SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing 18047 FitnessBrowser__Keio:18047 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)
100% identity, 100% coverage: 1:1227/1227 of query aligns to 1:1227/1227 of P13009

query
sites
P13009

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M1 (= M1) modified: Initiator methionine, Removed
C247 (= C247) binding Zn(2+)
C310 (= C310) binding Zn(2+); mutation C->A,S: Loss of zinc binding. Loss of catalytic activity.
C311 (= C311) binding Zn(2+); mutation C->A,S: Loss of zinc binding. Loss of catalytic activity.
E694 (= E694) binding methylcob(III)alamin
GDVHD 756:760 (= GDVHD 756:760) binding methylcob(III)alamin
D757 (= D757) mutation to E: Decreases activity by about 70%.; mutation to N: Decreases activity by about 45%.
H759 (= H759) binding axial binding residue; mutation to G: Loss of catalytic activity.
S804 (= S804) binding methylcob(III)alamin
T808 (= T808) binding methylcob(III)alamin
S810 (= S810) mutation to A: Decreases activity by about 40%.
A860 (= A860) binding methylcob(III)alamin
D946 (= D946) binding S-adenosyl-L-methionine
R1134 (= R1134) binding S-adenosyl-L-methionine
YY 1189:1190 (= YY 1189:1190) binding S-adenosyl-L-methionine

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)
54% identity, 100% coverage: 6:1227/1227 of query aligns to 20:1265/1265 of Q99707

query
sites
Q99707

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D

R61 (≠ C47) natural variant: R -> K
C255 (≠ T242) to Y: in dbSNP:rs1140598
GSR 382:384 (≠ GSA 367:369) binding (6S)-5,6,7,8-tetrahydrofolate
D449 (= D434) binding (6S)-5,6,7,8-tetrahydrofolate
N470 (= N455) binding (6S)-5,6,7,8-tetrahydrofolate
D537 (= D522) binding (6S)-5,6,7,8-tetrahydrofolate
N579 (= N564) binding (6S)-5,6,7,8-tetrahydrofolate
R585 (= R570) binding (6S)-5,6,7,8-tetrahydrofolate
R591 (= R576) binding (6S)-5,6,7,8-tetrahydrofolate
D919 (≠ Q893) to G: in dbSNP:rs1805087
D963 (vs. gap) mutation to E: Decreases binding to MTRR; when associated with N-1071.
K1071 (= K1035) mutation to N: Decreases binding to MTRR; when associated with E-963.

3bulA E. Coli i690c/g743c meth c-terminal fragment (649-1227) (see paper)
100% identity, 47% coverage: 651:1227/1227 of query aligns to 1:577/577 of 3bulA

query
sites
3bulA

Q

Q

A

A

E

E

W

W

R

R

S

S

W

W

E

E

V

V

N

N

K

K

R

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L

L

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Y

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M

D

D

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N

N

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D

D

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N

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G

G

D
|
D

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H
|
H

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D

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G

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K

N

N

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|
V

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D

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|
G

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|
L

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|
S

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G

L
|
L

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|
I

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|
T

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|
S

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R

Q

Q

G

G

F

F

T

T

I

I

P

P

L

L

I

I

G
|
G

A

A

T

T

S

S

K

K

A

A

H

H

T

T

A

A

V

V

K

K

I

I

E

E

Q

Q

N

N

Y

Y

S

S

G

G

P

P

T

T

V

V

Y

Y

V

V

Q
|
Q

N
|
N

A
|
A

S

S

R

R

T
|
T

V

V

G

G

V

V

A

A

L

L

S

S

D

D

T

T

Q

Q

R

R

D

D

F

F

V

V

A

A

R

R

T

T

R

R

K

K

E

E

Y

Y

E

E

T

T

V

V

R

R

I

I

Q

Q

H

H

G

G

R

R

K

K

P

P

R

R

T

T

P

P

V

V

T

T

L

L

E

E

A

A

R

R

D

D

N

N

D

D

F

F

A

A

F

F

D

D

W

W

Q

Q

A

A

Y

Y

T

T

P

P

V

V

A

A

H

H

R

R

L

L

G

G

V

V

Q

Q

E

E

V

V

E

E

A

A

S

S

I

I

E

E

T

T

L

L

R

R

N

N

Y

Y

I

I

D

D

W

W

T

T

P

P

F

F

M
|
M

T

T

W

W

S

S

L

L

A

A

G

G

K

K

Y

Y

P

P

R

R

I

I

L

L

E

E

D

D

E

E

V

V

G

G

V

V

E

E

A

A

Q

Q

R

R

L

L

F

F

K

K

D

D

A

A

N

N

D

D

M

M

L

L

D

D

K

K

L

L

S

S

A

A

E

E

K

K

T

T

L

L

N

N

P

P

R

R

G

G

V

V

G

G

L

L

F

F

P

P

A

A

N

N

R

R

V

V

G

G

D

D

I

I

E

E

I

I

Y

Y

R

R

D

D

E

E

T

T

R

R

T

T

H

H

V

V

I

I

N

N

V

V

S

S

H

H

L

L

R

R

Q

Q

T

T

E

E

K

K

T

T

G

G

F

F

A

A

N

N

Y

Y

C

C

L

L

A

A

D

D

F

F

V

V

A

A

P

P

K

K

L

L

S

S

G

G

K

K

A

A

D

D

Y

Y

I

I

G

G

A

A

F

F

A

A

V

V

T

T

G

G

L

L

E

E

D

D

A

A

L

L

A

A

D

D

A

A

F

F

E

E

A

A

Q

Q

H

H

D

D

Y

Y

N

N

K

K

I

I

M

M

V

V

K

K

A

A

L

L

A

A

D
|
D

R

R

L

L

A

A

E

E

A

A

F

F

A

A

E

E

Y

Y

L

L

H

H

E

E

R

R

V

V

R

R

K

K

V

V

Y

Y

W

W

G

G

Y

Y

A

A

P

P

N

N

E

E

N

N

L

L

S

S

N

N

E

E

L

L

I

I

R

R

E

E

N

N

Y

Y

Q

Q

G

G

I

I

R

R

P

P

A
|
A

P
|
P

G
|
G

Y
|
Y

P

P

A

A

C

C

P

P

E

E

H
|
H

T

T

E

E

K
|
K

A

A

T

T

I

I

W

W

E

E

L

L

E

E

V

V

E

E

K

K

H

H

T

T

G

G

M

M

K

K

L

L

T

T

E

E

S

S

F

F

A

A

M
|
M

W

W

P

P

G
|
G

A

A

S

S

V
|
V

S
|
S

G

G

W

W

Y

Y

F

F

S

S

H

H

P

P

D

D

S

S

K

K

Y

Y

A

A

V

V

A

A

Q

Q

I

I

Q

Q

R

R

D

D

Q

Q

V

V

E

E

D

D

Y

Y

A

A

R

R

K

K

G

G

M

M

S

S

V

V

T

T

E

E

V

V

E

E

R

R

W

W

L

L

A

A

P

P

N

N

L

L

G

G

Y

Y

D

D

A

A

D

D

active site: D107 (= D757), H109 (= H759), S160 (= S810)
binding cobalamin: H109 (= H759), V116 (= V766), G152 (= G802), L153 (= L803), S154 (= S804), L156 (= L806), I157 (= I807), T158 (= T808), G183 (= G833), G184 (= G834), Q208 (= Q858), N209 (= N859), A210 (= A860), T213 (= T863), M302 (= M952), D443 (= D1093), A486 (= A1136), P487 (= P1137), G488 (= G1138), Y489 (= Y1139), H495 (= H1145), K498 (= K1148), M521 (= M1171), G524 (= G1174), V527 (= V1177), S528 (= S1178)

