SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing 3608907 Dshi_2298 alanine racemase domain protein (RefSeq) 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 9 hits to proteins with known functional sites (download)

1sftA Alanine racemase (see paper)
34% identity, 42% coverage: 7:162/373 of query aligns to 10:167/382 of 1sftA

query
sites
1sftA

E

E

V

V

D

D

L

L

C

D

K

A

I

I

R

Y

H

D

N

N

A

V

Q

E

T

N

L

L

A

R

G

-

R

R

L

L

T

L

P

P

R

D

G

D

L

T

G

H

I

I

T

M

A

A

V

V

T

V

K
|
K

A

A

V

N

C

A

-
x
Y

-

G

-

H

G

G

N

D

P

V

A

Q

I

V

A

A

R

R

A

T

M

A

L

L

E

E

G

A

G

G

A

A

V

S

G

R

L

L

A

A

E

V

A

A

R

F

L

L

R

D

N

E

V

A

R

L

R

A

L

L

R

R

E

E

A

K

G

G

L

I

T

E

C

A

A

P

V

I

T

L

L

V

I
x
L

R

G

T

A

P

S

M

R

L

P

S

A

E

D

A

A

A

A

E

L

V

A

V

A

-

Q

-

Q

R

R

L

I

C

A

E

L

T

T

S

V

F

F

N

R

S

S

D

D

-

W

L

L

R

E

V

E

I

A

S

S

A

A

L

L

S

Y

A

S

E

G

S

P

C

F

P

P

R

I

R

H

A

-

A

-

H

-

G

-

I

F

I

H

L

L

M

K

V

M

E

D

M

T

G

G

D

M

L

G

R
|
R

E

L

G

G

I

V

L

K

P

D

E

E

E

E

L

E

G

T

A

K

L

-

A

-

L

-

R

R

V

I

R

V

A

A

L

L

-

I

-

E

-

R

-

H

P

P

G

H

V

F

V

V

L

L

Q

E

G

G

I

L

G

Y

A

T

N
x
H

F

F

A

A

active site: K38 (= K36), R135 (= R131), H165 (≠ N160)
binding pyridoxal-5'-phosphate: K38 (= K36), Y42 (vs. gap), L84 (≠ I79), R135 (= R131), H165 (≠ N160)

Sites not aligning to the query:

active site: 218, 264, 310, 312
binding pyridoxal-5'-phosphate: 203, 218, 220, 221, 353

1ftxA Crystal structure of alanine racemase in complex with d-alanine phosphonate
34% identity, 42% coverage: 7:162/373 of query aligns to 10:167/380 of 1ftxA

query
sites
1ftxA

E

E

V

V

D

D

L

L

C

D

K

A

I

I

R

Y

H

D

N

N

A

V

Q

E

T

N

L

L

A

R

G

-

R

R

L

L

T

L

P

P

R

D

G

D

L

T

G

H

I

I

T

M

A

A

V

V

T

V

K
|
K

A

A

V

N

C

A

-
x
Y

-

G

-

H

G

G

N

D

P

V

A

Q

I

V

A

A

R

R

A

T

M

A

L

L

E

E

G

A

G

G

A

A

V

S

G

R

L

L

A

A

E

V

A

A

R

F

L

L

R

D

N

E

V

A

R

L

R

A

L

L

R

R

E

E

A

K

G

G

L

I

T

E

C

A

A

P

V

I

T

L

L

V

I

L

-

G

-

A

R

S

T

R

P

P

M

A

L

D

S

A

E

A

A

L

A

A

E

A

V

Q

V

Q

R

R

L

I

C

A

E

L

T

T

S

V

F

F

N

R

S

S

D

D

-

W

L

L

R

E

V

E

I

A

S

S

A

A

L

L

S

Y

A

S

E

G

S

P

C

F

P

P

R

I

R

H

A

-

A

-

H

-

G

-

I

F

I

H

L

L

M

K

V

M

E

D

M

T

G

G

D

M

L

G

R
|
R

E

L

G

G

I

V

L

K

P

D

E

E

E

E

L

E

G

T

A

K

L

-

A

-

L

-

R

R

V

I

R

V

A

A

L

L

-

I

-

E

-

R

-

H

P

P

G

H

V

F

V

V

L

L

Q

E

G

G

I

L

G

Y

A

T

N
x
H

F

F

A

A

active site: K38 (= K36), R135 (= R131), H165 (≠ N160)
binding (1s)-1-[((1e)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylene)amino]ethylphosphonic acid: K38 (= K36), Y42 (vs. gap), R135 (= R131), H165 (≠ N160)

