SitesBLAST

R237 (= R6) mutation to A: Slightly reduced binding to NFIL3 promoter.
N286 (= N55) Required for binding to the NFIL3 promoter; mutation to A: Significantly reduced binding to NFIL3 promoter.
R290 (= R59) mutation to A: Slightly reduced binding to NFIL3 promoter.

1lfuP Nmr solution structure of the extended pbx homeodomain bound to DNA (see paper)
92% identity, 99% coverage: 2:74/74 of query aligns to 2:74/82 of 1lfuP

query
sites
1lfuP

A
|
A

R
|
R

K
|
K

R
|
R

R

R

N

N

F
|
F

S

N

K

K

Q

Q

A

A

S

T

E

E

I

I

L

L

N

N

E

E

Y

Y

F

F

Y

Y

S

S

H

H

L

L

S

S

N

N

P
|
P

Y
|
Y

P

P

S

S

E

E

A

A

K

K

E

E

L

L

A

A

R

K

K

K

C

S

G

G

I

I

T

T

V

V

S

S

Q

Q

V

V

S

S

N

N

W

W

F

F

G

G

N

N

K

K

R
|
R

I
|
I

R

R

Y

Y

K

K

N

N

I

I

G

G

K

K

A

F

Q

Q

E

E

A

A

N

N

L

I

Y

Y

binding : A2 (= A2), R3 (= R3), R4 (= R4), R4 (= R4), K5 (= K5), K5 (= K5), R6 (= R6), F9 (= F9), P28 (= P28), Y29 (= Y29), R57 (= R57), I58 (= I58)

Sites not aligning to the query:

binding : 1

P41779 Homeobox protein ceh-20 from Caenorhabditis elegans (see 2 papers)
86% identity, 100% coverage: 1:74/74 of query aligns to 187:260/338 of P41779

query
sites
P41779

D
|
D

A
|
A

R
|
R

K
|
K

R
|
R

N
|
N

F
|
F

S
|
S

K
|
K

Q
|
Q

A
|
A

S
x
T

E
|
E

I
x
V

L
|
L

N
|
N

E
|
E

Y
|
Y

F
|
F

Y
|
Y

S
x
G

H
|
H

L
|
L

S
|
S

N
|
N

P
|
P

Y
|
Y

P
|
P

S
|
S

E
|
E

A
|
A

K
|
K

E
|
E

E
x
D

L
|
L

A
|
A

R
|
R

K
x
Q

C
|
C

G
x
N

I
|
I

T
|
T

V
|
V

S
|
S

Q
|
Q

V
|
V

S
|
S

N
|
N

W
|
W

F
|
F

G
|
G

N
|
N

K
|
K

R
|
R

I
|
I

R
|
R

Y
|
Y

K
|
K

N
|
N

I
x
M

G
x
A

K
|
K

A
|
A

Q
|
Q

E
|
E

A
|
A

N
x
S

L
x
M

Y
|
Y

P214 (= P28) mutation to L: In ay42; loss of dopamine transporter dat-1 expression in midbody neurons (PDE).
R245 (= R59) mutation to H: In mu290; egg laying defects, abnormal migration of QR neuroblast lineage cells and BDU interneurons, and vulval protrusions. Loss of expression of dopamine pathway genes, including dopamine transporter dat-1, in midbody neurons (PDE).

Sites not aligning to the query:

102:338 mutation Missing: In ay38; loss of dopamine transporter dat-1 expression in midbody neurons (PDE).

