SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing PP_4894 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)

3quiA Crystal structure of pseudomonas aeruginosa hfq in complex with adpnp (see paper)
94% identity, 83% coverage: 2:72/86 of query aligns to 1:71/71 of 3quiA

query
sites
3quiA

S

S

K

K

G

G

H

H

S

S

L

L

Q

Q

D

D

P

P

Y

Y

L

L

N

N

T

T

L

L

R

R

K

K

E

E

K

R

V

V

P

P

V

V

S

S

I

I

Y
|
Y

L

L

V

V

N

N

G

G

I
|
I

K

K

L

L

Q

Q

G

G

S

Q

I

I

E

E

S

S

F

F

D

D

Q

Q

F

F

V

V

V

I

L

L

L

L

K

K

N

N

T

T

V

V

S

S

Q
|
Q

M

M

V

V

Y

Y

K

K

H

H

A

A

I

I

S

S

T
|
T

V

V

V

V

P

P

A

S

R

R

P

P

V

V

R

R

L

L

P

P

S

S

binding adenosine-5'-diphosphate: Y24 (= Y25), I29 (= I30), Q51 (= Q52), T60 (= T61)

3m4gF H57a hfq from pseudomonas aeruginosa (see paper)
93% identity, 83% coverage: 2:72/86 of query aligns to 1:71/71 of 3m4gF

query
sites
3m4gF

S

S

K

K

G

G

H
|
H

S

S

L

L

Q

Q

D
|
D

P

P

Y

Y

L

L

N

N

T

T

L

L

R

R

K

K

E

E

K

R

V

V

P

P

V

V

S

S

I

I

Y

Y

L

L

V

V

N

N

G

G

I

I

K

K

L

L

Q

Q

G

G

S

Q

I

I

E

E

S

S

F

F

D

D

Q

Q

F

F

V

V

V

I

L

L

L

L

K

K

N

N

T

T

V

V

S

S

Q

Q

M

M

V

V

Y

Y

K

K

H

A

A

A

I

I

S

S

T

T

V

V

V

V

P

P

A

S

R

R

P

P

V

V

R

R

L

L

P

P

S

S

binding zinc ion: H4 (= H5), D8 (= D9)

3quiE Crystal structure of pseudomonas aeruginosa hfq in complex with adpnp (see paper)
94% identity, 78% coverage: 4:70/86 of query aligns to 1:67/67 of 3quiE

query
sites
3quiE

G

G

H

H

S

S

L

L

Q

Q

D

D

P

P

Y

Y

L

L

N

N

T

T

L

L

R

R

K

K

E

E

K

R

V

V

P

P

V

V

S

S

I

I

Y
|
Y

L

L

V

V

N

N

G

G

I

I

K

K

L
|
L

Q

Q

G

G

S

Q

I

I

E

E

S

S

F

F

D

D

Q

Q

F

F

V

V

V

I

L

L

L

L

K

K

N

N

T

T

V

V

S

S

Q
|
Q

M

M

V

V

Y

Y

K

K

H

H

A

A

I

I

S

S

T
|
T

V

V

V

V

P

P

A

S

R

R

P

P

V

V

R

R

L

L

binding adenine: L29 (= L32), Q49 (= Q52)
binding phosphoaminophosphonic acid-adenylate ester: Y22 (= Y25), T58 (= T61)

4j6wA Crystal structure of hfq from pseudomonas aeruginosa in complex with ctp (see paper)
94% identity, 78% coverage: 5:71/86 of query aligns to 1:67/67 of 4j6wA

query
sites
4j6wA

H
|
H

S

S

L

L

Q
|
Q

D

D

P

P

Y

Y

L

L

N

N

T

T

L

L

R

R

K

K

E

E

K

R

V

V

P

P

V

V

S

S

I

I

Y
|
Y

L

L

V

V

N

N

G
|
G

I

I

K

K

L

L

Q

Q

G

G

S

Q

I

I

E

E

S

S

F
|
F

D
|
D

Q
|
Q

F
|
F

V

V

V

I

L

L

L

L

K

K

N

N

T

T

V

V

S

S

Q

Q

M

M

V

V

Y
|
Y

K
|
K

H
|
H

A

A

I

I

S

S

T
|
T

V

V

V

V

P

P

A

S

R

R

P

P

V

V

R

R

L

L

P

P

binding cytidine-5'-monophosphate: H1 (= H5), Q4 (= Q8), Q37 (= Q41), F38 (= F42), K52 (= K56)
binding cytidine-5'-triphosphate: Y21 (= Y25), G25 (= G29), F38 (= F42), Y51 (= Y55), H53 (= H57), T57 (= T61)
binding magnesium ion: F35 (= F39), D36 (= D40), K52 (= K56)

