Alignment of TRAD_HUMAN_whole with 2pgd-1

Alignment of TRAD_HUMAN_whole with 2pgd-1

PSSM Score Key
-10																			10

Bad																			Good

TRAD_H_PSS	Predicted Secondary Structure for your Sequence
TRAD_H_Seq	Your Sequence
2pgd-1_Seq	Library Sequence
2pgd-1_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

TRAD_H_PSS

C

C

C

C

C

C

C

H

H

H

H

E

E

E

E

E

E

E

E

E

C

H

H

H

H

H

H

.

H

H

C

C

C

C

C

C

H

H

H

H

H

H

H

H

H

H

H

H

H

H

TRAD_H_Seq

M

A

A

G

Q

N

G

H

E

E

W

V

G

S

A

Y

L

F

V

E

S

S

L

D

K

V

V

.

L

S

D

A

Y

A

H

P

Q

Q

K

V

A

V

Y

R

A

L

Q

A

A

L

-------

G

+

-

-

K

V

-

+

-

-

Y

+

-

-

Q

-

-

-

-

+

Y

-

-

+

-

+

L

2pgd-1_Seq

.

.

.

.

.

.

.

.

.

.

.

.

G

A

G

H

.

.

.

.

.

.

F

V

K

M

V

H

N

G

I

E

Y

G

D

M

Q

L

I

C

E

A

Y

H

L

M

K

D

V

L

2pgd-1_SS

.

.

.

.

.

.

.

.

.

.

.

.

H

H

H

H

.

.

.

.

.

.

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

C

CORE

.

.

.

.

.

.

.

.

.

.

.

.

0

0

0

0

.

.

.

.

.

.

2

2

0

1

4

0

0

2

2

0

0

4

0

0

0

8

4

0

0

9

0

0

6

4

0

0

2

3

TRAD_H_PSS		H	C	C	C	C	C	C	C	H	H		H	H	H	H	H	H	C	C	C	C		E	E	E	E	E	E	H	H	H	C		C	C	H	H	H	H	H	H	H	H		H	H	H	C	C	C	C	H	H	H
TRAD_H_Seq		A	E	S	G	G	S	P	D	V	L		Q	M	L	K	I	H	R	S	D	P		Q	L	I	V	Q	L	R	F	C	G		R	Q	P	C	G	R	F	L	R	A		Y	R	E	G	X	X	X	X	X	X
-------								-		-	-		+	M	-	K	+																									+	-			+			+
2pgd-1_Seq		.	.	.	.	.	G	L	G	H	K		E	M	A	K	A	.	.	.	.	.		.	.	.	.	.	.	.	.	.	.		.	.	.	.	.	.	.	F	E	E		W	N	K	T	E	L	D	S	F	L
2pgd-1_SS		.	.	.	.	.	C	C	C	H	H		H	H	H	H	H	.	.	.	.	.		.	.	.	.	.	.	.	.	.	.		.	.	.	.	.	.	.	H	H	H		H	H	C	C	C	C	C	E	H	H
CORE		.	.	.	.	.	0	2	0	0	0		0	1	1	0	2	.	.	.	.	.		.	.	.	.	.	.	.	.	.	.		.	.	.	.	.	.	.	4	0	0		2	0	0	0	0	3	0	0	0	1

TRAD_H_PSS

H

H

H

H

H

H

H

H

C

C

C

C

C

C

E

E

E

E

E

C

C

C

H

H

H

H

H

H

H

C

.

.

.

.

.

.

.

C

C

C

H

H

H

H

H

H

H

H

H

C

TRAD_H_Seq

X

X

X

X

X

X

X

X

X

X

H

S

V

P

L

Q

L

E

L

R

A

G

A

E

R

L

D

A

L

L

.

.

.

.

.

.

.

A

D

E

E

R

C

L

S

C

I

L

A

Q

-------

-

-

-

-

G

-

-

L

+

-

+

-

-

-

+

S

+

-

-

2pgd-1_Seq

I

E

I

T

A

S

I

L

K

F

Q

D

.

.

.

.

.

.

.

A

D

G

K

H

L

L

P

K

I

R

D

S

A

G

Q

K

G

T

G

K

W

T

A

I

S

A

L

E

Y

G

2pgd-1_SS

H

H

H

H

H

H

H

H

H

C

E

C

.

.

.

.

.

.

.

C

C

C

C

E

C

H

H

H

C

C

C

C

C

C

C

C

C

H

H

H

H

H

H

H

H

H

H

H

H

C

CORE

5

0

0

1

2

0

0

2

0

0

0

0

.

.

.

.

.

.

.

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

1

0

0

3

2

0

2

4

0

0

0

0

TRAD_H_PSS

C

C

C

C

H

H

H

H

H

H

H

H

H

H

E

E

E

E

.

.

.

E

E

E

C

C

C

C

C

C

C

C

C

C

C

C

C

C

C

C

H

H

H

H

H

H

H

H

H

H

TRAD_H_Seq

Q

P

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

.

.

.

