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 74 a.a. (MNRKQRSIPL...) to proteins with known functional sites using BLASTp with E ≤ 0.001.

Or try Sites on a Tree

Found 16 hits to proteins with known functional sites (download)

P03069 General control transcription factor GCN4; Amino acid biosynthesis regulatory protein; General control protein GCN4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 4 papers)
99% identity, 99% coverage: 2:74/74 of query aligns to 209:281/281 of P03069

query
sites
P03069

N

N

R

R

K

K

Q

Q

R

R

S

S

I

I

P

P

L

L

S

S

P

P

I

I

V

V

P

P

E

E

S

S

D

D

P

P

A

A

L

L

K
|
K

R
|
R

A
|
A

R
|
R

N
|
N

T
|
T

E
|
E

A
|
A

R
|
R

S
|
S

R
|
R

A
|
A

R
|
R

K
|
K

L
|
L

Q
|
Q

R
|
R

M
|
M

K
|
K

Q

Q

L
|
L

E
|
E

D
|
D

K
|
K

V
|
V

E
|
E

L
|
L

S
|
S

K
|
K

N
|
N

Y
|
Y

H
|
H

M
x
L

E
|
E

N
|
N

E
|
E

V
|
V

A
|
A

R
|
R

L
|
L

K

K

L

L

V

V

G

G

E

E

R

R

231:249 (vs. 24:42, 100% identical) Nuclear localization signal
231:251 (vs. 24:44, 100% identical) Basic motif
253:274 (vs. 46:67, 95% identical) Leucine-zipper

Sites not aligning to the query:

89:100 Required for transcriptional activation
97:98 FF→AA: Reduces transcriptional activation activity; when associated with A-107; A-110; A-113; A-120; A-123 and A-124.
106:125 Required for transcriptional activation
107 M→A: Reduces transcriptional activation activity; when associated with A-97; A-98; A-110; A-113; A-120; A-123 and A-124.
110 Y→A: Reduces transcriptional activation activity; when associated with A-97; A-98; A-107; A-113; A-120; A-123 and A-124.
113 L→A: Reduces transcriptional activation activity; when associated with A-97; A-98; A-107; A-110; A-120; A-123 and A-124.
120:124 WTSLF→ATSAA: Reduces transcriptional activation activity; when associated with A-97; A-98; A-107; A-110 and A-113.
165 modified: Phosphothreonine; by PHO85
167:200 Nuclear localization signal

1ysaC The gcn4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: crystal structure of the protein-DNA complex (see paper)
98% identity, 76% coverage: 19:74/74 of query aligns to 2:57/57 of 1ysaC

query
sites
1ysaC

D

D

P

P

A

A

L

L

K

K

R
|
R

A

A

R
|
R

N
|
N

T
|
T

E

E

A
|
A

A

A

R

R

R
|
R

S

S

R
|
R

A

A

R
|
R

K

K

L

L

Q

Q

R

R

M

M

K

K

Q

Q

L

L

E

E

D

D

K

K

V

V

E

E

L

L

S

S

K

K

N

N

Y

Y

H

H

M

L

E

E

N

N

E

E

V

V

A

A

R

R

L

L

K

K

L

L

V

V

G

G

E

E

R

R

binding : R8 (= R25), R10 (= R27), N11 (= N28), T12 (= T29), A14 (= A31), R17 (= R34), R19 (= R36), R21 (= R38)

1llmC Crystal structure of a zif23-gcn4 chimera bound to DNA (see paper)
62% identity, 80% coverage: 15:73/74 of query aligns to 31:87/87 of 1llmC

query
sites
1llmC

P

P

E

F

S

A

S
x
C

D

D

P

I

A
x
C

A

G

L
x
R

K

K

R
x
F

A

A

R
|
R

N
x
S

T
x
D

E
|
E

A

-

R

-

R

R

S
x
K

R
|
R

A
x
H

R

R

K

D

L

I

Q
|
Q

R
x
H

-

I

M

L

K

P

Q

I

L

L

E

E

D

D

K

K

V

V

E

E

L

L

S

S

K

K

N

N

Y

Y

H

H

M

L

E

E

N

N

E

E

V

V

A

A

R

R

L

L

K

K

L

L

V

V

G

G

E

E

binding zinc ion: C34 (≠ S18), C37 (≠ A21), H50 (≠ A37), H55 (≠ R42)
binding : R39 (≠ L23), F41 (≠ R25), R43 (= R27), S44 (≠ N28), D45 (≠ T29), E46 (= E30), K48 (≠ S35), R49 (= R36), H50 (≠ A37), Q54 (= Q41)