Q45EK2 Homeobox protein ceh-60 from Caenorhabditis elegans (see paper)
54% identity, 91% coverage: 4:70/74 of query aligns to 182:248/360 of Q45EK2

query
sites
Q45EK2

R

R

K

K

R

R

N

N

F

F

S

D

K

K

Q

N

A

T

S

T

E

D

I

I

L

L

N

Q

E

N

Y

W

F

F

Y

H

S

D

H

H

L

R

S

Q

N

N

P

P

Y

Y

P

P

S

S

E

D

E

Q

A

E

K

K

E

A

E

E

L

L

A

A

R

K

K

Q

C

C

G

N

I

I

T

K

V

I

S

S

Q

Q

V

V

S

N

N

N

W

W

F

F

G

G

N

N

K

Q

R

R

I

I

R

R

Y

T

K

K

K

Q

N
x
Q

I
x
A

G
x
L

K
x
R

A
x
M

Q
|
Q

E
|
E

E
x
D

Sites not aligning to the query:

241:360 mutation Missing: In lst466; increased accumulation of intestinal fat in adults. Significant reduction in cuticle permeability.

O14770 Homeobox protein Meis2; Meis1-related protein 1 from Homo sapiens (Human) (see 2 papers)
49% identity, 69% coverage: 9:59/74 of query aligns to 283:333/477 of O14770

query
sites
O14770

F

F

S

P

K

K

Q

V

A

A

S

T

E

N

I

I

L

M

N

R

E

A

Y

W

F

L

Y

F

S

Q

H

H

L

L

S

T

N

H

P

P

Y

Y

P

P

S

S

E

E

A

Q

K

K

E

K

E

Q

L

L

A

A

R

Q

K

D

C

T

G

G

I

L

T

T

V

I

S

L

Q

Q

V

V

S

N

N

N

W

W

F

F

G

I

N

N

K

A

R

R

I
x
R

R

R

R332 (≠ I58) mutation to M: Impairs DNA binding and PBX1-dependent transcriptional activation. No effect on interaction with PBX1.

Sites not aligning to the query:

85 L→A: Impairs interaction with PBX1; when associated with A-88.
88 L→A: Impairs interaction with PBX1; when associated with A-85. HELIX 285 297.
94:97 EKCE→NNGT: Impairs interaction with PBX1.
151 I→A: Impairs interaction with PBX1; when associated with A-154.
154 L→A: Impairs interaction with PBX1; when associated with A-151.
158:159 LL→AA: Impairs interaction with PBX1; when associated with A-161.
161 L→A: Impairs interaction with PBX1; when associated with 158-A-A-159.

4xrmB Homodimer of tale type homeobox transcription factor meis1 complexes with specific DNA (see paper)
49% identity, 69% coverage: 9:59/74 of query aligns to 5:55/64 of 4xrmB

query
sites
4xrmB

F
|
F

S

P

K

K

Q

V

A

A

S

T

E

N

I

I

L

M

N

R

E

A

Y

W

F

L

Y

F

S

Q

H

H

L

L

S

T

N

H

P

P

Y
|
Y

P

P

S

S

E

E

A

Q

K
|
K

E

K

E

Q

L

L

A

A

R

Q

K

D

C

T

G

G

I

L

T

T

V

I

S

L

Q
|
Q

V

V

S

N

N

N

W

W

F

F

G
x
I

N
|
N

K

A

R
|
R

I
x
R

R
|
R

binding : F5 (= F9), Y25 (= Y29), K31 (= K35), Q44 (= Q48), I50 (≠ G54), N51 (= N55), R53 (= R57), R54 (≠ I58), R55 (= R59)

8vtsB Meis1 homeobox domain bound to paromomycin fragment (see paper)
49% identity, 69% coverage: 9:59/74 of query aligns to 1:51/56 of 8vtsB

query
sites
8vtsB

F

F

S

P

K

K

Q

V

A

A

S

T

E

N

I

I

L

M

N

R

E

A

Y

W

F

L

Y

F

S

Q

H
|
H

L

L

S

T

N

H

P

P

Y

Y

P

P

S

S

E

E

A
x
Q

K

K

E

K

E

Q

L

L

A

A

R

Q

K

D

C

T

G

G

I

L

T

T

V

I

S

L

Q

Q

V

V

S

N

N

N

W

W

F

F

G

I

N

N

K

A

R

R

I

R

R

R

binding ribostamycin: H16 (= H24), Q26 (≠ A34)

