SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing mRNA_3004 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 19 hits to proteins with known functional sites (download)

Q9FKB0 Sm-like protein LSM5; AtLSM5; Protein SUPERSENSITIVE TO ABA AND DROUGHT 1; AtSAD1; U6 snRNA-associated Sm-like protein LSM5 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
70% identity, 95% coverage: 3:83/85 of query aligns to 6:86/88 of Q9FKB0

query
sites
Q9FKB0

S

S

T

Q

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L

L

L

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P

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E
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E

L

L

V

I

D

D

R

R

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C

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G

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S

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K

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M

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E

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F

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D

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Y

Y

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N

N

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M

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L

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E

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Y

Y

E

E

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A

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K

R

S

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K

K

L

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D

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Q

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I

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L

N

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G

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N

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A

A

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P

E

E

D

D

E12 (= E9) mutation to K: In sad1; decreased germination rate, dwarf plants with round-shaped leaves and increased sensitivity to inhibition of seed germination and plant growth by exogenous ABA.

3swnA Structure of the lsm657 complex: an assembly intermediate of the lsm1 7 and lsm2 8 rings (see paper)
63% identity, 92% coverage: 4:81/85 of query aligns to 1:76/76 of 3swnA

query
sites
3swnA

T

T

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I

L

L

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P

L

L

E

E

L

L

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I

D

D

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K

A

C

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N

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K

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E

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F

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G

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T

L

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F

F

D

D

Y

Y

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V

N

N

M

I

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V

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K

D

D

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V

T

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E
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E

Y

Y

E

D

T

T

T

V

A

T

E

-

G

-

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G

K

V

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S
x
E

K

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L
x
H

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L

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N

N

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G

N

N

N

G

I

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A

C

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M

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I

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P

G

G

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G

G

K

P

P

binding zinc ion: E46 (= E49), E55 (≠ S60), H57 (≠ L62)

6ppqE Structure of s. Pombe lsm1-7 with RNA, polyuridine with 3' adenosine (see paper)
62% identity, 91% coverage: 5:81/85 of query aligns to 1:75/75 of 6ppqE

query
sites
6ppqE

I

I

L

L

P

P

L

L

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E

L

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A

C

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G

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N

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K

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E

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F

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A

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L

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G

F

F

D

D

Y

Y

V

V

N

N

M

I

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V

L

L

E

K

D

D

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V

T

T

E

E

Y

Y

E

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T

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A

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E

-

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-

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M

L

L

N
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N

G

G

N
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N

N

G

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M

A

C

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M

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L

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I

P

P

G

G

R

G

G

K

P

P

binding : N62 (= N68), N64 (= N70)

P40089 U6 snRNA-associated Sm-like protein LSm5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 2 papers)
48% identity, 87% coverage: 5:78/85 of query aligns to 6:84/93 of P40089

query
sites
P40089

I

I

L

L

P

P

L

L

E

E

L

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I

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D

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K

A

T

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F

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E

G

G

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T

L

L

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G

F

F

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D

Y

F

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V

N

N

M

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L

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E

D

D

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A

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E

E

Y

W

E

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A

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E

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K

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V

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M

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Q

-

H

L

H

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G

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M

L

L

N
x
S

G

G

N

N

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I

A

A

M

I

I

L

V

V

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P

G

G

S74 (≠ N68) mutation to A: Slightly increases affinity for poly-U RNA ends.

1lojC Crystal structure of a methanobacterial sm-like archaeal protein (smap1) bound to uridine-5'-monophosphate (ump) (see paper)
37% identity, 86% coverage: 7:79/85 of query aligns to 4:73/77 of 1lojC

query
sites
1lojC

P

P

L

L

E

D

L

A

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L

D

G

R

N

A

S

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G

N

S

S

K

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E

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F

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Y
x
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M

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N

M

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N

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E

E

E

Y

L

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A

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N
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G

N
x
D

N

N

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A

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Y

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S

P

R

G

G

R

K

binding uridine: H36 (≠ Y39), N38 (= N41), R62 (≠ N68), D64 (≠ N70)

1lojA Crystal structure of a methanobacterial sm-like archaeal protein (smap1) bound to uridine-5'-monophosphate (ump) (see paper)
37% identity, 86% coverage: 7:79/85 of query aligns to 6:75/76 of 1lojA

query
sites
1lojA

P

P

L

L

E

D

L

A

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D

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N

A

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F

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x
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N
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N