3ivaA Structure of the b12-dependent methionine synthase (meth) c-teminal half with adohcy bound (see paper)
100% identity, 47% coverage: 651:1226/1227 of query aligns to 1:576/576 of 3ivaA

query
sites
3ivaA

Q

Q

A

A

E

E

W

W

R

R

S

S

W

W

E

E

V

V

N

N

K

K

R

R

L

L

E

E

Y

Y

S

S

L

L

V

V

K

K

G

G

I

I

T

T

E

E

F

F

I

I

E

E

Q

Q

D

D

T

T

E

E

A

A

R

R

Q

Q

A

A

T

T

R

R

P

P

I

C

E

E

V

V

I

I

E

E

G

G

P

P

L

L

M

M

D

D

G

G

M

M

N

N

V

V

G

G

D

D

L

L

F

F

G

G

E

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

Y

Y

L

L

E

E

P

P

F

F

I

I

E

E

A

A

S

S

K

K

E

E

Q

Q

G

C

K

K

T

T

N

N

G

G

K

K

M

M

V

V

I

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

Q

Q

C

C

N

N

Y

Y

E

E

I

I

V

V

D

D

L

L

G

G

V

V

M

M

V

V

P

P

A

A

E

E

K

K

I

I

L

L

R

R

T

T

A

A

K

K

E

E

V

V

N

N

A

A

D

D

L

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

N

N

V

V

A

A

K

K

E

E

M

M

E

E

R

R

Q

Q

G

G

F

F

T

T

I

I

P

P

L

L

I

I

G
|
G

A

A

T

T

S

S

K

K

A

A

H

H

T

T

A

A

V

V

K

K

I

I

E

E

Q

Q

N

N

Y

Y

S

S

G

G

P

P

T

T

V

V

Y

Y

V

V

Q
|
Q

N
|
N

A

A

S

S

R

R

T

T

V

V

G

G

V

V

A

A

L

L

S

S

D

D

T

T

Q

Q

R

R

D

D

F

F

V

V

A

A

R

R

T

T

R

R

K

K

E

E

Y

Y

E

E

T

T

V

V

R

R

I

I

Q

Q

H

H

G

G

R

R

K

K

P

P

R

R

T

T

P

P

V

V

T

T

L

L

E

E

A

A

R

R

D

D

N

N

D

D

F

F

A

A

F

F

D

D

W

W

Q

Q

A

A

Y

Y

T

T

P

P

V

V

A

A

H

H

R

R

L

L

G

G

V

V

Q

Q

E

E

V

V

E

E

A

A

S

S

I

I

E

E

T

T

L

L

R

R

N

N

Y

Y

I

I

D

D

W

W

T

T

P

P

F

F

M

M

T
|
T

W

W

S

S

L

L

A

A

G

G

K

K

Y

Y

P

P

R

R

I

I

L

L

E

E

D

D

E

E

V

V

G

G

V

V

E

E

A

A

Q

Q

R

R

L

L

F

F

K

K

D

D

A

A

N

N

D

D

M

M

L

L

D

D

K

K

L

L

S

S

A

A

E

E

K

K

T

T

L

L

N

N

P

P

R

R

G

G

V

V

G

G

L

L

F

F

P

P

A

A

N

N

R

R

V

V

G

G

D

D

I

I

E

E

I

I

Y

Y

R

R

D

D

E

E

T

T

R

R

T

T

H

H

V

V

I

I

N

N

V

V

S

S

H

H

L

L

R

R

Q

Q

T

T

E

E

K

K

T

T

G

G

F

F

A

A

N

N

Y

Y

C

C

L

L

A

A

D

D

F

F

V

V

A

A

P

P

K

K

L

L

S

S

G

G

K

K

A

A

D

D

Y

Y

I

I

G

G

A

A

F

F

A

A

V

V

T

T

G

G

L

L

E

E

D

D

A

A

L

L

A

A

D

D

A

A

F

F

E

E

A

A

Q

Q

H

H

D

D

Y

Y

N

N

K

K

I

I

M

M

V

V

K

K

A

A

L

L

A

A

D
|
D

R

R

L

L

A

A

E
|
E

A

A

F

F

A

A

E

E

Y

Y

L

L

H

H

E

E

R

R

V

V

R

R

K

K

V

V

Y

Y

W

W

G

G

Y

Y

A

A

P

P

N

N

E

E

N

N

L

L

S

S

N

N

E

E

L

L

I

I

R

R

E

E

N

N

Y

Y

Q

Q

G

G

I

I

R
|
R

P
|
P

A
|
A

P

P

G
|
G

Y
|
Y

P

P

A
|
A

C

C

P

P

E

E

H
|
H

T

T

E

E

K

K

A

A

T

T

I

I

W

W

E

E

L

L

E

E

V

V

E

E

K

K

H

H

T

T

G

G

M

M

K

K

L

L

T

T

E

E

S

S

F

F

A
|
A

M
|
M

W

W

P

P

G
|
G

A

A

S

S

V
|
V

S
|
S

G

G

W

W

Y

Y

F

F

S

S

H

H

P

P

D

D

S

S

K

K

Y
|
Y

Y

Y

A

A

V

V

A

A

Q

Q

I

I

Q

Q

R

R

D

D

Q

Q

V

V

E

E

D

D

Y

Y

A

A

R

R

K

K

G

G

M

M

S

S

V

V

T

T

E

E

V

V

E

E

R

R

W

W

L

L

A

A

P

P

N

N

L

L

G

G

Y

Y

D

D

A

A

active site: D107 (= D757), H109 (= H759), S160 (= S810)
binding cobalamin: H109 (= H759), G112 (= G762), V116 (= V766), G152 (= G802), L153 (= L803), S154 (= S804), L156 (= L806), I157 (= I807), T158 (= T808), G183 (= G833), G184 (= G834), Q208 (= Q858), N209 (= N859), T303 (= T953), D443 (= D1093), A486 (= A1136), G488 (= G1138), Y489 (= Y1139), H495 (= H1145), A520 (= A1170), M521 (= M1171), G524 (= G1174), V527 (= V1177), S528 (= S1178)
binding s-adenosyl-l-homocysteine: E447 (= E1097), R484 (= R1134), P485 (= P1135), Y489 (= Y1139), A491 (= A1141), Y539 (= Y1189)

1mskA Methionine synthase (activation domain) (see paper)
100% identity, 27% coverage: 901:1227/1227 of query aligns to 1:327/327 of 1mskA