Sites not aligning to the query:

active site: 218, 264, 310, 312
binding (1s)-1-[((1e)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylene)amino]ethylphosphonic acid: 202, 203, 218, 220, 221, 264, 310, 311, 353

1bd0A Alanine racemase complexed with alanine phosphonate (see paper)
34% identity, 42% coverage: 7:162/373 of query aligns to 10:167/381 of 1bd0A

query
sites
1bd0A

E

E

V

V

D

D

L

L

C

D

K

A

I

I

R

Y

H

D

N

N

A

V

Q

E

T

N

L

L

A

R

G

-

R

R

L

L

T

L

P

P

R

D

G

D

L

T

G

H

I

I

T

M

A

A

V

V

T

V

K
|
K

A

A

V

N

C

A

-
x
Y

-

G

-

H

G

G

N

D

P

V

A

Q

I

V

A

A

R

R

A

T

M

A

L

L

E

E

G

A

G

G

A

A

V

S

G

R

L

L

A

A

E

V

A

A

R

F

L

L

R

D

N

E

V

A

R

L

R

A

L

L

R

R

E

E

A

K

G

G

L

I

T

E

C

A

A

P

V

I

T

L

L

V

I

L

R

G

T

A

P

S

M

R

L

P

S

A

E

D

A

A

A

A

E

L

V

A

V

A

-

Q

-

Q

R

R

L

I

C

A

E

L

T

T

S

V

F

F

N

R

S

S

D

D

-

W

L

L

R

E

V

E

I

A

S

S

A

A

L

L

S

Y

A

S

E

G

S

P

C

F

P

P

R

I

R

H

A

-

A

-

H

-

G

-

I

F

I

H

L

L

M

K

V

M

E

D

M

T

G

G

D

M

L

G

R
|
R

E

L

G

G

I

V

L

K

P

D

E

E

E

E

L

E

G

T

A

K

L

-

A

-

L

-

R

R

V

I

R

V

A

A

L

L

-

I

-

E

-

R

-

H

P

P

G

H

V

F

V

V

L

L

Q

E

G

G

I

L

G

Y

A

T

N
x
H

F

F

A

A

active site: K38 (= K36), R135 (= R131), H165 (≠ N160)
binding {1-[(3-hydroxy-methyl-5-phosphonooxy-methyl-pyridin-4-ylmethyl)-amino]-ethyl}-phosphonic acid: K38 (= K36), Y42 (vs. gap), R135 (= R131), H165 (≠ N160)

Sites not aligning to the query:

active site: 218, 264, 310, 312
binding {1-[(3-hydroxy-methyl-5-phosphonooxy-methyl-pyridin-4-ylmethyl)-amino]-ethyl}-phosphonic acid: 202, 203, 218, 220, 221, 264, 310, 311, 353

1l6gA Alanine racemase bound with n-(5'-phosphopyridoxyl)-d-alanine (see paper)
34% identity, 42% coverage: 7:162/373 of query aligns to 10:167/382 of 1l6gA