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L

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N

D

D

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A

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E

E

E

Y

L

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T

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A

-

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G

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S

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K

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L

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G

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L

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I

N
x
R

G

G

N
x
D

N

N

I

I

A

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M

Y

I

I

V

S

P

R

G

G

R

K

binding uridine-5'-monophosphate: H38 (≠ Y39), N40 (= N41), R64 (≠ N68), D66 (≠ N70)

7abgj pre-Bact-1 spliceosome (see paper)
32% identity, 81% coverage: 7:75/85 of query aligns to 7:77/81 of 7abgj

query
sites
7abgj

P

P

L

I

E

N

L

L

V

I

D

F

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A

Y

I

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G

Q

S

N

K

R

-

S

-

R

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I

-

Q

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V

W

W

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I
x
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M

E

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N

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R

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I

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G

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C

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G

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F

D

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D

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Y
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Y

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M

N

N

M

L

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L

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D

D

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A

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E

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Y

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K

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M

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L

N

K

G

G

N

D

N

N

I

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A

T

M

L

I

L

binding : Y26 (≠ I22), Y43 (= Y39)

1m8vA Structure of pyrococcus abyssii sm protein in complex with a uridine heptamer (see paper)
34% identity, 84% coverage: 7:77/85 of query aligns to 4:71/72 of 1m8vA

query
sites
1m8vA

P

P

L
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L

E
x
D

L

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D
x
H

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S

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D

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F

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G

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Y

D

D

D

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Y
x
H

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L

N
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N

M

V

V

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L

E

A

D

D

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A

T

-

E

-

Y

-

E

E

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M

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I

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G

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K

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N
x
R

G

G

N
x
D

N

N

I

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A

L

M

A

I

I

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S

P

P

binding uridine-5'-monophosphate: H36 (≠ Y39), N38 (= N41), R62 (≠ N68), D64 (≠ N70)
binding : L5 (= L8), D6 (≠ E9), H9 (≠ D12), Y33 (≠ F36)

Sites not aligning to the query:

binding : 3

1i5lE Crystal structure of an sm-like protein (af-sm1) from archaeoglobus fulgidus complexed with short poly-u RNA (see paper)
35% identity, 85% coverage: 7:78/85 of query aligns to 3:71/71 of 1i5lE

query
sites
1i5lE

P

P

L

L

E

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T

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D

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G

F

Y

D

D

D
x
I

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x
H

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M

N
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N

M

L

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V

L

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E

L

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D

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E

E

E

Y

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N

T

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A

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-

G

G

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R

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G

N
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D

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F

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V

S

P

P

G

A

binding : I34 (≠ D38), H35 (≠ Y39), N37 (= N41), R61 (≠ N68), D63 (≠ N70)

1i5lC Crystal structure of an sm-like protein (af-sm1) from archaeoglobus fulgidus complexed with short poly-u RNA (see paper)
35% identity, 85% coverage: 7:78/85 of query aligns to 5:73/74 of 1i5lC

query
sites
1i5lC

P

P

L

L

E

D

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D

N

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G

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L

L

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G

G

F

Y

D

D

D

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x
H

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M

N
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N

M

L

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V

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L

E

L

D

D

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A

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E

E

E

Y

I

E

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N

T

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A

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E

-

G

G

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G

G

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S

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I

N
x
R

G

G

N
x
D

N

T

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A

V

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F

I

V

V

S

P

P

G

A

binding uridine: H37 (≠ Y39), N39 (= N41), R63 (≠ N68), D65 (≠ N70)

8xi2e Cryo-em structure of the chlamydomonas c Complex (see paper)
34% identity, 81% coverage: 7:75/85 of query aligns to 5:75/80 of 8xi2e

query
sites
8xi2e

P

P

L

I

E

N

L

L

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D

F

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A

F

I

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G

Q

S

S

K

K

-

Q

-

K

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V

-

Q

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I

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W

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x
F

M

D

K

Q

T

A

E

D

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L

E

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E

G

G

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I

G

G

F

F

D

D

D

E

Y
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Y

V

M

N

N

M

L

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V

L

L

E

D

D

E

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A

T

E

E

E

Y

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E

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A

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R

K

K

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T

S

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K

-

L

L

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G

Q

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T

I

L

L

N

K

G

G

N
x
D

N

N

I

I

A

T

M

L

I

I

binding : F24 (≠ I22), Y41 (= Y39), D70 (≠ N70)