Sites not aligning to the query:

binding zinc ion: 6, 9, 22, 26
binding : 11, 14, 15, 17, 18, 22, 25

Q00096 Cross-pathway control protein A from Aspergillus niger (see paper)
62% identity, 72% coverage: 1:53/74 of query aligns to 171:222/245 of Q00096

query
sites
Q00096

M

V

N

N

R

A

K

R

Q

Q

R

R

S

K

I

-

P

P

L

L

S

P

P

P

I

I

V

K

P

F

E

D

S

S

S

A

D

D

P

P

A

A

L

M

K
|
K

R
|
R

A
|
A

R
|
R

N
|
N

T
|
T

E
|
E

A
|
A

R
|
R

R
x
K

S
|
S

R
|
R

A
|
A

R
|
R

K
|
K

L
|
L

Q
x
E

R
|
R

M

Q

K

G

Q

E

L

M

E

E

D

R

K

R

V

I

E

E

L

L

193:211 (vs. 24:42, 89% identical) Nuclear localization signal

3i5cB Crystal structure of a fusion protein containing the leucine zipper of gcn4 and the ggdef domain of wspr from pseudomonas aeruginosa (see paper)
97% identity, 41% coverage: 42:71/74 of query aligns to 1:30/198 of 3i5cB

query
sites
3i5cB

R

R

M

M

K

K

Q

Q

L

L

E

E

D

D

K

K

V

V

E

E

L

L

S

S

K

K

N

N

Y

Y

H

H

M

L

E

E

N

N

E

E

V

V

A

A

R

R

L

L

K

K

L

L

V

V

Sites not aligning to the query:

binding 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one): 53, 56, 57, 100, 100, 101, 101, 102, 104, 125, 129

3crpB A heterospecific leucine zipper tetramer (see paper)
82% identity, 45% coverage: 42:74/74 of query aligns to 2:34/34 of 3crpB

query
sites
3crpB

R

K

M

V

K
|
K

Q

Q

L

L

E

E

D
|
D

K

A

V

V

E

E

L

L

S

S

K

A

N

N

Y

Y

H

H

M

L

E

E

N

N

E

A

V

V

A

A

R

R

L

L

K

K

L

L

V

V

G

G

E

E

R

R

binding : K4 (= K44), D8 (= D48)

Sites not aligning to the query:

binding : 1

6xneC Gcn4-p1 peptide trimer with p-methylphenylalanine residue at position 16 (me-f16)
93% identity, 41% coverage: 42:71/74 of query aligns to 1:30/30 of 6xneC

query
sites
6xneC

R

R

M

M

K

K

Q
|
Q

L

L

E

E

D

D

K
|
K

V

V

E

E

L

L

S

S

K

K

N

A

Y

Y

H

H

M

L

E

E

N

N

E

E

V

V

A

A

R

R

L

L

K

K

L

L

V

V

binding magnesium ion: Q4 (= Q45), K8 (= K49)

1swiC Gcn4-leucine zipper core mutant as n16a complexed with benzene (see paper)
93% identity, 41% coverage: 42:71/74 of query aligns to 1:30/30 of 1swiC

query
sites
1swiC

R

R

M

M

K

K

Q

Q

L

L

E

E

D

D

K

K

V

V

E

E

L
|
L

L

L

S

S

K

K

N
x
A

Y

Y

H

H

M

L

E

E

N

N

E

E

V

V

A

A

R

R

L

L

K

K

L

L

V

V

binding benzene: L12 (= L53), A16 (≠ N57)

1rb4A Antiparallel trimer of gcn4-leucine zipper core mutant as n16a tetragonal automatic solution (see paper)
93% identity, 41% coverage: 42:71/74 of query aligns to 1:30/30 of 1rb4A

query
sites
1rb4A

R

R

M
|
M

K

K

Q

Q

L

L

E

E

D

D

K

K

V
|
V

E
|
E

E

E

L

L

S

S

K

K

N

A

Y
|
Y

H

H

M
x
L

E
|
E

N

N

E

E

V
|
V

A

A

R

R

L
|
L

K
|
K

K

K

L

L

V

V

binding : M2 (= M43), V9 (= V50), E10 (= E51), Y17 (= Y58), L19 (≠ M60), E20 (= E61), V23 (= V64), L26 (= L67), K27 (= K68)