query
sites
1l6gA

E

E

V

V

D

D

L

L

C

D

K

A

I

I

R

Y

H

D

N

N

A

V

Q

E

T

N

L

L

A

R

G

-

R

R

L

L

T

L

P

P

R

D

G

D

L

T

G

H

I

I

T

M

A

A

V

V

T

V

K
|
K

A

A

V

N

C

A

-
x
Y

-

G

-

H

G

G

N

D

P

V

A

Q

I

V

A

A

R

R

A

T

M

A

L

L

E

E

G

A

G

G

A

A

V

S

G

R

L

L

A

A

E

V

A

A

R

F

L

L

R

D

N

E

V

A

R

L

R

A

L

L

R

R

E

E

A

K

G

G

L

I

T

E

C

A

A

P

V

I

T

L

L

V

I

L

R

G

T

A

P

S

M

R

L

P

S

A

E

D

A

A

A

A

E

L

V

A

V

A

-

Q

-

Q

R

R

L

I

C

A

E

L

T

T

S

V

F

F

N

R

S

S

D

D

-

W

L

L

R

E

V

E

I

A

S

S

A

A

L

L

S

Y

A

S

E

G

S

P

C

F

P

P

R

I

R

H

A

-

A

-

H

-

G

-

I

F

I

H

L

L

M

K

V

M

E

D

M

T

G

G

D

M

L

G

R
|
R

E

L

G

G

I

V

L

K

P

D

E

E

E

E

L

E

G

T

A

K

L

-

A

-

L

-

R

R

V

I

R

V

A

A

L

L

-

I

-

E

-

R

-

H

P

P

G

H

V

F

V

V

L

L

Q

E

G

G

I

L

G

Y

A

T

N
x
H

F

F

A

A

active site: K38 (= K36), R135 (= R131), H165 (≠ N160)
binding n-(5'-phosphopyridoxyl)-d-alanine: K38 (= K36), Y42 (vs. gap), R135 (= R131), H165 (≠ N160)

Sites not aligning to the query:

active site: 218, 264, 310, 312
binding n-(5'-phosphopyridoxyl)-d-alanine: 203, 218, 220, 221, 264, 310, 311, 353

1l6fA Alanine racemase bound with n-(5'-phosphopyridoxyl)-l-alanine (see paper)
34% identity, 42% coverage: 7:162/373 of query aligns to 10:167/382 of 1l6fA

query
sites
1l6fA

E

E

V

V

D

D

L

L

C

D

K

A

I

I

R

Y

H

D

N

N

A

V

Q

E

T

N

L

L

A

R

G

-

R

R

L

L

T

L

P

P

R

D

G

D

L

T

G

H

I

I

T

M

A

A

V

V

T

V

K
|
K

A

A

V

N

C

A

-
x
Y

-

G

-

H

G

G

N

D

P

V

A

Q

I

V

A

A

R

R

A

T

M

A

L

L

E

E

G

A

G

G

A

A

V

S

G

R

L

L

A

A

E

V

A

A

R

F

L

L

R

D

N

E

V

A

R

L

R

A

L

L

R

R

E

E

A

K

G

G

L

I

T

E

C

A

A

P

V

I

T

L

L

V

I

L

R

G

T

A

P

S

M

R

L

P

S

A

E

D

A

A

A

A

E

L

V

A

V

A

-

Q

-

Q

R

R

L

I

C

A

E

L

T

T

S

V

F

F

N

R

S

S

D

D

-

W

L

L

R

E

V

E

I

A

S

S

A

A

L

L

S

Y

A

S

E

G

S

P

C

F

P

P

R

I

R

H

A

-

A

-

H

-

G

-

I

F

I

H

L

L

M

K

V

M

E

D

M

T

G

G

D

M

L

G

R
|
R

E

L

G

G

I

V

L

K

P

D

E

E

E

E

L

E

G

T

A

K

L

-

A

-

L

-

R

R

V

I

R

V

A

A

L

L

-

I

-

E

-

R

-

H

P

P

G

H

V

F

V

V

L

L

Q

E

G

G

I

L

G

Y

A

T

N
x
H

F

F

A

A

active site: K38 (= K36), R135 (= R131), H165 (≠ N160)
binding alanyl-pyridoxal-5'-phosphate: K38 (= K36), Y42 (vs. gap), R135 (= R131), H165 (≠ N160)