6qw663 U4/U6 small nuclear ribonucleoprotein Prp3 (see paper)
31% identity, 84% coverage: 7:77/85 of query aligns to 4:84/85 of 6qw663

query
sites
6qw663

P

P

L

L

E

D

L

L

V

I

D

R

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A

S

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G

D

S

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M

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N

E

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R

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E

F

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G

T

R

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H

G

A

F

Y

D

D

D

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Y
x
H

V

L

N
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N

M

M

V

I

L

L

E

G

D

D

V

V

T

E

E

E

Y

T

-

V

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T

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I

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E

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I

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D

-

E

E

E

T

T

T

Y

A

E

E

E

G

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K

K

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S

S

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K

K

L

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G

N

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P

L

M

L

L

-

F

-

V

N
x
R

G
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G

N
x
D

N

G

I

V

A

V

M

L

I

V

V

A

P

P

binding : H36 (≠ Y39), N38 (= N41), R75 (≠ N68), G76 (= G69), D77 (≠ N70)

6ppqF Structure of s. Pombe lsm1-7 with RNA, polyuridine with 3' adenosine (see paper)
30% identity, 81% coverage: 7:75/85 of query aligns to 3:68/71 of 6ppqF

query
sites
6ppqF

P

P

L

N

E

E

L

F

V

L

D

N

R

K

A

V

I

I

G

G

S

K

K

K

V

V

W

L

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I

I

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M

L

K

S

T

S

E

G

R

V

E

D

F

Y

T

K

G

G

T

I

L

L

V

S

G

C

F

L

D

D

D

G

Y

Y

V

M

N

N

M

L

V

A

L

L

E

E

D

R

V

T

T

E

E

E

Y

Y

E

-

T

-

A

V

E

N

G

G

R

K

K

K

S

T

S

N

K

V

L

Y

G

G

Q

D

T

A

L

F

L

I

N
x
R

G

G

N
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N

N

N

I

V

A

L

M

Y

I

V

binding : R61 (≠ N68), N63 (= N70)

9eshH Structure of a b-state intermediate committed to discard (bd-i state) (see paper)
29% identity, 80% coverage: 8:75/85 of query aligns to 13:77/80 of 9eshH

query
sites
9eshH

L

F

E

K

L

L

V

L

D

Q

R

Q

A

H

I

T

G

P

S

V

K

S

V

I

W

W

V

L

I
x
F

M
x
E

K
x
Q

T

T

E

D

R

I

E

R

F

L

T

Q

G

G

T

Q

L

I

V

R

G

G

F

F

D

D

D

E

Y
x
F

V

M

N

N

M

I

V

V

L

L

E

D

D

D

V

A

T

V

E

Q

Y

V

E

D

T

A

T

K

A

N

E

N

G

K

R

R

K

-

S

-

K

E

L

L

G

G

Q

R

T

I

L

L

N

K

G

G

N

D

N

N

I

I

A

T

M

L

I

I

binding : F27 (≠ I22), E28 (≠ M23), Q29 (≠ K24), F44 (≠ Y39)

6ppnC Structure of s. Pombe lsm2-8 with unprocessed u6 snrna (see paper)
32% identity, 84% coverage: 7:77/85 of query aligns to 2:74/75 of 6ppnC

query
sites
6ppnC

P

P

L

L

E

D

L

L

V

V

D

R

R

L

A

S

I

L

G

D

S

E

K

I

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W

Y

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I

K

M

L

K

R

T

G

E

D

R

R

E

E

F

L

T

N

G

G

T

R

L

L

V

H

G

A

F

Y

D

D

D

E

Y
x
H

V

L

N
|
N

M

M

V

V

L

L

E

G

D

D

V

A

T

E

E

E

Y

I

E

V

T

T

T

I

A

F

E

K

G

A

R

L

K

K

S

T

S

I

K

R

L

K

G

H

Q

Y

T

E

L

M

L

L

-

F

-

V

N
x
R

G
|
G

N
x
D

N

S

I

V

A

I

M

L

I

I

V

A

P

P

binding : H34 (≠ Y39), N36 (= N41), R65 (≠ N68), G66 (= G69), D67 (≠ N70)