Q60954 Homeobox protein Meis1; Myeloid ecotropic viral integration site 1 from Mus musculus (Mouse) (see 2 papers)
49% identity, 69% coverage: 9:59/74 of query aligns to 279:329/390 of Q60954

query
sites
Q60954

F

F

S

P

K

K

Q

V

A

A

S

T

E

N

I

I

L

M

N

R

E

A

Y

W

F

L

Y

F

S

Q

H

H

L

L

S

T

N

H

P

P

Y

Y

P

P

S

S

E

E

A

Q

K

K

E

K

E

Q

L

L

A

A

R

Q

K

D

C

T

G

G

I

L

T

T

V

I

S

L

Q

Q

V

V

S

N

N
|
N

W

W

F

F

G

I

N

N

K

A

R

R

I

R

R

R

N321 (= N51) mutation to S: Loss of binding to other proteins.

Sites not aligning to the query:

213 W→A: No effect on cooperative binding with PBX1 to CYP17.

Q9GZN2 Homeobox protein TGIF2; 5'-TG-3'-interacting factor 2; TGF-beta-induced transcription factor 2; TGFB-induced factor 2 from Homo sapiens (Human) (see paper)
40% identity, 77% coverage: 3:59/74 of query aligns to 19:75/237 of Q9GZN2

query
sites
Q9GZN2

R

R

R

K

K

R

R

R

R

G

N

N

F

L

S

P

K

K

Q

E

A

S

S

V

E

K

I

I

L

L

N

R

E

D

Y

W

F

L

Y

Y

S

L

H

H

L

R

S

Y

N

N

P

A

Y

Y

P

P

S

S

E

E

E

Q

A

E

K

K

E

L

E

S

L

L

A

S

R

G

K

Q

C

T

G

N

I

L

T

S

V

V

S

L

Q

Q

V

I

S

C

N

N

W

W

F

F

G

I

N

N

K

A

R

R

I

R

R

R

Sites not aligning to the query:

182 modified: Phosphothreonine; T→V: Decrease of phosphorylation. Strong decrease of phosphorylation; when associated with V-186.
186 modified: Phosphothreonine; T→V: Decrease of phosphorylation. Strong decrease of phosphorylation; when associated with V-182.

Q24248 Homeobox protein araucan from Drosophila melanogaster (Fruit fly) (see paper)
35% identity, 97% coverage: 1:72/74 of query aligns to 254:325/717 of Q24248

query
sites
Q24248

D

D

A

L

R

A

K

R

R

R

R

K

N

N

F

A

S

T

K

R

Q

E

A

S

S

T

E

A

I

T

L

L

N

K

E

A

Y

W

F

L

Y

N

S

E

H

H

L

K

S

K

N

N

P

P

Y

Y

P

P

S

T

E

K

E

G

A

E

K

K

E

I

E

M

L

L

A

A

R

I

K

I

C

T

G

K

I

M

T

T

V

L

S

T

Q

Q

V

V

S

S

N

T

W

W

F

F

G

A

N

N

K

A

R

R

I

R

R

R

Y

L

K

K

N

E

I

N

G

K

K

M

A

T

Q

W

E

E

E

P

A

K

N

N

Sites not aligning to the query:

336 modified: Phosphoserine

Q6NZ04 Homeobox protein six1b; Homeobox protein six1a; Sine oculis homeobox homolog 1a; Sine oculis homeobox homolog 1b from Danio rerio (Zebrafish) (Brachydanio rerio) (see paper)
49% identity, 69% coverage: 9:59/74 of query aligns to 131:178/284 of Q6NZ04

query
sites
Q6NZ04

F

F

S

K

K
x
E

Q

K

A

S

S

R

E

G

I

V

L

L

N

R

E

E

Y

W

F

-

Y

Y

S

T

H

H

L

-

S

-

N

N

P

P

Y

Y

P

P

S

S

E

P

E

R

A

E

K

K

E

R

E

E

L

L

A

A

R

E

K

A

C

T

G

G

I

L

T

T

V

T

S

T

Q

Q

V

V

S

S

N

N

W

W

F

F

G

K

N

N

K

R

R

R

I

Q

R

R

E133 (≠ K11) mutation Missing: Impairs transcription factor activity.