3quiD Crystal structure of pseudomonas aeruginosa hfq in complex with adpnp (see paper)
94% identity, 78% coverage: 6:72/86 of query aligns to 1:67/67 of 3quiD

query
sites
3quiD

S

S

L

L

Q
|
Q

D

D

P

P

Y

Y

L

L

N

N

T

T

L

L

R

R

K

K

E

E

K

R

V

V

P

P

V

V

S

S

I

I

Y
|
Y

L

L

V

V

N

N

G

G

I

I

K

K

L

L

Q

Q

G

G

S

Q

I

I

E

E

S

S

F

F

D

D

Q
|
Q

F
|
F

V

V

V

I

L

L

L

L

K

K

N

N

T

T

V

V

S

S

Q

Q

M

M

V

V

Y

Y

K

K

H
|
H

A

A

I

I

S

S

T
|
T

V

V

V

V

P

P

A

S

R

R

P

P

V

V

R

R

L

L

P

P

S

S

binding phosphoaminophosphonic acid-adenylate ester: Q3 (= Q8), Y20 (= Y25), Q36 (= Q41), F37 (= F42), H52 (= H57), T56 (= T61)

4mmlA D40a hfq from pseudomonas aeruginosa (see paper)
93% identity, 78% coverage: 4:70/86 of query aligns to 1:67/67 of 4mmlA

query
sites
4mmlA

G

G

H

H

S

S

L

L

Q
|
Q

D

D

P

P

Y

Y

L

L

N

N

T

T

L

L

R

R

K

K

E

E

K

R

V

V

P

P

V

V

S

S

I

I

Y

Y

L

L

V

V

N

N

G

G

I

I

K

K

L

L

Q

Q

G

G

S

Q

I

I

E

E

S

S

F

F

D

A

Q
|
Q

F
|
F

V

V

V

I

L

L

L

L

K

K

N

N

T

T

V

V

S

S

Q

Q

M

M

V

V

Y

Y

K

K

H

H

A

A

I

I

S

S

T

T

V

V

V

V

P

P

A

S

R

R

P

P

V

V

R

R

L

L

binding uridine-5'-monophosphate: Q5 (= Q8), Q38 (= Q41), F39 (= F42)

4j6xA Crystal structure of hfq from pseudomonas aeruginosa in complex with utp (see paper)
94% identity, 77% coverage: 6:71/86 of query aligns to 1:66/66 of 4j6xA

query
sites
4j6xA

S

S

L

L

Q

Q

D

D

P

P

Y

Y

L

L

N
|
N

T

T

L

L

R
|
R

K

K

E

E

K

R

V

V

P

P

V

V

S

S

I

I

Y

Y

L

L

V

V

N

N

G

G

I

I

K

K

L

L

Q

Q

G

G

S

Q

I

I

E

E

S
|
S

F
|
F

D

D

Q

Q

F

F

V

V

V

I

L

L

L

L

K

K

N

N

T

T

V

V

S

S

Q

Q

M

M

V

V

Y

Y

K

K

H

H

A

A

I

I

S

S

T

T

V

V

V

V

P

P

A

S

R

R

P

P

V

V

R

R

L

L

P

P

binding uridine 5'-triphosphate: N8 (= N13), R11 (= R16), S33 (= S38), F34 (= F39)

4j6wD Crystal structure of hfq from pseudomonas aeruginosa in complex with ctp (see paper)
94% identity, 76% coverage: 5:69/86 of query aligns to 1:65/65 of 4j6wD

query
sites
4j6wD

H
|
H

S

S

L

L

Q
|
Q

D

D

P

P

Y

Y

L

L

N

N

T

T

L

L

R

R

K

K

E

E

K

R

V

V

P

P

V

V

S

S

I

I

Y
|
Y

L

L

V

V

N

N

G
|
G

I

I

K
|
K

L

L

Q

Q

G

G

S

Q

I

I

E

E

S

S

F

F

D

D

Q
|
Q

F
|
F

V

V

V

I

L

L

L

L

K

K

N

N

T

T

V

V

S

S

Q

Q

M

M

V

V

Y
|
Y

K
|
K

H
|
H

A

A

I

I

S

S

T
|
T

V

V

V

V

P

P

A

S

R

R

P

P

V

V

R

R

binding cytidine-5'-monophosphate: H1 (= H5), Q4 (= Q8), Q37 (= Q41), F38 (= F42), K52 (= K56), H53 (= H57)
binding cytidine-5'-diphosphate: F38 (= F42), Y51 (= Y55), H53 (= H57)
binding cytidine-5'-triphosphate: Y21 (= Y25), G25 (= G29), K27 (= K31), T57 (= T61)
binding magnesium ion: F38 (= F42), K52 (= K56), H53 (= H57)

