SitesBLAST

binding : K6 (= K10), W7 (= W11), K24 (vs. gap), D25 (= D28), F27 (= F30), Q45 (= Q48), S48 (≠ T51), F49 (= F52), E52 (≠ V55), A55 (≠ Q58), K56 (= K59), A57 (≠ G60), G61 (≠ D64), N62 (≠ E65), V63 (= V66), S65 (≠ A68)

Sites not aligning to the query:

binding : 1, 66

O54310 Cold shock-like protein from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (see paper)
57% identity, 86% coverage: 7:66/70 of query aligns to 3:62/66 of O54310

query
sites
O54310

G

G

T

K

V

V

K

K

W

W

F

F

N
x
D

D

S

E

K

K

K

G

G

F

Y

G

G

F

F

I

I

T

T

P

K

E

D

S

E

G

G

P

G

D

D

L

V

F

F

V

V

H

H

F

W

R

S

A

A

I

I

Q

E

G

M

N

E

G

G

F

F

K

K

S

T

L

L

K

K

E

E

G

G

Q

Q

K

V

V

V

T

E

F

F

V

E

A

I

V

Q

Q

E

G

G

Q

K

K

K

G

G

M

P

Q

Q

A

A

D

A

E
x
H

V

V

D9 (≠ N13) mutation to N: Destabilization at high temperature.
H61 (≠ E65) mutation to N: No effect on thermal stability.

7f3iA Crystal structure of human ybx2 csd in complex with m5c RNA in space group p212121
41% identity, 94% coverage: 1:66/70 of query aligns to 6:76/93 of 7f3iA

query
sites
7f3iA

M

L

S

A

T

T

R

K

Q

V

S

L

G

G

T

T

V

V

K
|
K

W
|
W

F

F

N
|
N

D
x
V

E
x
R

K
x
N

G

G

F
x
Y

G

G

F
|
F

I

I

T

N

-

R

P

N

E

D

S

T

G

K

P

E

D
|
D

L

V

F
|
F

V

V

H
|
H

F

Q

R

T

A

A

I

I

Q

K

G

R

N

N

G

N

-

P

-

R

-

K

-

F

F

L

K

R

S

S

L

V

K

G

E

D

G

G

Q

E

K

T

V

V

T

E

F

F

V

D

A

V

V

V

Q

E

G

G

Q

E

K
|
K

G
|
G

M

A

Q

E

A

A

D

T

E

N

V

V

binding : K15 (= K10), W16 (= W11), N18 (= N13), V19 (≠ D14), R20 (≠ E15), N21 (≠ K16), Y23 (≠ F18), F25 (= F20), D34 (= D28), F36 (= F30), H38 (= H32), K69 (= K59), G70 (= G60)

Sites not aligning to the query:

binding : 89

6a6jA Crystal structure of zebra fish y-box protein1 (yb-1) cold-shock domain in complex with 6mer m5c RNA (see paper)
41% identity, 94% coverage: 1:66/70 of query aligns to 3:73/90 of 6a6jA

query
sites
6a6jA

M

I

S

A

T

T

R

K

Q

V

S

L

G

G

T

T

V

V

K

K

W
|
W

F

F

N
|
N

D

V

E

R

K

N

G

G

F

Y

G

G

F
|
F

I

I

T

N

-

R

P

N

E

D

S

T

G

K

P

E

D

D

L

V

F
|
F

V

V

H
|
H

F

Q

R

T

A

A

I

I

Q

K

G

K

N

N

G

N

-

P

-

R

-

K

-

Y

F

L

K

R

S

S

L

V

K

G

E

D

G

G

Q

E

K

T

V

V

T

E

F

F

V

D

A

V

V

V

Q

E

G

G

Q
x
E

K
|
K

G
|
G

M
x
A

Q
x
E

A

A

D

A

E

N

V

V

binding zinc ion: E65 (≠ Q58), E69 (≠ Q62)
binding : W13 (= W11), N15 (= N13), F22 (= F20), F33 (= F30), H35 (= H32), E65 (≠ Q58), K66 (= K59), G67 (= G60), A68 (≠ M61)