Sites not aligning to the query:

110 R→W: Abolishes regulation of hair cell proliferation. No effect on regulation of neuron proliferation.
129 Y→C: Impairs transcription factor activity.

6fqpA Crystal structure of tale homeobox domain transcription factor tgif1 with its consensus DNA (see paper)
37% identity, 80% coverage: 6:64/74 of query aligns to 1:59/67 of 6fqpA

query
sites
6fqpA

R
|
R

R

G

N
|
N

F
x
L

S

P

K

K

Q

E

A

S

S

V

E

Q

I

I

L

L

N

R

E

D

Y

W

F

L

Y

Y

S

E

H

H

L

R

S

Y

N

N

P

A

Y
|
Y

P

P

S

S

E

E

E

Q

A

E

K
|
K

E

A

E

L

L

L

A

S

R

Q

K

Q

C

T

G

H

I

L

T

S

V

T

S

L

Q
|
Q

V

V

S

C

N

N

W

W

F

F

G
x
I

N
|
N

K

A

R
|
R

I
x
R

R
|
R

Y

L

K

L

K

P

N

D

I

M

binding : R1 (= R6), R1 (= R6), N3 (= N8), L4 (≠ F9), Y24 (= Y29), K30 (= K35), Q43 (= Q48), I49 (≠ G54), N50 (= N55), R52 (= R57), R53 (≠ I58), R54 (= R59)

4egcA Crystal structure of mbp-fused human six1 bound to human eya2 eya domain (see paper)
47% identity, 72% coverage: 7:59/74 of query aligns to 483:532/539 of 4egcA

query
sites
4egcA

R

R

N

T

F

I

S

W

K

D

Q

K

A

S

S

R

E

G

I

V

L

L

N

R

E

E

Y

W

F

-

Y

Y

S

A

H

H

L

-

S

-

N

N

P

P

Y

Y

P

P

S

S

E

P

E

R

A

E

K

K

E

R

E

E

L

L

A

A

R

E

K

A

C

T

G

G

I

L

T

T

V

T

S

T

Q

Q

V

V

S

S

N

N

W

W

F

F

G

K

N

N

K

R

R

R

I

Q

R

R

Sites not aligning to the query:

binding alpha-D-glucopyranose: 14, 15, 62, 65, 66, 111, 153, 154, 155, 230, 340

Q62233 Homeobox protein SIX3; Sine oculis homeobox homolog 3 from Mus musculus (Mouse) (see 2 papers)
38% identity, 74% coverage: 1:55/74 of query aligns to 206:257/333 of Q62233

query
sites
Q62233

D

D

A

G

R

E

R

Q

K

K

R

T

R

H

N

C

F

F

S

K

K

E

Q

R

A

T

S

R

E

S

I

L

L

L

N

R

E

E

Y

W

F

Y

Y

-

S

-

H

-

L

L

S

Q

N

D

P

P

Y

Y

P

P

S
x
N

E
x
P

E
x
S

A

K

K

K

E

R

E

E

L

L

A

A

R

Q

K

A

C

T

G

G

I

L

T

T

V

P

S

T

Q

Q

V

V

S

G

N

N

W

W

F

F

G

K

N

N

NPS 233:235 (≠ SEE 31:33) Bind to RHO promoter; mutation Missing: Suppression of SIX3-binding to rhodopsin promoter. Impairs the ability of Six3 to stimulate RHO transcription.

Sites not aligning to the query:

73:120 Interaction with TLE5
88 F→E: Loss of interaction with TLE5 and TLE4.