query
sites
1mskA

T

T

P

P

V

V

T

T

L

L

E

E

A

A

R

R

D

D

N

N

D

D

F

F

A

A

F

F

D

D

W

W

Q

Q

A

A

Y

Y

T

T

P

P

V

V

A

A

H

H

R

R

L

L

G

G

V

V

Q

Q

E

E

V

V

E

E

A

A

S

S

I

I

E

E

T

T

L

L

R

R

N

N

Y

Y

I

I

D
|
D

W

W

T

T

P

P

F

F

M

M

T

T

W

W

S

S

L

L

A

A

G

G

K

K

Y

Y

P

P

R

R

I

I

L

L

E

E

D

D

E

E

V

V

G

G

V

V

E

E

A

A

Q

Q

R

R

L

L

F

F

K

K

D

D

A

A

N

N

D

D

M

M

L

L

D

D

K

K

L

L

S

S

A

A

E

E

K

K

T

T

L

L

N

N

P

P

R

R

G

G

V

V

G

G

L

L

F

F

P

P

A

A

N

N

R

R

V

V

G

G

D

D

I

I

E

E

I

I

Y

Y

R

R

D

D

E

E

T

T

R

R

T

T

H

H

V

V

I

I

N

N

V

V

S

S

H

H

L

L

R

R

Q

Q

T

T

E

E

K

K

T

T

G

G

F

F

A

A

N

N

Y

Y

C

C

L

L

A

A

D

D

F

F

V

V

A

A

P

P

K

K

L

L

S

S

G

G

K

K

A

A

D

D

Y

Y

I

I

G

G

A

A

F

F

A

A

V

V

T

T

G

G

L

L

E

E

D

D

A

A

L

L

A

A

D

D

A

A

F

F

E

E

A

A

Q

Q

H

H

D

D

Y

Y

N

N

K

K

I

I

M

M

V

V

K

K

A

A

L

L

A

A

D

D

R

R

L

L

A

A

E

E

A

A

F

F

A

A

E

E

Y

Y

L

L

H

H

E

E

R

R

V

V

R

R

K

K

V

V

Y

Y

W

W

G

G

Y

Y

A

A

P

P

N

N

E

E

N

N

L

L

S

S

N

N

E

E

L

L

I

I

R

R

E

E

N

N

Y

Y

Q

Q

G

G

I

I

R
|
R

P
|
P

A

A

P

P

G

G

Y
|
Y

P

P

A
|
A

C

C

P

P

E

E

H

H

T

T

E

E

K

K

A

A

T

T

I

I

W

W

E

E

L

L

E

E

V

V

E

E

K

K

H

H

T

T

G

G

M

M

K

K

L

L

T

T

E

E

S

S

F

F

A

A

M

M

W

W

P

P

G

G

A

A

S

S

V

V

S

S

G

G

W

W

Y

Y

F

F

S

S

H

H

P

P

D

D

S

S

K

K

Y
|
Y

Y

Y

A

A

V

V

A

A

Q

Q

I

I

Q

Q

R

R

D

D

Q

Q

V

V

E

E

D

D

Y

Y

A

A

R

R

K

K

G

G

M

M

S

S

V

V

T

T

E

E

V

V

E

E

R

R

W

W

L

L

A

A

P

P

N

N

L

L

G

G

Y

Y

D

D

A

A

D

D

binding s-adenosylmethionine: D46 (= D946), R234 (= R1134), P235 (= P1135), Y239 (= Y1139), A241 (= A1141), Y289 (= Y1189)

6bdyA Crystal structure of the meth reactivation domain bound to sinefungin (see paper)
100% identity, 27% coverage: 901:1226/1227 of query aligns to 1:326/326 of 6bdyA

query
sites
6bdyA

T

T

P

P

V

V

T

T

L

L

E

E

A

A

R

R

D

D

N

N

D

D

F

F

A

A

F

F

D

D

W

W

Q

Q

A

A

Y

Y

T

T

P

P

V

V

A

A

H

H

R

R

L

L

G

G

V

V

Q

Q

E

E

V

V

E

E

A

A

S

S

I

I

E

E

T

T

L

L

R

R

N

N

Y

Y

I

I

D
|
D

W

W

T

T

P

P

F

F

M

M

T

T

W

W

S

S

L

L

A

A

G

G

K

K

Y

Y

P

P

R

R

I

I

L

L

E

E

D

D

E

E

V

V

G

G

V

V

E

E

A

A

Q

Q

R

R

L

L

F

F

K

K

D

D

A

A

N

N

D

D

M

M

L

L

D

D

K

K

L

L

S

S

A

A

E

E

K

K

T

T

L

L

N

N

P

P

R

R

G

G

V

V

G

G

L

L

F

F

P

P

A

A

N

N

R

R

V

V

G

G

D

D

I

I

E

E

I

I

Y

Y

R

R

D

D

E

E

T

T

R

R

T

T

H

H

V

V

I

I

N

N

V

V

S

S

H

H

L

L

R

R

Q

Q

T

T

E

E

K

K

T

T

G

G

F

F

A

A

N

N

Y

Y

C

C

L

L

A

A

D

D

F

F

V

V

A

A

P

P

K

K

L

L

S

S

G

G

K

K

A

A

D

D

Y

Y

I

I

G

G

A

A

F

F

A

A

V

V

T

T

G

G

L

L

E

E

D

D

A

A

L

L

A

A

D

D

A

A

F

F

E

E

A

A

Q

Q

H

H

D

D

Y

Y

N

N

K

K

I

I

M

M

V

V

K

K

A

A

L

L

A

A

D

D

R

R

L

L

A

A

E

E

A

A

F

F

A

A

E

E

Y

Y

L

L

H

H

E

E

R

R

V

V

R

R

K

K

V

V

Y

Y

W

W

G

G

Y

Y

A

A

P

P

N

N

E

E

N

N

L

L

S

S

N

N

E

E

L

L

I

I

R

R

E

E

N

N

Y

Y

Q

Q

G

G

I

I

R
|
R

P
|
P

A
|
A

P

P

G

G

Y
|
Y

P
|
P

A
|
A

C

C

P

P

E

E

H

H

T

T

E

E

K

K

A

A

T

T

I

I

W

W

E

E

L

L

E

E

V

V

E

E

K

K

H

H

T

T

G

G

M

M

K

K

L

L

T

T

E

E

S

S

F

F

A

A

M

M

W

W

P

P

G

G

A

A

S

S

V

V

S

S

G

G

W

W

Y

Y

F

F

S

S

H

H

P

P

D

D

S

S

K

K

Y
|
Y

Y

Y

A

A

V

V

A

A

Q

Q

I

I

Q

Q

R

R

D

D

Q

Q

V

V

E

E

D

D

Y

Y

A

A

R

R

K

K

G

G

M

M

S

S

V

V

T

T

E

E

V

V

E

E

R

R

W

W

L

L

A

A

P

P

N

N

L

L

G

G

Y

Y

D

D

A

A

binding sinefungin: D46 (= D946), R234 (= R1134), P235 (= P1135), A236 (= A1136), Y239 (= Y1139), P240 (= P1140), A241 (= A1141), Y289 (= Y1189)

4cczA Crystal structure of human 5-methyltetrahydrofolate-homocysteine methyltransferase, the homocysteine and folate binding domains
54% identity, 51% coverage: 6:636/1227 of query aligns to 4:611/611 of 4cczA

