SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Other sequence analysis tools:

Find papers: PaperBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Comparing 59 a.a. (MKVKSAAKKR...) to proteins with known functional sites using BLASTp with E ≤ 0.001.

Or try Sites on a Tree

Found 12 hits to proteins with known functional sites (download)

7ood1 Mycoplasma pneumoniae 50s subunit of ribosomes in chloramphenicol- treated cells (see paper)
100% identity, 100% coverage: 1:59/59 of query aligns to 1:59/59 of 7ood1

query
sites
7ood1

M

M

K
|
K

V
|
V

K
|
K

S
|
S

A
|
A

A

A

K
|
K

K
|
K

R
|
R

F

F

K

K

L

L

T

T

K
|
K

S

S

G

G

Q

Q

I

I

K
|
K

R
|
R

K

K

H

H

A
|
A

Y
|
Y

T

T

S
|
S

H
|
H

L
|
L

A
|
A

P
|
P

H
|
H

K

K

T

T

T

T

K
|
K

Q
|
Q

K
|
K

R
|
R

H
|
H

L

L

R
|
R

K
|
K

Q
|
Q

G

G

T

T

V

V

S
|
S

A

A

S
|
S

D
|
D

F

F

K

K

R
|
R

I

I

G

G

N

N

L

L

I

I

binding : K2 (= K2), V3 (= V3), K4 (= K4), S5 (= S5), A6 (= A6), K8 (= K8), K9 (= K9), R10 (= R10), K15 (= K15), K20 (= K20), R21 (= R21), A24 (= A24), Y25 (= Y25), S27 (= S27), H28 (= H28), L29 (= L29), A30 (= A30), P31 (= P31), H32 (= H32), K36 (= K36), Q37 (= Q37), K38 (= K38), R39 (= R39), H40 (= H40), R42 (= R42), K43 (= K43), Q44 (= Q44), S48 (= S48), S50 (= S50), D51 (= D51), R54 (= R54)

8buu3 50S ribosomal protein L13 (see paper)
58% identity, 100% coverage: 1:59/59 of query aligns to 3:61/65 of 8buu3

query
sites
8buu3

M
|
M

K
|
K

V
x
T

K
x
H

S
x
R

A

G

A

S

K

A

K
|
K

R
|
R

F

F

K
|
K

L

K

T
|
T

K
x
G

S
|
S

G

G

Q
x
K

I

L

K
|
K

R
|
R

K

S

H
|
H

A
|
A

Y
|
Y

T

T

S
|
S

H
|
H

L
|
L

A
x
F

P
x
A

H
x
N

K

K

T

S

T
x
Q

K
|
K

Q
|
Q

K
|
K

R
|
R

H
x
K

L

L

R
|
R

K
|
K

Q

S

G

A

T

V

V

V

S
|
S

A

A

S
x
G

D
|
D

F

F

K
|
K

R
|
R

I

I

G

K

N
x
Q

L

M

I

L

binding : M3 (= M1), K4 (= K2), T5 (≠ V3), H6 (≠ K4), R7 (≠ S5), K11 (= K9), R12 (= R10), K14 (= K12), T16 (= T14), G17 (≠ K15), S18 (= S16), K20 (≠ Q18), K22 (= K20), R23 (= R21), H25 (= H23), A26 (= A24), Y27 (= Y25), S29 (= S27), H30 (= H28), L31 (= L29), F32 (≠ A30), A33 (≠ P31), N34 (≠ H32), Q37 (≠ T35), K38 (= K36), Q39 (= Q37), K40 (= K38), R41 (= R39), K42 (≠ H40), R44 (= R42), K45 (= K43), S50 (= S48), G52 (≠ S50), D53 (= D51), K55 (= K53), R56 (= R54), Q59 (≠ N57)