N

L

K

C

G

S

G

A

R

G

G

D

G

E

V

A

S

A

P

L

Q

X

X

X

X

X

X

X

X

-------

P

+

-

-

-

G

+

-

+

+

+

-

-

-

+

2pgd-1_Seq

V

P

V

T

L

I

G

E

A

V

F

A

R

C

L

S

S

L

K

D

E

R

I

Q

A

S

K

K

L

K

G

P

Q

N

I

P

F

E

G

D

K

K

S

F

L

E

D

I

R

K

2pgd-1_SS

C

C

C

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

C

C

C

C

C

C

C

C

C

C

C

C

H

H

H

H

H

H

H

H

H

H

CORE

2

0

4

0

7

4

0

0

3

1

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

1

0

0

0

0

0

0

3

3

0

0

7

0

0

TRAD_H_PSS

H

H

H

H

H

H

H

H

H

.

H

H

E

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

H

H

H

H

H

H

H

H

H

TRAD_H_Seq

X

X

X

X

X

X

X

X

X

.

A

Q

T

F

.

.

L

F

Q

G

Q

P

V

V

N

R

P

L

S

L

K

D

Q

Q

T

F

A

R

S

V

G

L

K

W

R

K

V

G

R

S

-------

A

Q

-

F

L

-

Q

-

-

+

-

+

-

-

L

+

+

-

-

-

-

R

-

G

-

-

-

R

+

+

-

2pgd-1_Seq

A

L

Y

A

S

K

I

I

S

Y

A

Q

G

F

M

L

L

R

Q

A

A

T

E

F

G

W

T

L

N

Y

G

G

I

A

L

M

W

R

.

G

G

C

I

I

R

.

.

S

V

F

2pgd-1_SS

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

C

C

C

C

C

H

H

H

H

H

H

H

H

C

.

C

C

C

C

C

C

.

.

E

H

H

CORE

4

8

0

0

6

0

3

4

5

1

2

0

2

2

1

5

3

0

0

1

1

0

0

0

0

0

0

2

0

0

0

0

2

2

0

0

1

0

.

0

0

0

0

1

0

.

.

0

0

1

TRAD_H_PSS

H

H

H

C

C

C

C

C

.

C

C

C

C

C

C

C

H

H

H

H

C

C

C

C

C

H

H

H

H

H

H

H

H

H

H

H

H

H

.

.

.

.

H

H

C

C

C

C

C

H

TRAD_H_Seq

L

Q

R

G

C

R

A

L

.

R

D

P

A

L

D

S

L

A

Y

E

Y

E

R

E

G

L

Y

E

Q

A

F

Q

L

L

R

R

F

V

.

.

.

.

Q

A

E

G

R

R

A

T

-------

L

+

+

-

-

-

A

-

R

+

P

-

L

+

L

-

-

-

+

-

-

E

+

-

+

-

+

R

R

-

+

Q

A

+

-

-

-

+

2pgd-1_Seq

L

G

K

I

K

D

A

F

D

R

N

P

G

L

Q

N

L

L

L

D

D

F

F

K

S

A

V

E

N

C

Q

D

S

W

R

R

A

I

S

T

G

V

Q

A

G

I

P

M

P

C

2pgd-1_SS

H

H

H

H

H

H

H

H

H

H

C

C

C

C

C

C

H

H

H

C

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

C

C

C

C

H

H

CORE

1

0

0

2

0

0

2

1

0

0

0

0

0

1

0

0

3

4

0

0

0

0

2

0

0

1

3

0

0

0

0

0

0

1

0

0

4

2

0

1

2

0

0

0

0

2

0

2

0

4

TRAD_H_PSS

H

H

H

.

.

.

.

.

.

.

.

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

C

.

.

.

.

.

.

.

.

.

.

.

.

.

.

C

C

C

C

C

C

TRAD_H_Seq

L

Q

R

.

.

.

.

.

.

.

.

L

V

E

A

L

E

E

N

E

L

T

S

L

A

E

D

L

L

G

.

.

.

.

.

.

.

.

.

.

.

.

.

.

L

T

D

P

N

G

-------

+

-

-

-

-

+

L

-

-

N

L

+

-

D

-

G

-

T

+

-

G

2pgd-1_Seq

F

T

T

A

L

S

F

Y

D

G

Y

R

H

A

M

L

P

A

N

.

L

I

Q

A

Q

R

D

Y

F

G

A

H

T

Y

E

L

L

A

K

P

G

Q

F

I

H

T

N

W

T

G

2pgd-1_SS

H

H

H

H

H

H

H

H

H

H

H

H

C

C

C

C

H

H

H

.

H

H

H

H

H

H

H

H

H

H

C

C

C

E

E

C

C

C

C

C

C

C

E

E

C

C

C

C

C

C

CORE

8

0

1

6

0

0

1

1

0

0

0

0

0

0

0

0

0

0

0

.

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

TRAD_H_PSS		C	C	C
TRAD_H_Seq		G	L	A
-------		-	-
2pgd-1_Seq		H	G	G
2pgd-1_SS		C	C	C
CORE		0	0	0