5uk7C Escherichia coli hfq bound to dsdna
87% identity, 78% coverage: 2:68/86 of query aligns to 1:67/67 of 5uk7C

query
sites
5uk7C

S
x
A

K
|
K

G

G

H

Q

S

S

L

L

Q

Q

D

D

P
|
P

Y

F

L

L

N
|
N

T

A

L

L

R

R

K
x
R

E

E

K

R

V

V

P

P

V

V

S

S

I

I

Y

Y

L

L

V

V

N

N

G

G

I

I

K

K

L

L

Q

Q

G

G

S

Q

I

I

E

E

S

S

F

F

D

D

Q

Q

F

F

V

V

V

I

L

L

L

L

K

K

N

N

T

T

V

V

S

S

Q

Q

M

M

V

V

Y

Y

K

K

H

H

A

A

I

I

S

S

T

T

V

V

V

V

P

P

A

S

R

R

P

P

V

V

binding : A1 (≠ S2), K2 (= K3), P9 (= P10), N12 (= N13), R16 (≠ K17)

4v2sA Crystal structure of hfq in complex with the srna rydc (see paper)
88% identity, 76% coverage: 4:68/86 of query aligns to 1:65/71 of 4v2sA

query
sites
4v2sA

G

G

H

Q

S

S

L

L

Q

Q

D

D

P

P

Y

F

L

L

N

N

T

A

L

L

R

R

K

R

E

E

K

R

V

V

P

P

V

V

S

S

I

I

Y

Y

L

L

V

V

N

N

G

G

I

I

K

K

L

L

Q

Q

G

G

S

Q

I

I

E

E

S

S

F

F

D

D

Q
|
Q

F
|
F

V

V

V

I

L

L

L

L

K

K

N

N

T

T

V

V

S

S

Q

Q

M

M

V

V

Y
|
Y

K

K

H
|
H

A

A

I

I

S

S

T

T

V

V

V

V

P

P

A

S

R

R

P

P

V

V

binding : Q38 (= Q41), F39 (= F42), Y52 (= Y55), H54 (= H57)

2ylcA Structure of salmonella typhimurium hfq in complex with u6 RNA (see paper)
88% identity, 74% coverage: 5:68/86 of query aligns to 1:64/66 of 2ylcA

query
sites
2ylcA

H

Q

S

S

L

L

Q

Q

D

D

P

P

Y

F

L

L

N

N

T

A

L

L

R

R

K

R

E

E

K

R

V

V

P

P

V

V

S

S

I

I

Y

Y

L

L

V

V

N

N

G

G

I

I

K

K

L

L

Q

Q

G

G

S

Q

I

I

E

E

S

S

F

F

D

D

Q

Q

F
|
F

V

V

V

I

L

L

L

L

K

K

N

N

T

T

V

V

S

S

Q

Q

M

M

V

V

Y

Y

K

K

H
|
H

A

A

I

I

S

S

T

T

V

V

V

V

P

P

A

S

R

R

P

P

V

V

binding uridine-5'-monophosphate: F38 (= F42), H53 (= H57)

3gibA Crystal structure of the complex of the e. Coli hfq with poly(a) (see paper)
89% identity, 73% coverage: 6:68/86 of query aligns to 1:63/64 of 3gibA

query
sites
3gibA

S

S

L

L

Q

Q

D

D

P

P

Y

F

L

L

N

N

T

A

L

L

R

R

K

R

E

E

K

R

V

V

P

P

V

V

S

S

I

I

Y
|
Y

L

L

V

V

N

N

G
|
G

I
|
I

K
|
K

L
|
L

Q
|
Q

G

G

S

Q

I

I

E

E

S

S

F

F

D

D

Q

Q

F

F

V

V

V

I

L

L

L

L

K

K

N
|
N

T

T

V

V

S

S

Q
|
Q

M

M

V

V

Y

Y

K

K

H

H

A

A

I

I

S

S

T
|
T

V

V

V

V

P

P

A

S

R

R

P

P

V

V

binding : Y20 (= Y25), G24 (= G29), I25 (= I30), K26 (= K31), L27 (= L32), Q28 (= Q33), N43 (= N48), Q47 (= Q52), T56 (= T61)