Sites not aligning to the query:

binding : 1, 2, 65

8uu97 Large ribosomal subunit protein bL35 (see paper)
53% identity, 100% coverage: 1:59/59 of query aligns to 3:61/65 of 8uu97

query
sites
8uu97

M
|
M

K
|
K

V
x
T

K
x
H

S
x
R

A

G

A

S

K

A

K
|
K

R
|
R

F

F

K
|
K

L

R

T
|
T

K

G

S
|
S

G

G

Q

K

I

L

K

K

R
|
R

K

R

H

H

A
x
G

Y
x
F

T

T

S
|
S

H
|
H

L

M

A
x
F

P
x
A

H
x
N

K

K

T

S

T
x
Q

K
|
K

Q
|
Q

K

K

R
|
R

H
x
K

L

L

R
|
R

K
|
K

Q

S

G

A

T

M

V

V

S

S

A

A

S

G

D
|
D

F

F

K

K

R
|
R

I

I

G

R

N
x
Q

L

M

I

V

binding : M3 (= M1), K4 (= K2), T5 (≠ V3), H6 (≠ K4), R7 (≠ S5), K11 (= K9), R12 (= R10), K14 (= K12), T16 (= T14), S18 (= S16), R23 (= R21), G26 (≠ A24), F27 (≠ Y25), S29 (= S27), H30 (= H28), F32 (≠ A30), A33 (≠ P31), N34 (≠ H32), Q37 (≠ T35), K38 (= K36), Q39 (= Q37), R41 (= R39), K42 (≠ H40), R44 (= R42), K45 (= K43), D53 (= D51), R56 (= R54), Q59 (≠ N57)

Sites not aligning to the query:

binding : 1, 2, 63

8p2f8 50S ribosomal protein L35 (see paper)
56% identity, 100% coverage: 1:59/59 of query aligns to 3:61/64 of 8p2f8

query
sites
8p2f8

M
|
M

K
|
K

V
x
T

K
x
H

S
x
R

A

G

A

A

K

A

K
|
K

R
|
R

F

V

K

K

L

R

T
|
T

K
x
A

S
|
S

G

G

Q

Q

I

L

K
|
K

R
|
R

K

S

H
x
R

A
|
A

Y
x
F

T
|
T

S
|
S

H
|
H

L
|
L

A
x
F

P
x
A

H
x
N

K

K

T

S

T
|
T

K
|
K

Q
|
Q

K
|
K

R
|
R

H
x
Q

L

L

R
|
R

K
|
K

Q

A

G

R

T

L

V

V

S
|
S

A

K

S
|
S

D
|
D

F

M

K
|
K

R
|
R

I

V

G

K

N
x
Q

L

L

I

L

binding magnesium ion: T28 (= T26), F32 (≠ A30)
binding : M3 (= M1), K4 (= K2), T5 (≠ V3), H6 (≠ K4), R7 (≠ S5), K11 (= K9), R12 (= R10), T16 (= T14), A17 (≠ K15), S18 (= S16), K22 (= K20), R23 (= R21), R25 (≠ H23), A26 (= A24), F27 (≠ Y25), S29 (= S27), H30 (= H28), L31 (= L29), F32 (≠ A30), A33 (≠ P31), N34 (≠ H32), T37 (= T35), K38 (= K36), Q39 (= Q37), K40 (= K38), R41 (= R39), Q42 (≠ H40), R44 (= R42), K45 (= K43), S50 (= S48), S52 (= S50), D53 (= D51), K55 (= K53), R56 (= R54), Q59 (≠ N57)

Sites not aligning to the query:

binding : 1, 2, 63

5ngmA3 structure of the 70S ribosome composing the S. aureus 100S complex (see paper)
56% identity, 100% coverage: 1:59/59 of query aligns to 3:61/64 of 5ngmA3