Sites not aligning to the query:

active site: 218, 264, 310, 312
binding alanyl-pyridoxal-5'-phosphate: 202, 203, 218, 220, 221, 264, 310, 311, 353

1epvA Alanine racemase with bound inhibitor derived from d- cycloserine (see paper)
34% identity, 42% coverage: 7:162/373 of query aligns to 10:167/382 of 1epvA

query
sites
1epvA

E

E

V

V

D

D

L

L

C

D

K

A

I

I

R

Y

H

D

N

N

A

V

Q

E

T

N

L

L

A

R

G

-

R

R

L

L

T

L

P

P

R

D

G

D

L

T

G

H

I

I

T

M

A

A

V

V

T

V

K
|
K

A

A

V

N

C

A

-
x
Y

-

G

-

H

G

G

N

D

P

V

A

Q

I

V

A

A

R

R

A

T

M

A

L

L

E

E

G

A

G

G

A

A

V

S

G

R

L

L

A

A

E

V

A

A

R

F

L

L

R

D

N

E

V

A

R

L

R

A

L

L

R

R

E

E

A

K

G

G

L

I

T

E

C

A

A

P

V

I

T

L

L

V

I
x
L

R

G

T

A

P

S

M

R

L

P

S

A

E

D

A

A

A

A

E

L

V

A

V

A

-

Q

-

Q

R

R

L

I

C

A

E

L

T

T

S

V

F

F

N

R

S

S

D

D

-

W

L

L

R

E

V

E

I

A

S

S

A

A

L

L

S

Y

A

S

E

G

S

P

C

F

P

P

R

I

R

H

A

-

A

-

H

-

G

-

I

F

I

H

L

L

M

K

V

M

E

D

M

T

G

G

D

M

L

G

R
|
R

E

L

G

G

I

V

L

K

P

D

E

E

E

E

L

E

G

T

A

K

L

-

A

-

L

-

R

R

V

I

R

V

A

A

L

L

-

I

-

E

-

R

-

H

P

P

G

H

V

F

V

V

L

L

Q

E

G

G

I

L

G

Y

A

T

N
x
H

F

F

A

A

active site: K38 (= K36), R135 (= R131), H165 (≠ N160)
binding d-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-n,o-cycloserylamide: K38 (= K36), Y42 (vs. gap), L84 (≠ I79), R135 (= R131), H165 (≠ N160)

Sites not aligning to the query:

active site: 218, 264, 310, 312
binding d-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-n,o-cycloserylamide: 203, 218, 220, 221, 264, 310, 311, 353

1xqlA Effect of a y265f mutant on the transamination based cycloserine inactivation of alanine racemase (see paper)
34% identity, 42% coverage: 7:162/373 of query aligns to 10:167/382 of 1xqlA