6lmrA Solution structure of cold shock domain and ssdna complex (see paper)
41% identity, 94% coverage: 1:66/70 of query aligns to 5:75/90 of 6lmrA

query
sites
6lmrA

M

I

S

A

T

T

R

K

Q

V

S

L

G

G

T

T

V

V

K

K

W
|
W

F

F

N
|
N

D

V

E
x
R

K

N

G

G

F

Y

G

G

F
|
F

I

I

T

N

-

R

P

N

E

D

S

T

G

K

P

E

D

D

L

V

F
|
F

V

V

H
|
H

F

Q

R

T

A

A

I

I

Q

K

G

K

N

N

G

N

-

P

-

R

-

K

-

Y

F

L

K

R

S

S

L

V

K

G

E

D

G

G

Q

E

K

T

V

V

T

E

F

F

V

D

A

V

V

V

Q

E

G

G

Q
x
E

K
|
K

G

G

M

A

Q
x
E

A

A

D

A

E

N

V

V

binding : W15 (= W11), N17 (= N13), R19 (≠ E15), F24 (= F20), F35 (= F30), H37 (= H32), E67 (≠ Q58), K68 (= K59), E71 (≠ Q62)

Sites not aligning to the query:

binding : 87, 88

7oiiB Cold-shock DNA-binding protein family (see paper)
59% identity, 54% coverage: 6:43/70 of query aligns to 1:39/39 of 7oiiB

query
sites
7oiiB

S
x
T

G

G

T
x
I

V
|
V

K
|
K

W
|
W

F

F

N

N

D

A

E

D

K

K

G

G

F

F

G

G

F
|
F

I

I

T
|
T

P

P

E
x
D

S

D

-
x
G

G

G

P

A

D

D

L

V

F
|
F

V

A

H

H

F

F

R

S

A

A

I

I

Q

Q

G

M

N

S

G

G

F

Y

K

R

S

A

binding : T1 (≠ S6), I3 (≠ T8), V4 (= V9), K5 (= K10), W6 (= W11), F15 (= F20), T17 (= T22), D19 (≠ E24), G21 (vs. gap), F26 (= F30)

P92186 Protein lin-28; Abnormal cell lineage protein 28 from Caenorhabditis elegans (see 3 papers)
40% identity, 84% coverage: 2:60/70 of query aligns to 50:109/227 of P92186

query
sites
P92186

S

T

T

P

R

R

Q

Y

S

F

G
|
G

T

S

V

C

K

K

W

W

F

F

N

N

D

V

E

S

K

K

G

G

F

Y

G

G

F

F

I

V

T

I

P

D

E

D

-

I

S

T

G

G

P

E

D

D

L

L

F

F

V

V

H

H

F

Q

R

S

A

N

I

L

Q

N

G
x
M

N

Q

G

G

F

F

K
x
R

S

S

L

L

K

D

E

E

G

G

Q

E

K

R

V

V

T

S

F

Y

V

Y

A

I

V

Q

Q

E

G

R

Q

S

K

N

G

G

G55 (= G7) mutation to S: In n1119; loss of function.
M87 (≠ G38) mutation to I: In ga73; when associated with Q-91.
R91 (≠ K42) mutation to Q: In ga73; when associated with I-87.

Sites not aligning to the query:

2:32 mutation Missing: Constitutively active and results in reduced lin-28 protein levels. Rescues the seam cell number and vulval developmental defects of the lin-28 n719 loss of function mutant.
11 D→A: Reduced ced-3-mediated cleavage in vitro.
23 E→A: Reduced ced-3-mediated cleavage in vitro.
24 D→A: Reduced ced-3-mediated cleavage in vitro.
31 D→A: Loss of ced-3-mediated cleavage in vitro. Partially prevents reduction of lin-28 protein levels in vivo. About 20 percent of mutants fail to reach adulthood. Defects in alae morphology.
31:32 Cleavage; by ced-3
32 N→M: Loss of ced-3-mediated cleavage in vitro. Prevents reduction of lin-28 protein levels in vitro.
128 G→E: In ma157.; G→R: In sy283.
133 P→S: In ve9.