query
sites
5ngmA3

M
|
M

K
|
K

V
x
T

K
x
H

S
x
R

A

G

A

A

K

A

K
|
K

R
|
R

F

V

K
|
K

L

R

T
|
T

K
x
A

S

S

G

G

Q

Q

I

L

K
|
K

R
|
R

K

S

H

R

A
|
A

Y
x
F

T
|
T

S
|
S

H
|
H

L

L

A
x
F

P

A

H
x
N

K

K

T

S

T

T

K
|
K

Q

Q

K

K

R
|
R

H
x
Q

L

L

R
|
R

K
|
K

Q

A

G

R

T

L

V

V

S
|
S

A
x
K

S
|
S

D
|
D

F

M

K

K

R
|
R

I

V

G

K

N
x
Q

L

L

I

L

binding : M3 (= M1), K4 (= K2), T5 (≠ V3), H6 (≠ K4), R7 (≠ S5), K11 (= K9), R12 (= R10), K14 (= K12), T16 (= T14), A17 (≠ K15), K22 (= K20), R23 (= R21), A26 (= A24), F27 (≠ Y25), T28 (= T26), S29 (= S27), H30 (= H28), F32 (≠ A30), N34 (≠ H32), K38 (= K36), R41 (= R39), Q42 (≠ H40), R44 (= R42), K45 (= K43), S50 (= S48), K51 (≠ A49), S52 (= S50), D53 (= D51), R56 (= R54), Q59 (≠ N57)

Sites not aligning to the query:

binding : 1, 2, 63

5myjB7 of 70S ribosome from Lactococcus lactis (see paper)
52% identity, 92% coverage: 6:59/59 of query aligns to 8:61/64 of 5myjB7

query
sites
5myjB7

A
|
A

A

S

K

A

K

K

R

R

F

F

K

K

L

R

T
|
T

K

G

S
x
N

G

G

Q

G

I

L

K

K

R
|
R

K

F

H
x
R

A
|
A

Y
|
Y

T

T

S
|
S

H
|
H

L
x
R

A
x
F

P
x
H

H
x
G

K
|
K

T

S

T

V

K
|
K

Q
|
Q

K
x
R

R
|
R

H

Q

L

L

R
|
R

K

K

Q

A

G

S

T
x
M

V

V

S

S

A

K

S

G

D
|
D

F

F

K

K

R
|
R

I

I

G

R

N
x
R

L

M

I

V

binding : A8 (= A6), T16 (= T14), N18 (≠ S16), R23 (= R21), R25 (≠ H23), A26 (= A24), Y27 (= Y25), S29 (= S27), H30 (= H28), R31 (≠ L29), F32 (≠ A30), H33 (≠ P31), G34 (≠ H32), K35 (= K33), K38 (= K36), Q39 (= Q37), R40 (≠ K38), R41 (= R39), R44 (= R42), M48 (≠ T46), D53 (= D51), R56 (= R54), R59 (≠ N57)

Sites not aligning to the query:

binding : 1, 2, 3, 4, 5, 7, 64

8cd15 phikz014 (see paper)
49% identity, 93% coverage: 1:55/59 of query aligns to 3:56/63 of 8cd15

query
sites
8cd15

M
|
M

K
|
K

V
x
T

K
|
K

S
|
S

A

G

A

A

K

A

K
|
K

R
|
R

F

F

K

K

L

K

T
|
T

K

-

S

A

G

G

Q

G

I

L

K

K

R

H

K

K

H
|
H

A
|
A

Y
x
F

T
x
K

S
|
S

H
|
H

L

I

A
x
L

P
x
T

H
x
K

K

M

T

T

T
|
T

K

K

Q
x
R

K
|
K

R
|
R

H
x
Q

L

L

R
|
R

K

G

Q

T

G

S

T

M

V

L

S

N

A
x
K

S
|
S

D

D

F

V

K

A

R
|
R

I

V

binding : M3 (= M1), K4 (= K2), T5 (≠ V3), K6 (= K4), S7 (= S5), K11 (= K9), R12 (= R10), T16 (= T14), H24 (= H23), A25 (= A24), F26 (≠ Y25), K27 (≠ T26), S28 (= S27), H29 (= H28), L31 (≠ A30), T32 (≠ P31), K33 (≠ H32), T36 (= T35), R38 (≠ Q37), K39 (= K38), R40 (= R39), Q41 (≠ H40), R43 (= R42), K50 (≠ A49), S51 (= S50), R55 (= R54)