O95343 Homeobox protein SIX3; Sine oculis homeobox homolog 3 from Homo sapiens (Human) (see 5 papers)
38% identity, 74% coverage: 1:55/74 of query aligns to 205:256/332 of O95343

query
sites
O95343

D

D

A

G

R

E

R

Q

K

K

R

T

R

H

N

C

F

F

S

K

K

E

Q

R

A

T

S

R

E

S

I

L

L

L

N

R

E

E

Y

W

F

Y

Y

-

S

-

H

-

L

L

S

Q

N

D

P

P

Y

Y

P

P

S

N

E

P

E

S

A

K

K

K

E

R

E

E

L

L

A

A

R

Q

K

A

C

T

G

G

I

L

T

T

V

P

S

T

Q

Q

V
|
V

S

G

N

N

W

W

F

F

G

K

N

N

V250 (= V49) to A: in HPE2; Significantly decreased its ability to activate NR4A3; dbSNP:rs121917880

Sites not aligning to the query:

37 G → C: in SCHZC and HPE2; dbSNP:rs199823175
87 F→E: Decreased interaction with TLE5 and loss of interaction with TLE1.
95 V→P: Loss of interaction with TLE1 and TLE5; when associated with P-99.
99 L→P: Loss of interaction with TLE1 and TLE5; when associated with P-95.
257 R → P: in HPE2; Significantly decreased interaction with NR4A3; Significantly decreased its ability to activate NR4A3; dbSNP:rs121917879

P47239 Paired box protein Pax-7 from Mus musculus (Mouse) (see 2 papers)
33% identity, 93% coverage: 3:71/74 of query aligns to 213:281/503 of P47239

query
sites
P47239

R

R

R

K

K

Q

R

R

N

S

F

R

S

T

K

T

Q

F

A

T

S

A

E

E

I

Q

L

L

N

E

E

E

Y

L

F

E

Y

K

S

A

H

F

L

E

S

R

N

T

P

H

Y

Y

P

P

S

D

E

I

E

Y

A

T

K

R

E

E

L

L

A

A

R

Q

K

R

C

T

G

K

I

L

T

T

V

E

S

A

Q

R

V

V

S

Q

N

V

W

W

F

F

G

S

N

N

K

R

R

R

I

A

R

R

Y

W

K

R

K

K

N

Q

I

A

G

G

K

A

A

N

Q

Q

E

L

E

A

A

A

Sites not aligning to the query:

27:208 Sufficient to mediate interaction with PAXBP1
105 modified: N6-acetyllysine; K→R: Abolished acetylation by KAT8, leading to reduced transcription factor activity; when associated with R-139.
139 modified: N6-acetyllysine; K→R: Abolished acetylation by KAT8, leading to reduced transcription factor activity; when associated with R-105.

P23760 Paired box protein Pax-3; HuP2 from Homo sapiens (Human) (see 8 papers)
33% identity, 89% coverage: 3:68/74 of query aligns to 217:282/479 of P23760

query
sites
P23760

R

R

R

K

K

Q

R

R

N

S

F

R

S

T

K

T

Q

F

A

T

S

A

E

E

I

Q

L

L

N

E

E

E

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R270 (≠ K56) to C: in WS1 and WS3; dbSNP:rs1228590199
R273 (= R59) to K: in WS1; uncertain significance; dbSNP:rs1020175890

Sites not aligning to the query:

80 H → D: in WS1; results in decreased transcriptional activation of MITF; no effect on localization to nucleus; no effect on interaction with SOX10; dbSNP:rs387906947
81 G → A: in WS1; originally classified as Waardenburg syndrome type 2; dbSNP:rs587776586
201 modified: Phosphoserine
205 modified: Phosphoserine
209 modified: Phosphoserine
315 T → K: in dbSNP:rs2234675

O17894 Homeobox protein unc-39; Homeobox protein ceh-35; Uncoordinated protein 39 from Caenorhabditis elegans (see 3 papers)
49% identity, 47% coverage: 29:63/74 of query aligns to 242:276/335 of O17894

query
sites
O17894

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Sites not aligning to the query:

203 R→Q: In e257; uncoordinated locomotion, withered tail morphology, egg-laying defects, protruding vulvae and multiple vulvae. Defective pharyngeal development, which results in animals appearing starved. Mesodermal lineage and neuronal cell migration and specification defects. Abolishes differentiation of RID peptidergic neurons.
220 I→IQF: In ct73; uncoordinated locomotion, withered tail morphology, egg-laying defects, protruding vulvae and multiple vulvae. Defective pharyngeal development, which results in animals appearing starved. Mesodermal lineage and neuronal cell migration and specification defects.
283 P→L: In rh72; uncoordinated locomotion, withered tail morphology, egg-laying defects, protruding vulvae and multiple vulvae. Defective pharyngeal development, which results in animals appearing starved. Mesodermal lineage and neuronal cell migration and specification defects.
298 P→L: In hp701; abolishes differentiation of RID peptidergic neurons.