query
sites
1xqlA

E

E

V

V

D

D

L

L

C

D

K

A

I

I

R

Y

H

D

N

N

A

V

Q

E

T

N

L

L

A

R

G

-

R

R

L

L

T

L

P

P

R

D

G

D

L

T

G

H

I

I

T

M

A

A

V

V

T

V

K
|
K

A

A

V

N

C

A

-
x
Y

-

G

-

H

G

G

N

D

P

V

A

Q

I

V

A

A

R

R

A

T

M

A

L

L

E

E

G

A

G

G

A

A

V

S

G

R

L

L

A

A

E

V

A

A

R

F

L

L

R

D

N

E

V

A

R

L

R

A

L

L

R

R

E

E

A

K

G

G

L

I

T

E

C

A

A

P

V

I

T

L

L

V

I
x
L

R

G

T

A

P

S

M

R

L

P

S

A

E

D

A

A

A

A

E

L

V

A

V

A

-

Q

-

Q

R

R

L

I

C

A

E

L

T

T

S

V

F

F

N

R

S

S

D

D

-

W

L

L

R

E

V

E

I

A

S

S

A

A

L

L

S

Y

A

S

E

G

S

P

C

F

P

P

R

I

R

H

A

-

A

-

H

-

G

-

I

F

I

H

L

L

M

K

V

M

E

D

M

T

G

G

D

M

L

G

R
|
R

E

L

G

G

I

V

L

K

P

D

E

E

E

E

L

E

G

T

A

K

L

-

A

-

L

-

R

R

V

I

R

V

A

A

L

L

-

I

-

E

-

R

-

H

P

P

G

H

V

F

V

V

L

L

Q

E

G

G

I

L

G

Y

A

T

N
x
H

F

F

A

A

active site: K38 (= K36), R135 (= R131), H165 (≠ N160)
binding pyridoxal-5'-phosphate: K38 (= K36), Y42 (vs. gap), L84 (≠ I79), H165 (≠ N160)
binding (5-hydroxy-4-{[(3-hydroxyisoxazol-4-yl)amino]methyl}-6-methylpyridin-3-yl)methyl dihydrogen phosphate: K38 (= K36), Y42 (vs. gap), L84 (≠ I79), R135 (= R131), H165 (≠ N160)
binding 4'-deoxy-4'-aminopyridoxal-5'-phosphate: Y42 (vs. gap), R135 (= R131), H165 (≠ N160)

Sites not aligning to the query:

active site: 218, 264, 310, 312
binding (r)-4-amino-isoxazolidin-3-one: 264, 311
binding pyridoxal-5'-phosphate: 203, 218, 220, 221, 353
binding (5-hydroxy-4-{[(3-hydroxyisoxazol-4-yl)amino]methyl}-6-methylpyridin-3-yl)methyl dihydrogen phosphate: 202, 203, 218, 220, 221, 264, 283, 311, 353
binding 4'-deoxy-4'-aminopyridoxal-5'-phosphate: 202, 203, 218, 220, 221, 353

1xqkA Effect of a y265f mutant on the transamination based cycloserine inactivation of alanine racemase (see paper)
34% identity, 42% coverage: 7:162/373 of query aligns to 10:167/382 of 1xqkA

query
sites
1xqkA

E

E

V

V

D

D

L

L

C

D

K

A

I

I

R

Y

H

D

N

N

A

V

Q

E

T

N

L

L

A

R

G

-

R

R

L

L

T

L

P

P

R

D

G

D

L

T

G

H

I

I

T

M

A

A

V

V

T

V

K
|
K

A

A

V

N

C

A

-
x
Y

-

G

-

H

G

G

N

D

P

V

A

Q

I

V

A

A

R

R

A

T

M

A

L

L

E

E

G

A

G

G

A

A

V

S

G

R

L

L

A

A

E

V

A

A

R

F

L

L

R

D

N

E

V

A

R

L

R

A

L

L

R

R

E

E

A

K

G

G

L

I

T

E

C

A

A

P

V

I

T

L

L

V

I
x
L

R

G

T

A

P

S

M

R

L

P

S

A

E

D

A

A

A

A

E

L

V

A

V

A

-

Q

-

Q

R

R

L

I

C

A

E

L

T

T

S

V

F

F

N

R

S

S

D

D

-

W

L

L

R

E

V

E

I

A

S

S

A

A

L

L

S

Y

A

S

E

G

S

P

C

F

P

P

R

I

R

H

A

-

A

-

H

-

G

-

I

F

I

H

L

L

M

K

V

M

E

D

M

T

G

G

D

M

L

G

R
|
R

E

L

G

G

I

V

L

K

P

D

E

E

E

E

L

E

G

T

A

K

L

-

A

-

L

-

R

R

V

I

R

V

A

A

L

L

-

I

-

E

-

R

-

H

P

P

G

H

V

F

V

V

L

L

Q

E

G

G

I

L

G

Y

A

T

N
x
H

F

F

A

A

active site: K38 (= K36), R135 (= R131), H165 (≠ N160)
binding (5-hydroxy-4-{[(3-hydroxyisoxazol-4-yl)amino]methyl}-6-methylpyridin-3-yl)methyl dihydrogen phosphate: K38 (= K36), Y42 (vs. gap), L84 (≠ I79), R135 (= R131), H165 (≠ N160)