3qo3A Crystal structure of escherichia coli hfq, in complex with atp (see paper)
87% identity, 71% coverage: 5:65/86 of query aligns to 1:61/61 of 3qo3A

query
sites
3qo3A

H

Q

S

S

L

L

Q

Q

D

D

P

P

Y

F

L

L

N

N

T

A

L

L

R

R

K

R

E

E

K

R

V

V

P

P

V

V

S

S

I

I

Y
|
Y

L

L

V

V

N

N

G
|
G

I

I

K

K

L

L

Q

Q

G

G

S

Q

I

I

E

E

S

S

F

F

D

D

Q

Q

F

F

V

V

V

I

L

L

L

L

K

K

N

N

T

T

V

V

S

S

Q

Q

M

M

V

V

Y

Y

K

K

H

H

A

A

I

I

S

S

T
|
T

V

V

V

V

P

P

A

S

binding adenosine-5'-triphosphate: Y21 (= Y25), G25 (= G29), T57 (= T61)

4pnoA Escherichia coli hfq-RNA complex at 0.97 a resolution (see paper)
87% identity, 73% coverage: 6:68/86 of query aligns to 1:62/64 of 4pnoA

query
sites
4pnoA

S

S

L

L

Q
|
Q

D

D

P

P

Y

F

L

L

N

N

T

A

L

L

R

R

K

R

E

E

K

R

V

V

P

P

V

V

S

S

I

I

Y

Y

L

L

V

V

N

N

G

G

I

I

K

K

L

L

Q

Q

G

G

S

Q

I

I

E

E

S

S

F

F

D

D

Q
|
Q

F
|
F

V

V

V

I

L

L

L

L

K

K

N

-

T

T

V

V

S

S

Q

Q

M

M

V

V

Y

Y

K
|
K

H
|
H

A

A

I

I

S

S

T

T

V

V

V

V

P

P

A

S

R

R

P

P

V

V

binding uridine-5'-monophosphate: Q3 (= Q8), Q36 (= Q41), F37 (= F42), K50 (= K56), H51 (= H57)

5szeA Crystal structure of aquifex aeolicus hfq-RNA complex at 1.5a (see paper)
57% identity, 70% coverage: 5:64/86 of query aligns to 4:64/71 of 5szeA

query
sites
5szeA

H

Y

S

K

L

L

Q

Q

D

E

P

S

Y

F

L

L

N
|
N

T

T

L

A

R
|
R

K

K

E

K

K

R

V

V

P

K

V

V

S

S

I

V

Y

Y

L

L

V

V

N

N

G

G

I

V

K

R

L

L

Q

Q

G

G

S

R

I

I

E

R

S
|
S

F
|
F

D

D

Q

L

F

F

V

T

V

I

L

L

L

L

K

E

N

D

T

G

V

K

S

Q

Q

Q

-

T

M

L

V

V

Y

Y

K

K

H

H

A

A

I

I

S

T

T

T

V

I

V

V

P

P

binding : N12 (= N13), R15 (= R16), S37 (= S38), F38 (= F39)

4nl3F Crystal structure of listeria monocytogenes hfq in complex with u6 rna (see paper)
51% identity, 78% coverage: 4:70/86 of query aligns to 5:72/75 of 4nl3F

query
sites
4nl3F

G

G

H
x
Q

S

G

L

L

Q
|
Q

D

D

P

Y

Y

Y

L

L

N

N

T

Q

L

L

R

R

K

K

E

E

K

K

V

I

P

L

V

A

S

T

I

V

Y

F

L

L

V

T

N

N

G

G

I

F

K

Q

L

L

Q

R

G

G

S

R

I

V

E

V

S

S

F

F

D

D

Q
x
N

F
|
F

V

T

V

V

L

L

L

L

K

D

-

V

N

E

T

G

V

K

S

Q

Q

Q

M

L

V

V

Y

F

K
|
K

H
|
H

A

A

I

I

S

S

T

T

V

F

V

S

P

P

A

Q

R

K

P

N

V

V

R

A

L

L

binding : Q6 (≠ H5), Q9 (= Q8), N42 (≠ Q41), F43 (= F42), K58 (= K56), H59 (= H57)

