Alignment of thymidine_kinase with 1nksA0

Alignment of thymidine_kinase with 1nksA0

PSSM Score Key
-10																			10

Bad																			Good

thymid_PSS	Predicted Secondary Structure for your Sequence
thymid_Seq	Your Sequence
1nksA0_Seq	Library Sequence
1nksA0_SS	Known Secondary Structure of the Library Sequence (Assigned by STRIDE)
CORE	A measure of the burial and number of contacts made by a residue. (9 very buried/making many contacts, 0 not buried/making few contacts

thymid_PSS

C

C

C

C

C

C

C

C

C

C

C

C

C

C

C

C

C

C

E

E

E

E

E

E

E

E

E

C

C

C

C

H

H

H

H

H

H

H

H

H

H

H

H

H

H

C

C

C

E

E

thymid_Seq

M

S

C

I

N

L

P

T

V

L

P

G

S

P

S

K

T

R

G

Q

I

Q

V

I

L

G

P

M

F

S

G

K

S

T

E

L

M

R

R

V

R

R

F

Q

I

A

Q

Y

K

C

-------

M

I

-

+

+

-

G

-

-

-

+

G

K

S

T

-

L

-

+

-

+

-

-

-

+

-

1nksA0_Seq

M

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

K

I

G

I

V

T

G

I

P

G

V

G

K

S

T

V

L

A

K

V

K

E

I

L

D

N

Q

G

I

N

N

1nksA0_SS

C

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

E

E

E

E

E

E

E

C

C

C

C

C

H

H

H

H

H

H

H

H

H

H

H

H

H

H

C

C

C

C

E

CORE

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

0

4

5

8

7

5

1

4

0

0

3

1

0

0

0

6

3

0

0

5

0

0

1

2

0

0

0

0

0

0

0

thymid_PSS		E	E	E	E	E	.	.	.	.	.		.	.	.	.	.	.	.	.	C	C		C	.	.	.	.	.	.	.	.	.		.	.	.	.	.	.	.	.	.	.		.	.	.	.	.	.	.	.	.	.
thymid_Seq		L	V	I	K	Y	.	.	.	.	.		.	.	.	.	.	.	.	.	A	K		D	.	.	.	.	.	.	.	.	.		.	.	.	.	.	.	.	.	.	.		.	.	.	.	.	.	.	.	.	.
-------			+	I		Y															A	K		D
1nksA0_Seq		K	I	I	N	Y	G	D	F	M	L		A	T	A	L	K	L	G	Y	A	K		D	R	D	E	M	R	K	L	S	V		E	K	Q	K	K	L	Q	I	D	A		A	K	G	I	A	E	E	A	R	A
1nksA0_SS		E	E	E	E	H	H	H	H	H	H		H	H	H	H	H	C	C	C	C	C		C	H	H	H	H	H	C	C	C	H		H	H	H	H	H	H	H	H	H	H		H	H	H	H	H	H	H	H	H	H
CORE		0	3	1	0	1	0	0	1	1	0		0	0	1	0	0	0	0	0	1	0		0	0	0	0	1	0	0	0	0	0		0	0	0	0	0	1	0	0	0	1		2	0	0	3	0	0	0	3	0	0

thymid_PSS

.

.

C

C

C

.

.

.

.

C

C

C

E

E

E

E

C

C

C

C

C

C

C

C

C

C

C

C

H

H

H

H

H

H

H

H

C

C

E

E

E

E

E

E

E

C

C

C

C

C

thymid_Seq

.

.

T

R

Y

.

.

.

.

S

S

S

F

C

T

H

D

R

N

T

M

E

A

L

P

A

C

L

L

R

D

V

A

Q

E

A

L

G

V

A

V

I

G

I

D

E

G

Q

F

F

-------

-

-

Y

-

+

-

-

-

-

-

-

+

-

L

P

-

-

V

-

E

-

-

-

V

I

-

+

-

E

-

1nksA0_Seq

G

G

E

G

Y

L

F

I

D

T

H

A

V

I

R

T

P

S

G

Y

L

P

G

L

P

.

.

.

.

S

Y

V

I

T

E

I

.

N

P

S

V

I

F

L

L

E

A

.

.

.

1nksA0_SS

H

C

C

C

E

E

E

E

E

E

C

C

E

E

E

E

C

C

E

E

E

E

C

C

C

.