Sites not aligning to the query:

binding : 1, 2, 58, 62, 63

7unu7 50S ribosomal protein L35
49% identity, 93% coverage: 1:55/59 of query aligns to 3:56/63 of 7unu7

query
sites
7unu7

M
|
M

K
|
K

V
x
T

K

K

S
|
S

A

G

A

A

K

A

K
|
K

R
|
R

F

F

K

K

L

K

T

T

K

-

S
x
A

G
|
G

Q

G

I

L

K
|
K

R

H

K

K

H
|
H

A
|
A

Y
x
F

T

K

S
|
S

H
|
H

L

I

A
x
L

P
x
T

H
x
K

K

M

T

T

T
|
T

K
|
K

Q
x
R

K
|
K

R
|
R

H

Q

L

L

R
|
R

K

G

Q

T

G

S

T

M

V

L

S

N

A

K

S

S

D

D

F

V

K

A

R
|
R

I

V

binding magnesium ion: F26 (≠ Y25), H29 (= H28)
binding : M3 (= M1), K4 (= K2), T5 (≠ V3), S7 (= S5), K11 (= K9), R12 (= R10), A17 (≠ S16), G18 (= G17), K21 (= K20), H24 (= H23), A25 (= A24), F26 (≠ Y25), S28 (= S27), H29 (= H28), L31 (≠ A30), T32 (≠ P31), K33 (≠ H32), T36 (= T35), K37 (= K36), R38 (≠ Q37), K39 (= K38), R40 (= R39), R43 (= R42), R55 (= R54)

Sites not aligning to the query:

binding : 1, 2, 58, 63

7nhk7 50S ribosomal protein L36 (see paper)
51% identity, 80% coverage: 9:55/59 of query aligns to 11:57/64 of 7nhk7

query
sites
7nhk7

K
|
K

R
|
R

F

V

K

K

L

R

T
|
T

K
x
G

S

G

G

G

Q

G

I

L

K
|
K

R
|
R

K

G

H
x
R

A
|
A

Y
x
F

T

T

S
|
S

H
|
H

L
x
R

A
x
F

P
x
H

H

G

K

K

T

T

T
x
K

K
|
K

Q
|
Q

K
x
R

R
|
R

H

Q

L

L

R
|
R

K
|
K

Q

A

G

S

T

M

V

V

S

A

A
x
K

S

G

D
|
D

F

Y

K

K

R
|
R

I

I

binding : K11 (= K9), R12 (= R10), T16 (= T14), G17 (≠ K15), K22 (= K20), R23 (= R21), R25 (≠ H23), A26 (= A24), F27 (≠ Y25), S29 (= S27), H30 (= H28), R31 (≠ L29), F32 (≠ A30), H33 (≠ P31), K37 (≠ T35), K38 (= K36), Q39 (= Q37), R40 (≠ K38), R41 (= R39), R44 (= R42), K45 (= K43), K51 (≠ A49), D53 (= D51), R56 (= R54)

Sites not aligning to the query:

binding : 1, 2, 3, 4, 5, 6, 7, 59, 63

8a3l2 50S ribosomal protein L36 (see paper)
46% identity, 88% coverage: 1:52/59 of query aligns to 3:54/64 of 8a3l2

query
sites
8a3l2

M
x
I

K
|
K

V
x
T

K

V

S
x
R

A

G

A

A

K

A

K
|
K

R
|
R

F

F

K

K

L

K

T
|
T

K

G

S
x
K

G

G

Q

G

I

F

K
|
K

R

H

K

K

H
|
H

A

A

Y
x
N

T

L

S
x
R

H
|
H

L
x
I

A
x
L

P
x
T

H
x
K

K

K

T

A

T
|
T

K
|
K

Q
x
R

K
|
K

R
|
R

H
|
H

L

L

R
|
R

K

P

Q
x
K

G

A

T
x
M

V

V

S
|
S

A
x
K

S

G

D
|
D

F

L

binding : I3 (≠ M1), K4 (= K2), T5 (≠ V3), R7 (≠ S5), K11 (= K9), R12 (= R10), T16 (= T14), K18 (≠ S16), K22 (= K20), H25 (= H23), N27 (≠ Y25), R29 (≠ S27), H30 (= H28), I31 (≠ L29), L32 (≠ A30), T33 (≠ P31), K34 (≠ H32), T37 (= T35), K38 (= K36), R39 (≠ Q37), K40 (= K38), R41 (= R39), H42 (= H40), R44 (= R42), K46 (≠ Q44), M48 (≠ T46), S50 (= S48), K51 (≠ A49), D53 (= D51)