4wzjMM Small nuclear ribonucleoprotein F (see paper)
34% identity, 100% coverage: 1:85/85 of query aligns to 1:79/80 of 4wzjMM

query
sites
4wzjMM

M

M

A

S

S

L

T

P

I

L

L

N

P

P

L

K

E

P

L

F

V

L

D

N

R

G

A

L

I

T

G

G

S

K

K

P

V

V

W

M

V

V

I

K

M

L

K
|
K

T
x
W

E

G

R

M

E

E

F

Y

T

K

G

G

T

Y

L

L

V

V

G

S

F

V

D

D

D
x
G

Y
|
Y

V
x
M

N
|
N

M

M

V

Q

L

L

E

A

D

N

V

T

T

E

E

E

Y

Y

E

-

T

-

A

I

E

D

G

G

R

A

K

L

S

S

S

G

K

H

L

L

G

G

Q

E

T

V

L

L

L

I

N
x
R

G

C

N
|
N

N

N

I

V

A

L

M

Y

I

I

V

-

P

-

G

-

R

R

G

G

P

V

E

E

D

E

E

E

Q

E

binding : K24 (= K24), W25 (≠ T25), G38 (≠ D38), Y39 (= Y39), M40 (≠ V40), N41 (= N41), R65 (≠ N68), N67 (= N70)

6ppnD Structure of s. Pombe lsm2-8 with unprocessed u6 snrna (see paper)
32% identity, 84% coverage: 5:75/85 of query aligns to 1:69/88 of 6ppnD

query
sites
6ppnD

I

M

L

L

P

P

L

L

E

T

L

L

V

L

D

N

R

A

A

T

I

Q

G

G

S

R

K

P

V

I

W

L

V

V

I

E

M

L

K

K

T

N

E

G

R

E

E

T

F

F

T

N

G

G

T

H

L

L

V

E

G

N

F

C

D

D

D

N

Y
|
Y

V

M

N
|
N

M

L

V

T

L

L

E

R

D

E

V

V

T

I

E

-

Y

-

E

R

T

T

T

M

A

P

E

D

G

G

R

D

K

K

S

F

K

R

L

L

G

P

Q

E

T

C

L

Y

L

I

N
x
R

G

G

N
|
N

N

N

I

I

A

K

M

Y

I

L

binding : Y35 (= Y39), N37 (= N41), R62 (≠ N68), N64 (= N70)

9dtre Structure of the yeast post-catalytic p complex spliceosome at 2.3 angstrom resolution (see paper)
32% identity, 67% coverage: 19:75/85 of query aligns to 22:83/86 of 9dtre

query
sites
9dtre

V

I

W

W

V

L

I
x
F

M
x
E

K
x
Q

T

I

E

G

R

I

E

R

F

I

T

K

G

G

T

K

L

I

V

V

G

G

F

F

D

D

D

E

Y
x
F

V

M

N

N

M

V

V

V

L

I

E

D

D

E

V

A

T

V

E

E

Y

I

E

P

T

V

-

N

T

S

A

A

E

D

G

G

R

K

-

E

-

D

-

V

-

E

K

K

S

G

S

T

K

P

L

L

G

G

Q

K

T

I

L

L

N

K

G

G

N

D

N
|
N

I

I

A

T

M

L

I

I

binding : F25 (≠ I22), E26 (≠ M23), Q27 (≠ K24), F42 (≠ Y39), N79 (= N71)

Q9Y7M4 Probable U6 snRNA-associated Sm-like protein LSm3 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
27% identity, 87% coverage: 7:80/85 of query aligns to 10:93/93 of Q9Y7M4

query
sites
Q9Y7M4

P

P

L

L

E

D

L

L

V

V

D

R

R

L

A

S

I

L

G

D

S

E

K

I

V

V

W

Y

V

V

I

K

M

L

K

R

T

G

E

D

R

R

E

E

F

L

T

N

G

G

T

R

L

L

V

H

G

A

F

Y

D

D

D

E

Y

H

V

L

N

N

M

M

V

V

L

L

E

G

D

D

V

A

T

E

E

E

Y

I

E

V

T

T

T

I

A

F

E

D

G

D

R

E

K

E

S

T

S

D

K

K

-

D

-

K

-

A

-

L

-

K

-

T

-

I

-

R

-

K

-

H

L

Y

G

E

Q

M

T

L

L

F

L

V

N

R

G

G

N

D

N
x
S

I

V

A

I

M

L

I

I

V

A

P

P

G

P

R

R

G

N

S84 (≠ N71) modified: Phosphoserine

Query Sequence

>mRNA_3004
MASTILPLELVDRAIGSKVWVIMKTEREFTGTLVGFDDYVNMVLEDVTEYETTAEGRKSS
KLGQTLLNGNNIAMIVPGRGPEDEQ

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