1ij0A Coiled coil trimer gcn4-pvls ser at buried d position (see paper)
90% identity, 42% coverage: 42:72/74 of query aligns to 1:31/31 of 1ij0A

query
sites
1ij0A

R

R

M

M

K

K

Q

Q

L

L

E

E

D

D

K

K

V

V

E

E

L

S

L

L

S

S

K

K

N

V

Y

Y

H
|
H

M

L

E

E

N

N

E
|
E

V

V

A

A

R

R

L

L

K

K

L

L

V

V

G

G

binding zinc ion: H18 (= H59), E22 (= E63)

5apwB Sequence matkdd inserted between gcn4 adaptors - structure t6 (see paper)
93% identity, 39% coverage: 43:71/74 of query aligns to 36:64/64 of 5apwB

query
sites
5apwB

M

M

K

K

Q

Q

L

L

E

E

D
|
D

K

K

V

V

E
|
E

E

E

L

L

S

S

K

K

N

V

Y

Y

H

H

M

L

E

E

N

N

E

E

V

V

A

A

R

R

L

L

K

K

L

L

V

V

binding calcium ion: D41 (= D48), E44 (= E51)

1favA The structure of an HIV-1 specific cell entry inhibitor in complex with the HIV-1 gp41 trimeric core (see paper)
71% identity, 38% coverage: 46:73/74 of query aligns to 1:28/78 of 1favA

query
sites
1favA

L

I

E

E

D

D

K

K

V

I

E

E

L

I

L

L

S

S

K

K

N

I

Y

Y

H

H

M

I

E

E

N

N

E

E

V

I

A

A

R

R

L

I

K

K

L

L

V

I

G

G

E

E

Sites not aligning to the query:

binding : 30, 37, 41, 44, 48, 51

1uo4B Structure based engineering of internal molecular surfaces of four helix bundles (see paper)
74% identity, 42% coverage: 43:73/74 of query aligns to 1:31/31 of 1uo4B

query
sites
1uo4B

M

M

K

K

Q

Q

L
x
I

E

E

D

D

K

K

V
x
G

E

E

L

I

L

L

S

S

K

K

N

L

Y

Y

H

H

M

I

E

E

N

N

E

E

V

L

A

A

R

R

L

I

K

K

L

L

V

L

G

G

E

E

binding iodobenzene: I4 (≠ L46), G8 (≠ V50)

2bniD Pli mutant e20c l16g y17h, antiparallel (see paper)
68% identity, 42% coverage: 43:73/74 of query aligns to 1:31/31 of 2bniD

query
sites
2bniD

M

M

K

K

Q

Q

L

I

E

E

D

D

K
|
K

V

L

E

E

L
x
I

L

L

S

S

K

K

N

G

Y

H

H

H

M

I

E

C

N

N

E
|
E

V

L

A

A

R

R

L
x
I

K

K

L

L

V

L

G

G

E

E

binding : K7 (= K49), I11 (≠ L53), E21 (= E63), I25 (≠ L67)

1unyB Structure based engineering of internal molecular surfaces of four helix bundles (see paper)
73% identity, 41% coverage: 42:71/74 of query aligns to 1:30/30 of 1unyB

query
sites
1unyB

R
|
R

M

M

K

K

Q
|
Q

L
x
I

E

E

D

D

K

K

V

L

E

E

E
|
E

L
x
I

L

L

S

S

K
|
K

N

L

Y

Y

H
|
H

M
x
I

E

E

N

N

E
|
E

V

L

A

A

R

R

L

G

K

K

L

L

V

L

binding : R1 (= R42), Q4 (= Q45), I5 (≠ L46), E11 (= E52), I12 (≠ L53), K15 (= K56), H18 (= H59), I19 (≠ M60), E22 (= E63)

1czqA Crystal structure of the d10-p1/iqn17 complex: a d-peptide inhibitor of HIV-1 entry bound to the gp41 coiled-coil pocket. (see paper)
63% identity, 41% coverage: 42:71/74 of query aligns to 1:30/45 of 1czqA

query
sites
1czqA

R

R

M

M

K

K

Q

Q

L

I

E

E

D

D

K

K

V

I

E

E

L

I

L

E

S

S

K

K

N

Q

Y

K

H

K

M

I

E

E

N

N

E

E

V

I

A

A

R

R

L

I

K

K

L
|
L

V

L

binding : L29 (= L70)

Sites not aligning to the query:

binding : 32, 35

Query Sequence

>74 a.a. (MNRKQRSIPL...)
MNRKQRSIPLSPIVPESSDPAALKRARNTEAARRSRARKLQRMKQLEDKVEELLSKNYHM
ENEVARLKKLVGER

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