4alpA The lin28b cold shock domain in complex with hexauridine (see paper)
42% identity, 90% coverage: 4:66/70 of query aligns to 6:76/87 of 4alpA

query
sites
4alpA

R

R

Q

G

S

S

G

G

T

H

V

C

K

K

W

W

F

F

N

N

D

V

E

R

K

M

G
|
G

F

F

G

G

F

F

I

I

T

S

-

M

-

T

-

S

-

R

-

E

-

G

-

S

P

P

E

L

S

E

G

N

P

P

-

V

D

D

L

V

F

F

V

V

H

H

F
x
Q

R

S

A

K

I

L

Q

Y

G

M

N

E

G

G

F
|
F

K
x
R

S

S

L

L

K

K

E

E

G

G

Q

E

K

P

V

V

T

E

F

F

V

T

A

F

V

K

Q

K

G

S

Q

S

K

K

G

G

M

F

Q

E

A

S

D

L

E

R

V

V

binding : G19 (= G17), Q43 (≠ F33), F51 (= F41), R52 (≠ K42)

P67809 Y-box-binding protein 1; YB-1; CCAAT-binding transcription factor I subunit A; CBF-A; DNA-binding protein B; DBPB; Enhancer factor I subunit A; EFI-A; Nuclease-sensitive element-binding protein 1; Y-box transcription factor from Homo sapiens (Human) (see 5 papers)
40% identity, 96% coverage: 1:67/70 of query aligns to 55:126/324 of P67809

query
sites
P67809

M
x
I

S
x
A

T
|
T

R
x
K

Q
x
V

S
x
L

G
|
G

T
|
T

V
|
V

K
|
K

W
|
W

F
|
F

N
|
N

D
x
V

E
x
R

K
x
N

G
|
G

F

Y

G

G

F

F

I

I

T

N

-

R

P

N

E

D

S

T

G

K

P

E

D

D

L

V

F

F

V

V

H

H

F

Q

R

T

A

A

I

I

Q

K

G

K

N

N

G

N

-

P

-

R

-

K

-

Y

F

L

K

R

S
|
S

L

V

K

G

E

D

G

G

Q

E

K

T

V

V

T

E

F

F

V

D

A

V

V

V

Q

E

G

G

Q

E

K

K

G

G

M

A

Q

E

A

A

D

A

E

N

V

V

I

T

W65 (= W11) Important for C5-methylcytosine-recognition; mutation to A: Abolished binding to C5-methylcytosine (m5C)-containing mRNAs.; mutation to F: Decreased binding to C5-methylcytosine (m5C)-containing mRNAs. Decreased ability to discriminate between m5C-containing and unmethylated mRNAs.
WFNVRN 65:70 (≠ WFNDEK 11:16) C5-methylcytosine binding
S102 (= S43) modified: Phosphoserine; by PKB/AKT1; mutation to A: Loss of phosphorylation by PKB/AKT1. Inhibits translocation to the nucleus and tumor cell growth.

Sites not aligning to the query:

1 modified: Initiator methionine, Removed
2 modified: N-acetylserine
15:71 Interaction with ss-DNA
137 modified: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)
165 modified: Phosphoserine
301 modified: N6-acetyllysine; K→A: Abrogates unconventional secretion.
304 modified: N6-acetyllysine; K→A: Abrogates unconventional secretion.