query
sites
4cczA

E

D

Q

E

L

I

R

N

A

A

Q

I

L

L

N

Q

E

K

R

R

I

I

L

M

V

V

L

L

D

D

G

G

M

M

G

G

T

T

M

M

I

I

Q

Q

S

R

Y

E

R

K

L

L

N

E

E

E

A

-

D

H

F

F

R

R

G

G

E

Q

R

E

F

F

A

K

D

D

W

H

P

A

C

R

D

P

L

L

K

K

G

G

N

N

D

D

L

I

L

L

V

S

L

I

S

T

K

Q

P

P

E

D

V

V

I

I

A

Y

A

Q

I

I

H

H

N

K

A

E

Y

Y

F

L

E

L

A

A

G

-

A

-

D

D

I

I

E

E

T

T

N

N

T

T

F

F

N

S

S

S

T

T

T

S

I

I

A

A

M

Q

A

A

D

D

Y

Y

Q

G

M

L

E

E

S

H

L

L

S

A

A

Y

E

R

I

M

N

N

F

M

A

C

A

S

A

A

K

G

L

V

A

A

R

R

A

K

C

A

A

A

D

E

E

E

W

V

T

T

A

L

R

Q

T

T

P

G

E

I

K

K

P

-

R

R

Y

F

V

V

A

A

G

G

V

A

L

L

G

G

P

P

T

T

N

N

R

K

T

T

A

L

S

S

I

V

S

S

P

P

D

S

V

V

N

E

D

R

P

P

A

D

F

Y

R

R

N

N

I

I

T

T

F

F

D

D

G

E

L

L

V

V

A

E

A

A

Y

Y

R

Q

E

E

S

Q

T

A

K

K

A

G

L

L

V

L

E

D

G

G

A

V

D

D

L

I

I

L

L

L

I

I

E

E

T

T

V

I

F

F

D

D

T

T

L

A

N

N

A

A

K

K

A

A

V

L

F

F

A

A

V

L

K

Q

T

N

E

L

F

F

E

E

A

E

L

K

G

Y

V

A

E

P

L

R

P

P

I

I

M

F

I

I

S

S

G

G

T

T

I

I

T

V

D

D

A

K

S

S

G

G

R

R

T

T

L

L

S

S

G

G

Q

Q

T

T

T

G

E

E

A

G

F

F

Y

V

N

I

S

S

L

V

R

S

H

H

A

G

E

E

A

P

L

L

T

C

F

I

G

G

L

L

N

N

C

C

A

A

L

L

G

G

P

A

D

A

E

E

L

M

R

R

Q

P

Y

F

V

I

Q

E

E

I

L

I

S

G

R

K

I

C

A

T

E

T

C

A

Y

Y

V

V

T

L

A

C

H

Y

P

P

N

N

A

A

G

G

L

-

P

-

N

-

A

-

F

-

G

-

E

-

Y

-

D

-

L

-

D

-

A

-

D

-

T

-

M

-

A

-

K

-

Q

-

I

-

R

-

E

-

W

F

A

A

Q

M

A

D

G

G

F

L

L

V

N

N

I

I

V

V

G

G

C

C

G

G

T

S

T

T

P

P

Q

D

H

H

I

I

A

R

A

E

M

I

S

A

R

E

A

A

V

V

E

K

G

N

L

C

A

K

P

P

R

R

K

V

L

P

P

P

E

A

I

T

P

A

V

F

A

E

C

G

R

H

-

M

-

L

L

L

S

S

G

G

L

L

E

E

P

P

L

F

N

R

I

I

G

G

E

P

D

Y

S

T

L

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

K

A

R

K

L

L

I

I

K

M

E

A

E

G

K

N

Y

Y

S

E

E

E

A

A

L

L

D

C

V

V

A

A

R

K

Q

V

Q

Q

V

V

E

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

M

M

L

L

D

D

A

G

E

P

A

S

A

A

M

M

V

T

R

R

F

F

L

C

N

N

L

L

I

I

A

A

G

S

E

E

P

P

D

D

I

I

A

A

R

K

V

V

P

P

I

L

M

C

I

I

D

D

S

S

K

N

W

F

D

A

V

V

I

I

E

E

K

A

G

G

L

L

K

K

C

C

I

C

Q

Q

G

G

K

K

G

C

I

I

V

V

N
|
N

S

S

I

I

S

S

M

L

K

K

E

E

G

G

V

E

D

D

A

D

F

F

I

L

H

E

H

K

A

A

K

R

L

K

L

I

R

K

Y

Y

G

G

A

A

V

M

V

V

M
|
M

A

A

F

F

D

D

E

E

Q

E

G

G

Q

Q

A

A

D

T

T

E

R

T

A

D

R

T

K

K

I

I

E

R

I

V

C

C

R

T

R

R

A

A

Y

Y

K

H

I

L

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

E

E

H

H

N

N

N

L

Y

Y

A

A

Q

I

D

N

F

F

I

I

G

H

A

A

C

T

E

K

D

V

I

I

K

K

R

E

E

T

L

L

P

P

H

G

A

A

L

R

I

I

S

S

G

G

G
|
G

V

L

S
|
S

N
|
N

V

L

S

S

F
|
F

S

S

F

F

R
|
R

G

G

N

M

D

E

P

A

V

I

R
|
R

E

E

A

A

I

M

H

H

A

G

V

V

F

F

L

L

Y

Y

Y

H

A

A

I

I

R

K

N

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

I

V

Y

Y

D

D

L

I

P

H

A

K

E

E

L

L

R

L

D

Q

A

L

V

C

E

E

D

D

V

L

I

I

L

W

N

N

R

K

R

D

D

P

D

E

G

A

T

T

E

E

R

K

L

L

E

R

L

Y

A

A

E

Q

binding (6s)-5,6,7,8-tetrahydrofolate: E336 (= E361), G342 (= G367), R344 (≠ A369), N430 (= N455), M458 (= M483), D497 (= D522), G536 (= G561), S538 (= S563), N539 (= N564), F542 (= F567), R545 (= R570), R551 (= R576)

1bmtA How a protein binds b12: a 3.O angstrom x-ray structure of the b12- binding domains of methionine synthase (see paper)
100% identity, 20% coverage: 651:896/1227 of query aligns to 1:246/246 of 1bmtA

query
sites
1bmtA

Q

Q

A

A

E

E

W

W

R

R

S

S

W

W

E

E

V

V

N

N

K

K

R

R

L

L

E

E

Y

Y

S

S

L

L

V

V

K

K

G

G

I

I

T

T

E

E

F

F

I

I

E

E

Q

Q

D

D

T

T

E

E

A

A

R

R

Q

Q

A

A

T

T

R

R

P

P

I

I

E

E

V

V

I

I

E
|
E

G

G

P

P

L

L

M
|
M

D

D

G

G

M
|
M

N

N

V

V

G
|
G

D

D

L

L

F

F

G

G

E

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

Y

Y

L

L

E

E

P

P

F

F

I

I

E

E

A

A

S

S

K

K

E

E

Q

Q

G

G

K

K

T

T

N

N

G

G

K

K

M

M

V

V

I

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

Q

Q

C

C

N

N

Y

Y

E

E

I

I

V

V

D

D

L

L

G

G

V

V

M

M

V

V

P

P

A

A

E

E

K

K

I

I

L

L

R

R

T

T

A

A

K

K

E

E

V

V

N

N

A

A

D

D

L

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

N

N

V

V

A

A

K

K

E

E

M

M

E

E

R

R

Q

Q

G

G

F

F

T

T

I

I

P

P

L

L

I

I

G
|
G

A
|
A

T

T

S

S

K

K

A

A

H

H

T

T

A

A

V

V

K

K

I

I

E

E

Q

Q

N

N

Y

Y

S

S

G

G

P

P

T

T

V

V

Y

Y

V
|
V

Q

Q

N
|
N

A
|
A

S

S

R

R

T

T

V

V

G

G

V

V

A

A

L

L

S

S

D

D

T

T

Q

Q

R

R

D

D

F

F

V

V

A

A

R

R

T

T

R

R

K

K

E

E

Y

Y

E

E

T

T

V

V

R

R

I

I

Q

Q

H

H

G

G

R

R

active site: D107 (= D757), H109 (= H759), S160 (= S810)
binding co-methylcobalamin: E44 (= E694), M48 (= M698), M51 (= M701), G55 (= G705), L65 (= L715), V68 (= V718), D107 (= D757), V108 (= V758), H109 (= H759), D110 (= D760), I111 (= I761), I115 (= I765), G152 (= G802), L153 (= L803), S154 (= S804), L156 (= L806), I157 (= I807), T158 (= T808), G183 (= G833), G184 (= G834), A185 (= A835), V207 (= V857), N209 (= N859), A210 (= A860)

8g3hA Structure of cobalamin-dependent methionine synthase (meth) in a resting state (see paper)
36% identity, 68% coverage: 8:842/1227 of query aligns to 6:806/841 of 8g3hA