3hsbB Crystal structure of ymah (hfq) from bacillus subtilis in complex with an RNA aptamer (see paper)
45% identity, 77% coverage: 6:71/86 of query aligns to 2:68/69 of 3hsbB

query
sites
3hsbB

S

N

L

I

Q

Q

D

D

P

Q

Y

F

L

L

N

N

T

Q

L

I

R

R

K

K

E

E

K

N

V

T

P

Y

V

V

S

T

I

V

Y
x
F

L
|
L

V

L

N

N

G
|
G

I
x
F

K
x
Q

L

L

Q
x
R

G

G

S

Q

I

V

E

K

S

G

F

F

D

D

Q

N

F

F

V

T

V

V

L

L

L

L

K

E

N

S

T

E

-

G

V

K

S

Q

Q

Q

M

L

V

I

Y

Y

K

K

H

H

A

A

I

I

S
|
S

T
|
T

V

F

V

A

P

P

A

Q

R

K

P

N

V

V

R

Q

L

L

P

E

binding : F21 (≠ Y25), L22 (= L26), G25 (= G29), F26 (≠ I30), Q27 (≠ K31), R29 (≠ Q33), S57 (= S60), T58 (= T61)

4y91F Crystal structure of a thermotoga maritima hfq homolog
46% identity, 79% coverage: 1:68/86 of query aligns to 4:72/73 of 4y91F

query
sites
4y91F

M

L

S

A

K

E

G

K

H

F

S

N

L

L

Q
|
Q

D

D

P

R

Y

F

L

L

N

N

T

H

L

L

R

R

K

V

E

N

K

K

V

I

P

E

V

V

S

K

I

V

Y

Y

L

L

V

V

N

N

G

G

I

F

K

Q

L

T

Q

K

G

G

S

F

I

I

E

R

S

S

F

F

D

D

Q
x
S

F
x
Y

V

T

V

V

L

L

L

L

K

E

N

S

T

G

V

N

S

Q

Q

Q

-

S

M

L

V

I

Y
|
Y

K
|
K

H
|
H

A

A

I

I

S

S

T

T

V

I

V

I

P

P

A

S

R

S

P

Y

V

V

binding : Q11 (= Q8), S44 (≠ Q41), Y45 (≠ F42), Y59 (= Y55), K60 (= K56), H61 (= H57)

1kq2H Crystal structure of an hfq-RNA complex (see paper)
37% identity, 65% coverage: 6:61/86 of query aligns to 2:58/62 of 1kq2H

query
sites
1kq2H

S

N

L

I

Q
|
Q

D

D

P

K

Y

A

L

L

N

E

T

N

L

F

R

K

K

A

E

N

K

Q

V

T

P

E

V

V

S

T

I

V

Y

F

L

F

V

L

N

N

G

G

I

F

K

Q

L

M

Q

K

G

G

S

V

I

I

E

E

S

E

F

Y

D

D

Q
x
K

F
x
Y

V

V

V

V

L

S

L

L

K

N

N

S

T

Q

V

G

S

K

Q

Q

-

H

M

L

V

I

Y

Y

K
|
K

H
|
H

A

A

I

I

S

S

T

T

binding : Q4 (= Q8), K37 (≠ Q41), Y38 (≠ F42), K53 (= K56), H54 (= H57)

3qsuB Structure of staphylococcus aureus hfq in complex with a7 RNA (see paper)
37% identity, 65% coverage: 6:61/86 of query aligns to 1:57/61 of 3qsuB

query
sites
3qsuB

S

N

L

I

Q

Q

D

D

P

K

Y

A

L

L

N

E

T

N

L

F

R

K

K

A

E

N

K

Q

V

T

P

E

V

V

S

T

I

V

Y

F

L

F

V

L

N
|
N

G

G

I
x
F

K

Q

L

M

Q

K

G

G

S

V

I

I

E

E

S

E

F

Y

D

D

Q

K

F

Y

V

V

V

V

L

S

L

L

K

N

N

S

T

Q

V

G

S
x
K

Q

Q

-
x
H

M

L

V

I

Y

Y

K

K

H

H

A

A

I

I

S

S

T

T

binding zinc ion: K46 (≠ S51), H48 (vs. gap)
binding : N23 (= N28), F25 (≠ I30)

Query Sequence

>PP_4894
MSKGHSLQDPYLNTLRKEKVPVSIYLVNGIKLQGSIESFDQFVVLLKNTVSQMVYKHAIS
TVVPARPVRLPSPTDSEHGDSEPGNA

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