.

.

.

H

H

H

H

H

H

H

.

C

C

C

E

E

E

E

E

E

C

.

.

.

CORE

0

0

0

0

0

3

6

5

0

3

0

8

3

0

0

0

0

0

0

0

0

0

1

7

0

.

.

.

.

0

0

1

7

0

0

4

.

0

4

0

2

9

6

6

7

0

2

.

.

.

thymid_PSS

C

H

H

H

H

H

H

H

H

H

H

H

C

C

C

E

E

E

E

E

C

C

C

C

C

H

H

H

C

C

C

C

C

H

H

H

H

H

H

H

H

H

H

H

H

H

C

C

H

H

thymid_Seq

P

D

I

M

E

F

C

E

A

M

A

N

A

G

K

T

V

I

V

A

A

L

D

G

T

F

Q

R

K

P

F

G

A

I

L

N

L

V

P

L

A

E

S

V

V

K

L

T

A

V

-------

-

-

-

-

-

+

-

-

-

K

-

D

-

T

-

R

-

+

-

E

S

V

+

L

-

-

1nksA0_Seq

D

P

K

I

I

L

S

R

.

.

.

.

.

Q

K

R

.

.

.

.

.

.

D

T

T

R

N

R

N

D

Y

S

D

.

.

.

.

.

.

.

.

E

S

V

I

.

L

E

T

I

1nksA0_SS

C

H

H

H

H

H

H

H

.

.

.

.

.

H

H

H

.

.

.

.

.

.

C

C

C

C

C

C

C

C

C

C

C

.

.

.

.

.

.

.

.

H

H

H

H

.

H

H

H

H

CORE

0

0

0

0

3

0

0

0

.

.

.

.

.

0

0

0

.

.

.

.

.

.

0

0

0

0

0

0

0

0

1

0

0

.

.

.

.

.

.

.

.

0

0

0

2

.

0

0

1

1

thymid_PSS		H	H	H	H	C	C	C	C	C	E		E	E	E	E	C	C	C	C	E	E		E	E	E	C	C	C	C	C	C	H		H	H	H	H	H	H	C	C	C	C		C	C	C	C	C	C	C	C	C	C
thymid_Seq		C	M	E	C	F	R	E	A	A	Y		T	K	R	L	G	T	E	K	E	V		E	V	I	G	G	A	D	K	Y	H		S	V	C	R	L	C	Y	F	K	K		A	S	G	Q	P	A	G	P	D	N
-------		-	+		-		-		A	-	-		-	-			-	+	-	-	-	V			V	I
1nksA0_Seq		N	F	A	R	Y	A	.	A	T	A		S	A	.	V	L	A	G	S	T	V		K	V	I	.	.	.	.	.	.	.		.	.	.	.	.	.	.	.	.	.		.	.	.	.	.	.	.	.	.	.
1nksA0_SS		H	H	H	H	H	H	.	H	H	H		H	H	.	H	H	H	C	C	E	E		E	E	E	.	.	.	.	.	.	.		.	.	.	.	.	.	.	.	.	.		.	.	.	.	.	.	.	.	.	.
CORE		0	0	7	0	0	1	.	8	0	0		5	5	.	0	1	3	0	3	0	4		0	1	5	.	.	.	.	.	.	.		.	.	.	.	.	.	.	.	.	.		.	.	.	.	.	.	.	.	.	.

thymid_PSS

C

C

C

C

C

C

C

C

C

C

C

H

H

H

H

H

H

H

H

C

C

C

H

H

H

H

C

C

C

C

C

C

thymid_Seq

K

E

N

C

P

V

P

G

K

P

G

E

A

V

A

A

R

K

L

F

A

P

Q

Q

I

L

Q

C

S

P

A

N

-------

V

-

-

-

+

-

-

A

A

+

-

-

-

1nksA0_Seq

.

.

.

.

.

V

N

V

E

G

D

P

S

I

A

A

N

E

I

I

R

S

M

K

.

.

.

.

.

.

.

.

1nksA0_SS

.

.

.

.

.

E

C

C

C

C

C

H

H

H

H

H

H

H

H

H

H

H

H

C

.

.

.

.

.

.

.

.

CORE

.

.

.

.

.

0

1

0

0

0

0

1

0

0

3

4

0

0

9

2

0

2

3

0

.

.

.

.

.

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.

.