query
sites
8g3hA

L

L

R

R

A

A

Q

-

L

L

N

S

E

Q

R

R

I

V

L

L

V

V

L

F

D

D

G

G

G

A

M

M

G

G

T

T

M

E

I

L

Q

Q

S

K

Y

R

R

D

L

L

N

T

E

P

A

E

D

D

F

Y

R

G

G

E

E

E

R

A

F

Y

A

Y

D

G

W

C

P

P

C

-

D

-

L

-

K

-

G

-

N

-

D

E

L

V

L

L

V

N

L

R

S

T

K

R

P

P

E

D

V

V

I

V

A

R

A

E

I

I

H

H

N

L

A

S

Y

Y

F

L

E

E

A

A

G

G

A

A

D

E

I

V

I

I

E

E

T

T

N

N

T

S

F

F

N

G

S

A

T

L

T

R

I

H

A

V

M

L

A

A

D

E

Y

Y

Q

G

M

L

E

G

S

E

L

E

S

A

A

E

E

E

I

L

N

A

F

Y

A

R

A

A

K

R

L

I

A

A

R

K

A

E

C

A

A

A

D

E

E

P

W

Y

T

G

A

A

R

-

T

-

P

-

E

-

K

-

P

-

R

-

Y

F

V

V

A

A

G

G

V

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

-

D

-

P

-

A

-

F

-

R

-

N

Q

I

I

T

S

F

W

D

E

G

E

L

L

V

F

A

S

A

A

Y

Y

R

K

E

E

S

A

T

V

K

R

A

G

L

L

V

V

E

R

G

G

A

V

D

D

L

L

I

I

L

L

I

L

E

E

T

T

V

A

F

Q

D

D

T

I

L

L

N

Q

A

V

K

R

A

C

A

A

V

V

F

L

A

A

V

A

K

R

T

E

E

A

F

M

E

A

A

E

L

L

G

G

V

V

E

E

L

L

P

P

I

L

M

Q

I

V

S

Q

G

V

T

T

I

F

T

-

D

E

A

A

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G

G

R

T

T

M

L

L

S

V

G

G

Q

T

T

D

T

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E

Q

A

A

F

A

Y

L

N

A

S

A

L

L

R

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H

S

A

L

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P

A

I

L

D

T

V

F

V

G

G

L

M

N

N

C

C

A

A

L

T

G

G

P

P

D

D

-

L

-

M

-

D

-

A

E

K

L

I

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Q

Y

Y

F

V

A

Q

Q

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E

L

S

S

T

R

R

I

F

A

V

E

A

C

C

Y

L

V

-

T

-

A

-

H

-

P

P

N

N

A

A

G

G

L

L

P

P

N

R

A

N

F

E

G

G

E

G

-

R

-

V

Y

Y

D

D

L

L

D

T

A

P

D

E

T

E

M

L

A

A

K

R

Q

W

I

H

R

L

E

K

W

F

A

V

Q

T

A

E

G

Y

F

G

L

V

N

N

I

A

V

V

G

G

C

C

G

G

T

T

T

G

P

P

Q

E

H

H

I

I

A

R

A

K

M

V

S

A

R

E

A

A

V

V

E

G

G

G

L

-

A

R

P

P

R

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K

P

L

V

P

H

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K

I

T

P

A

V

F

A

P

C

P

R

Q

L

V

S

A

G

S

L

L

-

Y

E

Q

P

A

L

V

N

P

I

L

G

R

E
x
Q

D

E

S
x
T

L
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

K

R

R

E

L

L

I

L

K

F

E

A

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G

K

D

Y

L

S

E

E

G

A

I

L

L

D

A

V

L

A

A

R

Q

Q

E

Q

Q

V

V

E

A

N

E

G

G

A

A

Q

H

I

V

I

L

D

D

I

L

N

S

M

V

D

A

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W

G

T

M

G

L

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D

D

A

E

E

L

A

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A

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M

M

V

K

R

R

F

V

L

L

N

S

L

K

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L

A

A

G

T

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G

P

-

D

-

I

-

A

V

R

T

V

V

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P

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F

M

M

I

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D

D

S

S

S

T

K

S

W

P

D

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V

V

I

M

E

E

K

E

G

A

L

L

K

K

C

R

I

L

Q

P

G

G

K

R

G

A

I

I

V

L

N

N

S

S

I

A

S

N

M

L

K

E

E

D

G

G

V

L

D

E

A

K

F

F

I

D

H

R

H

V

A

A

K

S

L

L

L

A

R

K

R

A

Y

H

G

G

A

A

V

L

V

V

V

A

M

L

A

A

F

I

D

D

E

E

Q

E

G

G

Q

M

A

A

D

K

T

T

R

R

A

V

R

K

K

K

I

V

E

E

I

V

C

A

R

L

R

R

A

M

Y

Y

K

E

I

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

E

E

H

T

N

R

N

P

Y

L

A

A

Q

R

D

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F

T

I

L

G

L

A

A

C

L

E

E

D

E

I

L

K

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R

E

E

R

L

L

P

P

H

G

A

V

L

G

I

F

S

V

G

L

G

G

V

V

S

S

N

N

V

V

S

S

F

F

S

G

F

L

R

K

G

P

N

K

D

-

P

-

V

A

R

R

E

R

A

V

I

L

H

N

A

S

V

V

F

F

L

L

Y

D

Y

E

A

A

I

R

R

K

N

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

I

P

Y

I

D

S

D

Q

L

I

P

P

A

E

E

E

L

A

R

Y

D

A

A

L

V

A

E

L

D

D

V

L

I

I

L

Y

N

D

R

R

D

-

D

E

G

G

T

Q

E

D

R

P

L

L

L

F

E

A

L

F

A

I

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K

F

Y

F

R

E

G

E

S

H

K

K

T

-

D

-

D

E

T

V

A

L

N

A

A

E

Q

D

Q

K

A

E

E

A

W

F

R

Q

S

A

W

L

E

P

V

V

N

E

K

E

R

R

L

L

E

R

Y

R

S

R

L

V

V

L

K

E

G

G

I

K

T

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E

V

F

G

I

L

E

E

Q

E

D

D

T

L

E

A

E

E

A

A

R

L

Q

G

Q

R

A

-

T

M

R

R

P

P

I

L

E

E

V

I

I

I

E

N

G

G

P

P

L

L

M

L

D

E

G

A

M

M

N

K

V

E

V

V

G

G

D

E

L

L

F
|
F

G

G

E

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

Y

Y

L

L

E

E

P

P

F

H

I

M

E

E

A

-

S

-

K

-

E

K

Q

K

G

G

K

E

T

G

N

K

G

G

K

K

M

L

V

V

I

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

Q

T

C

N

N

N

N

G

Y

Y

E

T

I

V

V

Y

D

N

L

L

G

G

V

I

M

K

V

V

P

P

A

I

E

E

K

E

I

M

L

L

R

K

T

A

A

V

K

D

E

E

V

V

N

K

A

P

D

H

L

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

N

E

V

N

A

L

K

E

E

Y

M

M

E

R

R

A

Q

R

G

G

F

Y

T

T

I

L

P

P

L

V

L
x
I

I
x
L

G
|
G

A
|
A

T

A

T

L

S

T

K

R

A

A

H

Y

T

V

binding cobalamin: Q328 (≠ E352), T330 (≠ S354), S331 (≠ L355), F675 (= F708), V685 (= V718), K693 (= K726), G720 (= G756), V722 (= V758), H723 (= H759), D724 (= D760), I725 (= I761), G726 (= G762), V730 (= V766), M767 (≠ L803), S768 (= S804), L770 (= L806), V772 (≠ T808), I795 (≠ L831), L796 (≠ I832), G797 (= G833), G798 (= G834), A799 (= A835)

Sites not aligning to the query:

binding cobalamin: 818, 819, 820, 821

3k13C Structure of the pterin-binding domain metr of 5- methyltetrahydrofolate-homocysteine methyltransferase from bacteroides thetaiotaomicron
67% identity, 23% coverage: 356:639/1227 of query aligns to 4:286/287 of 3k13C

query
sites
3k13C

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

K

L

R

R

L

L

I

V

K

N

E

E

E

K

K

K

Y

Y

S

D

E

E

A

A

L

L

D

S

V

I

A

A

R

R

Q

Q

V

V

E

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

M

L

L

L

D

D

A

A

E

R

A

T

A

E

M

M

V

T

R

T

F

F

L

L

N

N

L

L

I

I

A

M

G

S

E

E

P

P

D

E

I

I

A

A

R

R

V

V

P

P

I

V

M

M

I

I

D

D

S

S

K

K

W

W

D

E

V

V

I

I

E

E

K

A

G

G

L

L

K

K

C

C

I

L

Q

Q

G

G

K

K

G

S

I

I

V

V

N
|
N

S

S

I

I

S

S

M

L

K

K

E

E

G

G

V

E

D

E

A

V

F

F

I

L

H

E

H

H

A

A

K

R

L

I

R

K

R

Q

Y

Y

G

G

A

A

V

T

V

V

M

M

A

A

F

F

D

D

E

E

Q

K

G

G

Q

Q

A

A

D

D

T

T

R

A

A

A

R

R

K

K

I

I

E

E

I

V

C

C

R

E

R

R

A

A

Y

Y

K

R

I

L

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

E

E

H

H

N

N

Y

Y

A

A

Q

V

D

D

F

F

I

I

G

E

A

A

C

T

E

G

D

W

I

I

K

R

R

K

E

N

L

L

P

P

H

G

A

A

L

H

I

V

S

S

G

G

G
|
G

V

V

S
|
S

N
|
N

V

L

S

S

F

F

S

S

F

F

R
|
R

G

G

N

N

D

N

P

Y

V

I

R
|
R

E

E

A

A

I

M

H

H

A

A

V

V

F

F

L

L

Y

Y

Y

H

A

A

I

I

R

Q

N

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

-

I

L

Y

Y

D

S

D

D

L

I

P

P

A

A

E

D

L

T

R

L

D

E

A

K

V

I

E

E

D

D

V

V

I

V

L

L

N

N

R

R

D

P

D

D

G

A

T

A

E

E

R

R

L

L

L

I

E

E

L

L

A

A

E

E

K

A

Y

L

R

K

binding n-[4-({[(6s)-2-amino-4-hydroxy-5-methyl-5,6,7,8-tetrahydropteridin-6-yl]methyl}amino)benzoyl]-l-glutamic acid: E9 (= E361), G15 (= G367), R17 (≠ A369), N103 (= N455), D170 (= D522), G209 (= G561), S211 (= S563), N212 (= N564), R218 (= R570), R224 (= R576), I244 (= I596)