G5ED66 Paired box protein 3 homolog from Caenorhabditis elegans (see paper)
28% identity, 92% coverage: 2:69/74 of query aligns to 187:251/308 of G5ED66

query
sites
G5ED66

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Sites not aligning to the query:

29 P→L: In ga96; causes defects in embryonic development, larval body morphology and vulval development. Adult hermaphrodites have gonad migration defects in which one or both arms of the developing gonad fail to turn correctly. Decrease in the number of ventral hypodermal cells (Pn.p cells) and in the number of ventral cord neurons (Pn.a cells). Ectopic expression of scm in P cells in 27% of animals raised at the restrictive temperature, 25 degrees Celsius.

P0CY08 Mating-type protein ALPHA2; MATalpha2 protein; Alpha-2 repressor from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 7 papers)
33% identity, 89% coverage: 9:74/74 of query aligns to 136:200/210 of P0CY08

query
sites
P0CY08

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R173 (≠ V46) mutation to A: Reduces the ability of ALPHA2/MCM1 to repress a-specific genes. Disrupts interaction with SSN6.
S181 (≠ G54) mutation to A: In ALPHA2-3A; defective in binding DNA alone or in complex with MCM1, but binds DNA normally in complex with A1; when associated with A-182 and A-185.
N182 (= N55) mutation to A: In ALPHA2-3A; defective in binding DNA alone or in complex with MCM1, but binds DNA normally in complex with A1; when associated with A-181 and A-185.
R185 (= R59) mutation to A: In ALPHA2-3A; defective in binding DNA alone or in complex with MCM1, but binds DNA normally in complex with A1; when associated with A-181 and A-182.
I192 (≠ K66) mutation to A: Disrupts the ability of A1/ALPHA2 to repress haploid-specific genes.
L196 (≠ E70) mutation L->A,S: Disrupts the ability of A1/ALPHA2 to repress haploid-specific genes.
L199 (= L73) mutation to A: Disrupts the ability of A1/ALPHA2 to repress haploid-specific genes.
L200 (≠ Y74) mutation to A: Disrupts the ability of A1/ALPHA2 to repress haploid-specific genes.

Sites not aligning to the query:

1 modified: N-acetylmethionine
4 I→T: Reduces the ability of ALPHA2 to repress transcription, but binds normally to DNA and MCM1.
9 L→F: Reduces the ability of ALPHA2 to repress transcription, but binds normally to DNA and MCM1.
10 L→S: Reduces the ability of ALPHA2 to repress transcription, but binds normally to DNA and MCM1. Disrupts interaction with TUP1.
71 E→K: Reduces the ability of alpha2 to repress transcription, but binds normally to DNA and MCM1.
114 L→A: Reduces the ability of ALPHA2/MCM1 to repress a-specific genes.
115 V→A: Reduces the ability of ALPHA2/MCM1 to repress a-specific genes.
116 F→A: Reduces the ability of ALPHA2/MCM1 to repress a-specific genes.
117 N→A: Reduces the ability of ALPHA2/MCM1 to repress a-specific genes.
118 V→A: Reduces the ability of ALPHA2/MCM1 to repress a-specific genes.
119 V→A: Reduces the ability of ALPHA2/MCM1 to repress a-specific genes.
120 T→A: Reduces the ability of ALPHA2/MCM1 to repress a-specific genes.

Query Sequence

>74 a.a. (DARRKRRNFS...)
DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRY
KKNIGKAQEEANLY

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