4a75A The lin28b cold shock domain in complex with hexathymidine. (see paper)
41% identity, 93% coverage: 4:68/70 of query aligns to 8:80/89 of 4a75A

query
sites
4a75A

R

R

Q

G

S

S

G

G

T

H

V

C

K
|
K

W
|
W

F

F

N
|
N

D

V

E

R

K

M

G

G

F
|
F

G

G

F
|
F

I

I

T

S

-

M

-

T

-

S

-

R

-

E

-

G

-

S

P

P

E

L

S

E

G

N

P

P

-

V

D
|
D

L

V

F
|
F

V

V

H
|
H

F

Q

R

S

A

K

I

L

Q

Y

G

M

N

E

G

G

F

F

K

R

S

S

L

L

K

K

E

E

G

G

Q

E

K

P

V

V

T

E

F

F

V

T

A

F

V

K

Q

K

G
x
S

Q

S

K
|
K

G

G

M
x
F

Q

E

A

S

D

L

E

R

V

V

I

T

A

G

binding : K14 (= K10), W15 (= W11), N17 (= N13), F22 (= F18), F24 (= F20), D40 (= D28), F42 (= F30), H44 (= H32), S69 (≠ G57), K71 (= K59), F73 (≠ M61)

Q28618 Y-box-binding protein 1; YB-1; Nuclease-sensitive element-binding protein 1; Y-box transcription factor; p50 from Oryctolagus cuniculus (Rabbit) (see 2 papers)
40% identity, 96% coverage: 1:67/70 of query aligns to 55:126/324 of Q28618

query
sites
Q28618

M

I

S

A

T

T

R

K

Q

V

S

L

G

G

T

T

V

V

K

K

W

W

F

F

N

N

D

V

E

R

K

N

G

G

F

Y

G

G

F

F

I

I

T

N

-

R

P

N

E

D

S

T

G

K

P

E

D

D

L

V

F

F

V

V

H

H

F

Q

R

T

A

A

I

I

Q

K

G

K

N

N

G

N

-

P

-

R

-

K

-

Y

F

L

K

R

S
|
S

L

V

K

G

E

D

G

G

Q

E

K

T

V

V

T

E

F

F

V

D

A

V

V

V

Q

E

G

G

Q

E

K

K

G

G

M

A

Q

E

A

A

D

A

E

N

V

V

I

T

S102 (= S43) modified: Phosphoserine; by PKB/AKT1; mutation to A: Abolishes phosphorylation by PKB/AKT1.

Sites not aligning to the query:

219:220 Cleavage; by 20S proteasomal protease

B5DE31 Y-box-binding protein 1; YB-1; ZfY1; Y-box transcription factor from Danio rerio (Zebrafish) (Brachydanio rerio) (see paper)
40% identity, 96% coverage: 1:67/70 of query aligns to 35:106/310 of B5DE31

query
sites
B5DE31

M

I

S

A

T

T

R

K

Q

V

S

L

G

G

T

T

V

V

K

K

W
|
W

F
|
F

N
|
N

D
x
V

E
x
R

K
x
N

G

G

F

Y

G

G

F

F

I

I

T

N

-

R

P

N

E

D

S

T

G

K

P

E

D

D

L

V

F

F

V

V

H

H

F

Q

R

T

A

A

I

I

Q

K

G

K

N

N

G

N

-

P

-

R

-

K

-

Y

F

L

K

R

S

S

L

V

K

G

E

D

G

G

Q

E

K

T

V

V

T

E

F

F

V

D

A

V

V

V

Q

E

G

G

Q

E

K

K

G

G

M

A

Q

E

A

A

D

A

E

N

V

V

I

T

W45 (= W11) Important for C5-methylcytosine-recognition; mutation to A: Abolished binding to C5-methylcytosine (m5C)-containing mRNAs.; mutation to F: Decreased binding to C5-methylcytosine (m5C)-containing mRNAs. Decreased ability to discriminate between m5C-containing and unmethylated mRNAs.
WFNVRN 45:50 (≠ WFNDEK 11:16) C5-methylcytosine binding