8sseA Methionine synthase, c-terminal fragment, cobalamin and reactivation domains from thermus thermophilus hb8 (see paper)
31% identity, 43% coverage: 661:1192/1227 of query aligns to 4:506/507 of 8sseA

query
sites
8sseA

K

E

R

R

L

L

E

K

Y

R

S

R

L

V

V

V

K

E

G

G

I

R

T

K

E

Q

F

G

I

L

E

E

Q

A

D

D

T

L

E

E

A

A

R

L

Q

K

Q

A

A

G

T

H

R

K

P

P

I

L

E

D

V

L

I

I

E

N

G

G

P

P

L

L

M

L

D

A

G

G

M

M

N

K

V

E

V

V

G

G

D

D

L

L

F

F

G

G

E

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

Y

Y

L

L

E

E

P

P

F

H

I

M

E

E

A

-

S

-

K

-

E

K

Q

E

G

G

K

K

T

-

N

-

G

G

K

T

M

L

V

V

I

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

Q

S

C

N

N

N

N

G

Y

Y

E

R

I

V

V

V

D

N

L

L

G

G

V

I

M

K

V

V

P

P

A

I

E

E

K

E

I

I

L

L

R

K

T

A

A

V

K

E

E

A

V

H

N

K

A

P

D

H

L

A

I

V

G

G

L

M

S
|
S

G

G

L

L

I
x
L

T
x
V

P

K

S

S

L

T

D

L

E

V

M

M

V

K

N

E

V

N

A

L

K

E

E

Y

M

M

E

R

R

D

Q

R

G

G

F

Y

T

T

I

L

P

P

L

V

L
x
I

I

L

G
|
G

A
|
A

T

A

T

L

S

T

K

R

A

S

H

Y

T

V

A

E

V

-

K

-

I

-

E

E

Q

L

N

R

Y

A

S

I

G

Y

P

P

T

N

V

V

Y

Y

V

Y

Q

A

N

E

A

-

S

-

R

-

T

-

V

-

G

-

V

-

A

-

L

-

S

-

D

-

T

-

Q

-

R

-

D

D

D

A

F

F

V

E

A

G

R

L

T

R

R

L

K

M

E

E

Y

E

E

L

T

T

V

G

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x
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L

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x
S

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x
F

G
|
G

Y
|
Y

P

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A

C

C

P

P

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D

H

L

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x
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|
S

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F

V

S

H

H

H

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V

V

binding cobalamin: H97 (= H759), G100 (= G762), V104 (= V766), S142 (= S804), L145 (≠ I807), V146 (≠ T808), I169 (≠ L831), G171 (= G833), G172 (= G834), A173 (= A835), H405 (≠ K1089), V409 (≠ D1093), S451 (≠ A1136), F452 (≠ P1137), G453 (= G1138), Y454 (= Y1139), Q463 (≠ K1148), L485 (≠ M1171), E488 (≠ G1174), A490 (≠ S1176), S492 (= S1178)

1q8jA Cobalamin-dependent methionine synthase (1-566) from thermotoga maritima (cd2+, hcy, methyltetrahydrofolate complex) (see paper)
28% identity, 50% coverage: 12:625/1227 of query aligns to 11:559/559 of 1q8jA

query
sites
1q8jA

L

L

N

S

E

E

R

R

I

V

L

L

V

L

L

L

D

D

G

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|
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|
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A

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-

G

-

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|
G

V

L

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N
|
N

V

L

S

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F
|
F

S

G

F

L

R

-

G

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N

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P

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|
R

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S

A

Y

I

Y

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N

A

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F

F

L

L

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K

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G

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|
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N

N

A

P

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D

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M

D

K

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L

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-

A

-

V

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-

D

-

V

V

I

I

L

L

N

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K

D

E

binding 5-methyl-5,6,7,8-tetrahydrofolic acid: E320 (= E361), D390 (= D434), N411 (= N455), D473 (= D522), G505 (= G561), N508 (= N564), F511 (= F567), R516 (= R576), I536 (= I596)

3bofA Cobalamin-dependent methionine synthase (1-566) from thermotoga maritima complexed with zn2+ and homocysteine (see paper)
28% identity, 50% coverage: 12:625/1227 of query aligns to 11:559/560 of 3bofA

query
sites
3bofA

L

L

N

S

E

E

R

R

I

V

L

L

V

L

L

L

D

D

G

G

G

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M

Y

G

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M

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K

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N

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D

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|
C

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|
C

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R

A

K

K

K

F

L

K

W

R

A

L

E

I

M

K

Q

E

K

E

G

K

N

Y

E

S

E

E

I

A

V

L

I

D

K

V

E

A

A

R

K

Q

T

Q

Q

V

V

E

E

N

K

G

G

A

A

Q

E

I

V

I

L

D

D

I

V

N

N

M

F

D

G

-

I

E

E

G

S

M

Q

L

I

D

D

A

-

E

-

A

-

M

-

V

V

R

R

F

Y

L

V

-

E

N

K

L

I

I

V

A

Q

G

T

E

L

P

P

D

Y

I

V

A

S

R

N

V

V

P

P

I

L

M

S

I

L

D

D

S

I

S

Q

K

N

W

V

D

D

V

L

I

T

E

E

K

R

G

A

L

L

K

R

C

A

I

Y

Q

P

G

G

K

R

G

S

I

L

V

F

N

N

S

S

I

A

S

K

M

V

K

D

E

E

G

-

V

-

D

E

A

E

F

L

I

E

H

M

H

K

A

I

K

N

L

L

R

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

Q

D

G

V

Q

P

A

K

D

S

T

F

R

E

A

E

R

R

K

K

I

-

E

E

I

Y

C

F

R

E

R

K

A

A

Y

L

K

K

I

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

A

G

T

A

G

-

I

-

E

-

H

-

N

E

N

G

Y

K

A

P

Q

V

D

E

F

V

I

L

G

K

A

T

C

I

E

E

D

F

I

I

K

S

R

S

E

K

L

G

P

F

H

N

A

T

L

T

I

V

S

-

G

-

G

G

V

L

S

S

N

N

V

L

S

S

F

F

S

G

F

L

R

-

G

-

N

-

D

-

P

P

V

D

R

R

E

S

A

Y

I

Y

H

N

A

T

V

A

F

F

L

L

Y

V

Y

L

A

G

I

I

R

S

N

K

G

G

M

L

D

S

M

S

G

A

I

I

V

M

N

N

A

P

G

L

Q

D

L

E

A

T

I

L

Y

M

D

K

D

T

L

L

P

N

A

A

E

T

L

L

R

-

D

-

A

-

V

-

E

-

D

-

V

V

I

I

L

L

N

E

R

K

D

E

binding zinc ion: C207 (= C247), C272 (= C310)