Sites not aligning to the query:

binding : 1, 2, 63

4v9pA3 50S ribosomal protein L35 (see paper)
46% identity, 88% coverage: 1:52/59 of query aligns to 3:54/64 of 4v9pA3

query
sites
4v9pA3

M
x
I

K
|
K

V
x
T

K

V

S
x
R

A

G

A

A

K

A

K
|
K

R
|
R

F

F

K

K

L

K

T
|
T

K
x
G

S
x
K

G

G

Q

G

I

F

K
|
K

R

H

K

K

H
|
H

A
|
A

Y
x
N

T
x
L

S
x
R

H
|
H

L
x
I

A
x
L

P
x
T

H
x
K

K

K

T

A

T
|
T

K
|
K

Q
x
R

K
|
K

R
|
R

H
|
H

L

L

R
|
R

K

P

Q
x
K

G

A

T

M

V

V

S
|
S

A
x
K

S

G

D
|
D

F

L

binding magnesium ion: L28 (≠ T26), R29 (≠ S27)
binding : I3 (≠ M1), K4 (= K2), T5 (≠ V3), R7 (≠ S5), K11 (= K9), R12 (= R10), T16 (= T14), G17 (≠ K15), K18 (≠ S16), K22 (= K20), H25 (= H23), A26 (= A24), N27 (≠ Y25), R29 (≠ S27), H30 (= H28), I31 (≠ L29), L32 (≠ A30), T33 (≠ P31), K34 (≠ H32), T37 (= T35), K38 (= K36), R39 (≠ Q37), K40 (= K38), R41 (= R39), H42 (= H40), R44 (= R42), K46 (≠ Q44), S50 (= S48), K51 (≠ A49), D53 (= D51)

Sites not aligning to the query:

binding : 1, 2, 63

7f0d3 Cryo-em structure of mycobacterium tuberculosis 50s ribosome subunit bound with clarithromycin (see paper)
40% identity, 98% coverage: 2:59/59 of query aligns to 4:61/62 of 7f0d3

query
sites
7f0d3

K
|
K

V
x
T

K
x
H

S
|
S

A
x
G

A

A

K

S

K
|
K

R
|
R

F

F

K

R

L

R

T
|
T

K
x
G

S
x
T

G

G

Q
x
K

I

I

K

V

R
|
R

K

Q

H

K

A
|
A

Y
x
N

T

R

S
x
R

H
|
H

L
|
L

A
x
L

P

E

H

H

K

K

T

P

T

S

K

T

Q
x
R

K

T

R
|
R

H
x
R

L
|
L

R

D

K

G

Q
x
R

G

T

T

V

V

V

S

A

A

A

S
x
N

D

D

F

T

K
|
K

R
|
R

I

V

G

T

N

S

L

L

I

L

binding : K4 (= K2), T5 (≠ V3), H6 (≠ K4), S7 (= S5), G8 (≠ A6), K11 (= K9), R12 (= R10), T16 (= T14), G17 (≠ K15), T18 (≠ S16), K20 (≠ Q18), R23 (= R21), A26 (= A24), N27 (≠ Y25), R29 (≠ S27), H30 (= H28), L31 (= L29), L32 (≠ A30), R39 (≠ Q37), R41 (= R39), R42 (≠ H40), L43 (= L41), R46 (≠ Q44), N52 (≠ S50), K55 (= K53), R56 (= R54)

Sites not aligning to the query:

binding : 1, 2, 3, 62

Query Sequence

>59 a.a. (MKVKSAAKKR...)
MKVKSAAKKRFKLTKSGQIKRKHAYTSHLAPHKTTKQKRHLRKQGTVSASDFKRIGNLI

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