Q803L0 Protein lin-28 homolog A; Lin-28A from Danio rerio (Zebrafish) (Brachydanio rerio) (see paper)
40% identity, 89% coverage: 6:67/70 of query aligns to 35:104/202 of Q803L0

query
sites
Q803L0

S

S

G

G

T

V

V

C

K

K

W

W

F

F

N

N

D

V

E

R

K

M

G

G

F

F

G

G

F

F

-

L

-

S

-

M

-

T

-

H

-

R

-

E

-

G

I

I

T

C

P

L

E

D

S

S

G

P

P

V

D

D

L

V

F

F

V

V

H

H

F

Q

R

S

A

K

I

L

Q

H

G

M

N

E

G

G

F

F

K

R

S

S

L

L

K

K

E

E

G

G

Q

E

K

A

V

V

T

E

F

F

V

T

A

F

V

K

Q

R

G

S

Q

S

K

K

G

G

M

L

Q

E

A

S

D

L

E

Q

V

V

I

T

Sites not aligning to the query:

174 modified: Phosphoserine

Q9Z2C8 Y-box-binding protein 2; FRGY2 homolog; Germ cell-specific Y-box-binding protein from Mus musculus (Mouse) (see paper)
42% identity, 87% coverage: 7:67/70 of query aligns to 98:163/360 of Q9Z2C8

query
sites
Q9Z2C8

G
|
G

T
|
T

V
|
V

K
|
K

W
|
W

F
|
F

N
|
N

D
x
V

E
x
R

K
x
N

G
|
G

F
x
Y

G
|
G

F
|
F

I
|
I

T
x
N

-
x
R

P
x
N

E
x
D

S
x
T

G
x
K

P
x
E

D
|
D

L
x
V

F
|
F

V
|
V

H
|
H

F
x
Q

R
x
T

A
|
A

I
|
I

Q
x
K

G
x
R

N
|
N

G
x
N

-
x
P

-
x
R

-
x
K

-
x
F

F
x
L

K
x
R

S
|
S

L
x
V

K
x
G

E
x
D

G
|
G

Q
x
E

K
x
T

V
|
V

T
x
E

F
|
F

V
x
D

A
x
V

V
|
V

Q
x
E

G
|
G

Q
x
E

K
|
K

G
|
G

M
x
A

Q
x
R

A
|
A

D
x
A

E
x
N

V
|
V

I
x
T

Y109 (≠ F18) mutation to A: Abolishes cytoplasmic retention and mRNA-binding affinity; when associated with A-111.
F111 (= F20) mutation to A: Abolishes cytoplasmic retention and mRNA-binding affinity; when associated with A-109.

Sites not aligning to the query:

89:171 Required for cytoplasmic retention
219:360 Required for mRNA-binding

Q6ZN17 Protein lin-28 homolog B; Lin-28B from Homo sapiens (Human) (see paper)
40% identity, 91% coverage: 4:67/70 of query aligns to 29:100/250 of Q6ZN17

query
sites
Q6ZN17

R

R

Q

G

S

T

G

G

T

H

V

C

K

K

W

W

F

F

N

N

D

V

E

R

K

M

G

G

F

F

G

G

F

F

I

I

T

S

-

M

-

I

-

N

P

R

E

E

S

G

G

S

P

P

-

L

-

D

-

I

-

P

-

V

D

D

L

V

F

F

V

V

H

H

F

Q

R

S

A

K

I

L

Q

F

G

M

N

E

G

G

F

F

K

R

S

S

L

L

K

K

E

E

G

G

Q

E

K

P

V

V

T

E

F

F

V

T

A

F

V

K

Q

K

G

S

Q

S

K

K

G

G

M

L

Q

E

A

S

D

I

E

R

V

V

I

T

Sites not aligning to the query:

112:125 Bipartite nuclear localization signal
239:250 Nucleolar localization signal

Query Sequence

>PFLU_RS24015
MSTRQSGTVKWFNDEKGFGFITPESGPDLFVHFRAIQGNGFKSLKEGQKVTFVAVQGQKG
MQADEVIAEA

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