Sites not aligning to the query:

active site: 218, 264, 310, 312
binding (5-hydroxy-4-{[(3-hydroxyisoxazol-4-yl)amino]methyl}-6-methylpyridin-3-yl)methyl dihydrogen phosphate: 202, 203, 218, 220, 221, 264, 311, 353

P10724 Alanine racemase; EC 5.1.1.1 from Geobacillus stearothermophilus (Bacillus stearothermophilus) (see 8 papers)
34% identity, 42% coverage: 7:162/373 of query aligns to 11:168/388 of P10724

query
sites
P10724

E

E

V

V

D

D

L

L

C

D

K

A

I

I

R

Y

H

D

N

N

A

V

Q

E

T

N

L

L

A

R

G

-

R

R

L

L

T

L

P

P

R

D

G

D

L

T

G

H

I

I

T

M

A

A

V

V

T

V

K
|
K

A

A

V

N

C

A

-

Y

-

G

-

H

G

G

N

D

P

V

A

Q

I

V

A

A

R

R

A

T

M

A

L

L

E

E

G

A

G

G

A

A

V

S

G

R

L

L

A

A

E

V

A

A

R

F

L

L

R

D

N

E

V

A

R

L

R

A

L

L

R

R

E

E

A

K

G

G

L

I

T

E

C

A

A

P

V

I

T

L

L

V

I

L

R

G

T

A

P

S

M

R

L

P

S

A

E

D

A

A

A

A

E

L

V

A

V

A

-

Q

-

Q

R

R

L

I

C

A

E

L

T

T

S

V

F

F

N

R

S

S

D

D

-

W

L

L

R

E

V

E

I

A

S

S

A

A

L

L

S

Y

A

S

E

G

S

P

C

F

P

P

R

I

R

H

A

-

A

-

H

-

G

-

I

F

I

H

L

L

M
x
K

V

M

E

D

M

T

G

G

D

M

L

G

R
|
R

E

L

G

G

I

V

L

K

P

D

E

E

E

E

L

E

G

T

A

K

L

-

A

-

L

-

R

R

V

I

R

V

A

A

L

L

-

I

-

E

-

R

-

H

P

P

G

H

V

F

V

V

L

L

Q

E

G

G

I

L

G

Y

A

T

N
x
H

F

F

A

A

K39 (= K36) modified: N6-(pyridoxal phosphate)lysine; mutation to A: Loss of activity.
K129 (≠ M124) modified: N6-carboxylysine
R136 (= R131) binding
H166 (≠ N160) mutation to A: 6.5-fold decrease in activity.

Sites not aligning to the query:

219 R→A: 100-fold decrease in activity.; R→E: 1000-fold decrease in activity.; R→K: 4-fold decrease in activity.
265 Y→A: 5000-fold decrease in activity.; Y→F: Loss of activity.; Y→S: 2000-fold decrease in activity.
312 binding
354 Y→A: 54-fold increase in serine racemase activity.; Y→N: 81-fold increase in serine racemase activity.; Y→Q: 51-fold increase in serine racemase activity.

Query Sequence

>3608907 Dshi_2298 alanine racemase domain protein (RefSeq)
MKNPRLEVDLCKIRHNAQTLAGRLTPRGLGITAVTKAVCGNPAIARAMLEGGAVGLAEAR
LRNVRRLREAGLTCAVTLIRTPMLSEAAEVVRLCETSFNSDLRVISALSAESCPRRAAHG
IILMVEMGDLREGILPEELGALALRVRALPGVVLQGIGANFACFGGQAPEPAIMMALSDI
VVETERTCGVILQTVSGGNSANLPWAMGATPTGRITDLRLGEAILLGVEPVSGDRIAGLH
TDAITLVAEVIEAGFKSLPSRAAKATASGRRIRPSRTTRLILALGVQDTDVQGLVMPVGT
TFVGATSDHLVVVTQNALPRPGGEMRFQLNYSALMRAMAAPDIETVLRCDRPPTDASYAV
ADPVLAQHRHHQY

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