

-

G

-

K

K

I

I

L

V

M

L

A

A

T

T

V

V

K

E

G

G

D
|
D

V
x
L

H
|
H

D
|
D

I
|
I

G
|
G

K

K

N

N

I

I

V
x
F

G

R

V

T

V

M

L

A

A

E

C

A

N

S

N

G

Y

F

E

E

I

V

I

F

D

D

L

L

G

G

V

I

M

D

V

V

P

P

S

V

A

K

K

I

I

I

L

V

E

D

V

K

A

V

R

K

Q

E

E

V

K

N

V

P

D

E

A

I

I

V

G
|
G

L

L

S
|
S

G

G

L

V

I
x
L

T

T

P

L

S
x
A

L

L

D

D

E

S

M

M

V

R

H

E

V

T

A

V

S

D

E

A

L

L

E

K

R

A

E

E

G

G

F

L

-

R

-

N

D

D

I

L

P

K

L

V

L

I

I

I

G
|
G

active site: D95 (= D776), H97 (= H778), A148 (≠ S829)
binding co-methylcobalamin: L63 (≠ V731), D95 (= D776), L96 (≠ V777), H97 (= H778), D98 (= D779), I99 (= I780), G100 (= G781), F104 (≠ V785), G140 (= G821), S142 (= S823), L145 (≠ I826), G173 (= G852), G174 (= G853)

Sites not aligning to the query:

binding co-methylcobalamin: 175, 191, 192, 193, 194

2ycjA Methyltransferase bound with methyltetrahydrofolate (see paper)
28% identity, 19% coverage: 370:611/1256 of query aligns to 10:237/271 of 2ycjA

query
sites
2ycjA

F

F

V

I

N

M

V

I

G

G

E

E

R

R

T

I

N

N

V

-

T

-

G

G

S
x
M

A
x
F

K

K

-

D

F

I

R

R

K

E

L

A

I

I

T

L

T

N

G

K

D

D

Y

P

A

R

A

P

A

I

L

Q

D

E

V

W

A

A

R

R

D

R

Q

Q

V

A

A

E

N

K

G

G

A

A

Q

H

I

Y

I

L

D

D

I

V

N

N

M

T

D

G

E

P

G

T

L

A

I

D

D

D

S

P

T

V

R

R

A

V

M

M

V

E

E

W

F

L

L

V

N

K

L

T

V

I

A

Q

S

E

E

V

P

V

D

D

I

L

A

P

C

C

V

C

P

-

V

-

M

-

I

L

D
|
D

S

S

S

T

K

N

W

P

E

D

V

A

I

I

E

E

A

A

G

G

L

L

K

K

C

V

V

H

Q

R

G

G

K

H

A

A

L

M

V

I

N
|
N

S

S

I

T

S

S

L

A

K

D

E

Q

G

W

E

K

E

M

A

D

F

I

L

F

H

F

H

-

A

-

R

P

L

M

V

A

R

K

A

K

Y

Y

G

E

A

A

V

I

V

G

M

L

A

T

F

M

D

N

E

E

K

K

G

G

-

V

-

P

-

K

Q

D

A

A

D

N

S

D

R

R

A

S

R

Q

-

L

K

A

V

M

E

E

I

L

C

V

R

A

R

N

A

A

Y

-

R

-

L

-

T

-

E

D

E

A

V

H

G

G

F

I

P

P

P

M

E

T

D

E

I

L

I

Y

F

I

D
|
D

P

P

N

L

I

I

F

L

A

P

V

V

A

N

T

V

G

A

I

-

D

Q

E

E

H

H

N

-

Y

-

G

A

V

V

D

E

F

V

I

L

E

E

A

T

T

I

H

R

E

Q

I

I

-

K

I

L

A

M

T

A

L

N

P

P

H

A

V

P

H

R

V

T

S

V

G

L

G
|
G

V

L

S

S

N
|
N

L

V

S

S

F
x
Q

S

K

F

C

R

-

G

-

N

-

E

-

P

P

V

D

R
|
R

E

P

A

L

M

I

H

N

A

R

V

T

F

Y

L

L

Y

V

H

M

A

A

I

M

Q

T

A

A

G

G

M

L

D

D

M

A

G

A

I
|
I

V

M

binding 5-methyl-5,6,7,8-tetrahydrofolic acid: M20 (≠ S382), F21 (≠ A383), D84 (= D448), N105 (= N469), D169 (= D536), G205 (= G575), N208 (= N578), Q211 (≠ F581), R216 (= R590), I236 (= I610)

Query Sequence

>WP_012709542.1 NCBI__GCF_000018545.1:WP_012709542.1
MSAASLFGELSPKPDGSEIFRALNQAAAERILIMDGAMGTEIQQLGFVEDHFRGERFGGC
ACHQQGNNDLLTLTQPKAIEEIHYRYALAGADILETNTFSSTRIAQADYGMEDMVYDLNR
DGARLARRAAKRAEAEDGRRRFVAGALGPTNRTASISPDVNNPGYRAVSFDDLRLAYAEQ
VRGLIDGGADIILIETIFDTLNAKAAIFATQEVFAEKKIHLPVMVSGTITDLSGRTLSGQ
TPTAFWYSVRHAAPFTIGLNCALGADAMRAHIDELSTVADTLVCAYPNAGLPNEFGRYDE
SPETMAAQIEAFVRDGLVNIVGGCCGSTPAHIRAIAEAVQKYPPRQVPEIERRMRLSGLE
PFTLTDEIPFVNVGERTNVTGSAKFRKLITTGDYAAALDVARDQVANGAQIIDINMDEGL
IDSTRAMVEFLNLVASEPDIACVPVMIDSSKWEVIEAGLKCVQGKALVNSISLKEGEEAF
LHHARLVRAYGAAVVVMAFDEKGQADSRARKVEICRRAYRLLTEEVGFPPEDIIFDPNIF
AVATGIDEHNNYGVDFIEATHEIIATLPHVHVSGGVSNLSFSFRGNEPVREAMHAVFLYH
AIQAGMDMGIVNAGQLAVYDAIDPELREACEDVVLNRRPDATERLLEIAERYRGQGGAQG
KEKDLAWRQWPVAKRLEHALVNGITEFIEADTEEARLAAERPLHVIEGPLMAGMNVVGDL
FGAGKMFLPQVVKSARVMKQAVAVLLPYMEAEKLANGGEGTRASAGKILMATVKGDVHDI
GKNIVGVVLACNNYEIIDLGVMVPSAKILEVARQEKVDAIGLSGLITPSLDEMVHVASEL
EREGFDIPLLIGGATTSRVHTAVKINPRYGLGQTVYVTDASRAVGVVSSLLSPEARDGYK
ETVRAEYLKVADAHARNEAEKRRLPLSQARANASKLDWDAYRPKTPSFLGTRVFESWDLA
ELARYIDWTPFFQTWELKGVYPRILDDEHQGPAARQLFADAQAMLEKIIAEKWFAPKAVV
GFWPAGSAGDDIRLFTDERRERELATFFTLRQQLAKRDGRPNVALADFVAPVESGRRDYL
GGFVVTAGIEEVAIAERFERANDDYSSILVKALADRFAEAFAERMHEYVRKELWGYAPDE
SFTPQELIAEPYTGIRPAPGYPAQPDHTEKETLFRLLDAEAAIGVRLTENYAMWPGSSVS
GLYVGHPDAYYFGVAKIERDQVEDYATRKRMGVREVERWLSPILNYVPMRETQAAE

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