5vooA Methionine synthase folate-binding domain with methyltetrahydrofolate from thermus thermophilus hb8 (see paper)
36% identity, 23% coverage: 354:632/1227 of query aligns to 1:273/282 of 5vooA

query
sites
5vooA

S

S

L

L

F

F

V

L

N

-

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

K

R

R

E

L

M

I

L

K

F

E

A

E

R

K

D

Y

L

S

E

E

G

A

I

L

L

D

A

V

L

A

A

R

R

Q

E

Q

Q

V

V

E

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

M

G

L

R

D

D

A

-

E

E

A

L

A

E

M

D

V

L

R

R

F

W

L

L

N

L

L

-

I

-

A

-

G

-

E

-

P

P

D

H

I

L

A

A

R

T

-

A

-

L

-

T

V

V

P

P

I

V

M

M

I

V

D
|
D

S

S

S

T

K

S

W

P

D

E

V

A

I

M

E

E

K

L

G

A

L

L

K

K

C

Y

I

L

Q

P

G

G

K

R

G

V

I

L

V

L

N
|
N

S

S

I

A

S

N

M

L

K

E

E

D

G

G

V

L

D

E

A

R

F

F

I

D

H

R

H

V

A

A

K

S

L

L

L

A

R

K

R

A

Y

H

G

G

A

A

V

L

V

V

M

L

A

A

F

I

D

D

E

E

Q

K

G

G

Q

M

A

A

D

K

T

T

R

R

A

E

R

E

K

K

I

V

E

R

I

V

C

A

R

L

R

R

A

M

Y

Y

K

E

I

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

E

E

H

S

N

R

N

P

Y

L

A

A

Q

K

D

E

F

T

I

L

G

L

A

A

C

M

E

E

D

E

I

L

K

R

R

E

E

R

L

L

P

P

H

G

A

V

L

G

I

F

S

V

G

L

G
|
G

V

V

S

S

N
|
N

V

V

S

S

F
|
F

S

G

F

L

R

K

G

P

N

R

D

-

P

-

V

A

R
|
R

E

R

A

V

I

L

H

N

A

S

V

V

F

F

L

L

Y

D

Y

E

A

A

I

R

R

K

N

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

I

P

Y

I

D

S

D

Q

L

I

P

P

A

E

E

E

L

A

R

Y

D

A

A

L

V

A

E

L

D

D

V

L

I

I

L

Y

N

D

R

R

D

K

D

E

G

G

T

F

E

D

R

P

L

L

binding 5-methyl-5,6,7,8-tetrahydrofolic acid: E7 (= E361), R8 (= R362), G13 (= G367), S14 (= S368), K15 (≠ A369), D77 (= D434), N98 (= N455), D165 (= D522), G204 (= G561), N207 (= N564), F210 (= F567), R217 (= R576), I237 (= I596)

7xcnP Crystal structure of the mttb-mttc complex at 2.7 a resolution (see paper)
31% identity, 16% coverage: 673:872/1227 of query aligns to 20:215/215 of 7xcnP

query
sites
7xcnP

E

E

F

L

I

A

E

E

Q

E

D

V

T

A

E

N

E

E

A

A

R

L

Q

A

A

G

T

I

R

D

P

P

I

V

E

E

V

L

I

I

E

E

G

K

P

G

L

F

M

T

D

A

G

G

M

M

N

E

V

E

V

V

G

G

D

E

L

K

F

F

G

G

E

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

Y

V

L

I

E

T

P

P

F

E

I

M

E

E

A

K

S

R

K

K

E

S

Q

Q

G

T

K

K

T

S

N

L

G

G

K

T

M

V

V

A

I

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

Q

N

C

I

N

A

N

G

Y

F

E

K

I

V

V

V

D

D

L

L

G

G

V

R

M

D

V

V

P

P

A

I

E

N

K

T

I

F

L

V

R

E

T

K

A

V

K

K

E

E

V

L

N

K

A

P

D

Q

L

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

N

Q

V

I

A

E

K

E

E

Q

M

L

E

K

R

E

Q

A

G

G

F

V

-

R

-

D

T

Q

I

V

P

K

L

T

L
x
M

I

V

G
|
G

A

A

T

P

T

V

S

T

K

Q

A

-

H

D

T

W

A

A

V

D

K

K

I

I

E

-

Q

-

N

-

Y

-

S

-

G

G

P

A

T

D

V

I

Y

Y

V
x
G

Q

E

N
x
S

A
|
A

S

N

R

D

T

A

V

V

G

A

V

K

V

V

A

K

A

A

L

A

L

L

S

N

binding 5-hydroxybenzimidazolylcobamide: D104 (= D757), I105 (≠ V758), H106 (= H759), I108 (= I761), G109 (= G762), V113 (= V766), S150 (≠ L803), S151 (= S804), L153 (= L806), M154 (≠ I807), T155 (= T808), M180 (≠ L831), G182 (= G833), G183 (= G834), G200 (≠ V857), S202 (≠ N859), A203 (= A860)

2i2xB Crystal structure of methanol:cobalamin methyltransferase complex mtabc from methanosarcina barkeri (see paper)
37% identity, 15% coverage: 662:839/1227 of query aligns to 38:216/258 of 2i2xB

query
sites
2i2xB

R

E

L

L

E

I

Y

Y

S

P

L

I

V

A

K

K

G

A

I

I

T

F

E

E

F

G

I

E

E

E

Q

D

D

D

T

V

E

V

E

E

A

G

R

L

Q

Q

Q

A

A

A

T

I

R

E

-

A

-

G

-

K

-

D

P

P

I

I

E

D

V

L

I

I

E

D

G

D

P

A

L

L

M

M

D

V

G

G

M

M

N

G

V

V

G

I

D

R

L

L

F

Y

G

D

E

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

E

Y

Y

L

C

E

K

P

-

F

-

I

-

E

E

A

N

S

S

K

G

E

A

Q

T

G

P

K

K

T

T

N

K

G

G

K

T

M

V

V

V

I

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

Q

R

C

A

N

N

N

G

Y

Y

E

N

I

V

V

V

D

D

L

L

G

G

V

R

M

D

V

V

P

P

A

A

E

E

K

E

I

V

L

L

R

A

T

A

A

V

K

Q

E

K

V

E

N

K

A

P

D

I

L

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

N

E

V

V

A

N

K

D

E

M

M

L

E

L

R

E

Q

N

G

G

F

I

T

K

I

I

P

P

L

F

L
x
A

I

C

G
|
G

A
x
G

T

A

T

V

S

N

K

Q

active site: D134 (= D757), H136 (= H759), T187 (≠ S810)
binding 5-hydroxybenzimidazolylcob(iii)amide: G133 (= G756), D134 (= D757), V135 (= V758), H136 (= H759), D137 (= D760), I138 (= I761), G139 (= G762), V143 (= V766), T179 (≠ G802), T181 (≠ S804), L183 (= L806), M184 (≠ I807), T185 (= T808), A208 (≠ L831), G210 (= G833), G211 (= G834), G212 (≠ A835)

Sites not aligning to the query:

binding 5-hydroxybenzimidazolylcob(iii)amide: 228, 229, 230, 231

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)
37% identity, 15% coverage: 662:839/1227 of query aligns to 38:216/258 of Q46EH4

query
sites
Q46EH4

R

E

L

L

E

I

Y

Y

S

P

L

I

V

A

K

K

G

A

I

I

T

F

E

E

F

G

I

E

E

E

Q

D

D

D

T

V

E

V

E

E

A

G

R

L

Q

Q

Q

A

A

A

T

I

R

E

-

A

-

G

-

K

-

D

P

P

I

I

E

D

V

L

I

I

E

D

G

D

P

A

L

L

M

M

D

V

G

G

M

M

N

G

V

V

G

I

D

R

L

L

F

Y

G

D

E

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

E

Y

Y

L

C

E

K

P

-

F

-

I

-

E

E

A

N

S

S

K

G

E

A

Q

T

G

P

K

K

T

T

N

K

G

G

K

T

M

V

V

V

I

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

Q

R

C

A

N

N

N

G

Y

Y

E

N

I

V

V

V

D

D

L

L

G

G

V

R

M

D

V

V

P

P

A

A

E

E

K

E

I

V

L

L

R

A

T

A

A

V

K

Q

E

K

V

E

N

K

A

P

D

I

L

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

N

E

V

V

A

N

K

D

E

M

M

L

E

L

R

E

Q

N

G

G

F

I

T

K

I

I

P

P

L

F

L

A

I

C

G

G

A

G

T

A

T

V

S

N

K

Q

H129 (≠ A752) mutation to K: Does not affect cobalamin-binding.
H136 (= H759) mutation H->G,K: Abolishes cobalamin-binding.

Sites not aligning to the query:

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

4jgiB 1.5 angstrom crystal structure of a novel cobalamin-binding protein from desulfitobacterium hafniense dcb-2 (see paper)
35% identity, 11% coverage: 700:834/1227 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

E

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

Y

K

L

L

E

K

P

P

F

A

I

L

E

E

A

-

S

-

K

-

E

-

Q

-

G

-

K

-

T

K

N

R

G

A

K

K

M

I

V

V

I

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

Q

E

C

A

N

S

N

G

Y

F

E

E

I

V

V

F

D

D

L

L

G

G

V

I

M

D

V

V

P

P

A

V

E

K

K

I

I

I

L

V

R

D

T

K

A

V

K

K

E

E

V

V

N

N

A

P

D

E

L

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

N

E

V

T

A

V

K

D

E

A

M

L

E

K

R

A

Q

E

G

G

F

L

-

R

-

N

T

D

I

L

P

K

L

V

L

I

I

I

G
|
G

active site: D95 (= D757), H97 (= H759), A148 (≠ S810)
binding co-methylcobalamin: L63 (≠ V718), D95 (= D757), L96 (≠ V758), H97 (= H759), D98 (= D760), I99 (= I761), G100 (= G762), F104 (≠ V766), G140 (= G802), S142 (= S804), L145 (≠ I807), G173 (= G833), G174 (= G834)

Sites not aligning to the query:

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

3ezxA Structure of methanosarcina barkeri monomethylamine corrinoid protein
32% identity, 13% coverage: 680:838/1227 of query aligns to 26:185/212 of 3ezxA

query
sites
3ezxA

E

K

E

E

A

A

R

L

Q

A

A

G

T

V

R

P

P

A

I

L

E

D

V

I

I

I

E

T

G

K

P

G

L

L

M

S

D

V

G

G

M
|
M

N

K

V

I

V

V

G

G

D

D

L

K

F
|
F

G

E

E

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

Y

V

L

L

E

T

P

P

F

E

I

L

E

E

A

K

S

N

K

K

E

K

Q

E

G

A

K

-

T

-

N

-

G

G

K

L

M

A

V

I

I

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

Q

G

C

A

N

N

N

G

Y

F

E

Q

I

I

V

V

D

D

L

L

G

G

V

V

M

D

V

V

P

L

A

N

E

E

K

N

I

V

L

V

R

E

T

E

A

A

K

A

E

K

V

H

N

K

A

G

D

E

L

K

I

V

G

L

L

L

S
x
V

G

G

-
x
S

-

A

L
|
L

I
x
M

T
|
T

P

T

S
|
S

L

M

-

L

-

G

-

Q

-

K

D

D

E

L

M

M

V

D

N

R

V

L

A

N

K

E

E

E

M

K

E

L

R

R

Q

D

G

-

F

-

T

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 (= D757), H102 (= H759), S155 (= S810)
binding 5-hydroxybenzimidazolylcobamide: M47 (= M701), F54 (= F708), D100 (= D757), I101 (≠ V758), H102 (= H759), D103 (= D760), I104 (= I761), V109 (= V766), V147 (≠ S804), S149 (vs. gap), L151 (= L806), M152 (≠ I807), T153 (= T808), M178 (≠ L831), G180 (= G833), G181 (= G834)

Sites not aligning to the query:

binding 5-hydroxybenzimidazolylcobamide: 198, 200

5dmmA Crystal structure of the homocysteine methyltransferase mmum from escherichia coli, metallated form (see paper)
24% identity, 26% coverage: 8:321/1227 of query aligns to 3:284/288 of 5dmmA

query
sites
5dmmA

L

L

R

R

A

A

Q

L

L

L

N

D

E

K

R

Q

-

D

I

I

L

L

V

L

L

L

D

D

G

G

G

A

M

M

G

A

T

T

M

E

I

L

Q

E

S

A

Y

R

R

G

L

C

N

N

E

L

A

A

D

D

F

-

R

-

G

-

E

-

R

-

F

-

A

S

D

L

W

W

P

S

C

A

D

K

L

V

K

-

G

-

N

-

D

-

L

-

V

L

L

V

S

E

K

N

P

P

E

E

V

L

I

I

A

R

A

E

I

V

H

H

N

L

A

D

Y

Y

F

Y

E

R

A

A

G

G

A

A

D

Q

I

C

I

A

E

I

T

T

N

A

T

S

F

Y

N

Q

S

A

T

T

T

P

I

A

A

G

M

F

A

A

D

A

Y

R

Q

G

M

L

-

D

E

E

S

A

L

Q

S

S

A

K

E

A

I

L

N

I

F

G

A

K

A

S

A

V

K

E

L

L

A

A

R

R

A

K

C

A

A

R

D

E

E

A

W

Y

T

L

A

A

R

E

T

N

P

P

E

Q

K

A

-

G

P

T

R

L

Y

L

V

V

A

A

G

G

V

S

L

V

G

G

P

P

T

Y

N

G

R

-

T

-

A

A

S

Y

I

L

S

A

P

D

D

G

V

S

N

E

D

Y

P

R

A

G

F
x
D

R

Y

N
x
H

I

C

T

S

F

V

D

E

G

A

L

F

V

Q

A

A

A

F

Y

H

R

R

E

P

S

R

T

V

K

E

A

A

L

L

V

L

E

D

G

A

G

G

A

A

D

D

L

L

I

L

L

A

I

C

E

E

T

T

V

L

-

P

-

N

F

F

D

S

T

E

L

I

N

E

A

A

K

L

A

A

A

E

V

L

F

L

A

T

V

A

K

Y

T

P

E

R

F

A

E

R

A

A

L

-

G

-

V

-

E

-

L

-

P

-

I

-

M

W

I

F

S

S

G

F

T

T

I

L

T

R

D

D

A

S

S

E

G

H

R

L

T

S

L

D

S

G

G

T

Q

P

T

L

T

R

E

D

A

V

F

V

Y

A

N

L

S

L

L

A

R

G

H

Y

A

P

E

Q

A

V

L

V

T

A

F

L

G

G

L

I

N

N

C
|
C

A

-

L

I

G

A

P

L

D

E

E

N

L

T

R

T

Q

A

Y

A

V

L

Q

Q

E

H

L

L

S

H

R

G

I

L

A

T

E

V

C

L

Y

P

V

L

T

V

A

V

H

Y

P

P

N

N

A

S

G

G

L

-

P

-

N

-

A

-

F

-

G

-

E

-

Y

-

D

-

L

-

D

-

A

-

D

-

T

Q

M

L

A

A

K

D

Q

Y

I

L

R

P

E

Q

W

W

A

Q

Q

A

A

A

G

G

F

A

L

-

N

R

I

L

V

I

G

G

C
|
C

C

C

G

R

T

T

P

P

Q

A

H

D

I

I

A

A

M

L

binding zinc ion: D134 (≠ F151), H136 (≠ N153), C225 (= C247), C273 (= C310)

Query Sequence

>18047 FitnessBrowser__Keio:18047
MSSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSK
PEVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTA
RTPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILI
ETVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEA
LTFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQ
AGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVG
ERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLI
AGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAV
VVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQ
DFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAG
QLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVN
KRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVK
SARVMKQAVAYLEPFIEASKEQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDL
GVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA
HTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPR
TPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVEASIETLRNYIDWTPFFMTWSLAGKY
PRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRT
HVINVSHHLRQQTEKTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQH
DDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYP
ACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQV
EDYARRKGMSVTEVERWLAPNLGYDAD

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