SitesBLAST – Find functional sites

 

SitesBLAST

Comparing PFR28_05003 to proteins with known functional sites using BLASTp with E ≤ 0.001.

Or try Sites on a Tree, PaperBLAST, Conserved Domains, or compare to all protein structures

Found 20 (the maximum) hits to proteins with known functional sites (download)

8cd1Le phikz014 (see paper)
65% identity, 93% coverage: 1:68/73 of query aligns to 1:68/68 of 8cd1Le

query
sites
8cd1Le
M
|
M
K
|
K
T
 
A
D
 
D
I
 
I
H
|
H
P
 
P
E
 
T
Y
 
Y
P
 
E
V
 
A
V
 
I
A
 
E
V
 
A
T
 
T
C
 
C
S
 
S
C
 
C
G
 
G
N
 
N
K
 
V
F
 
I
E
 
K
T
 
T
R
 
R
S
 
S
T
 
T
Y
 
L
G
 
C
K
 
K
A
 
P
L
 
I
A
 
H
I
 
L
D
 
D
V
 
V
C
 
C
N
 
S
E
 
E
C
 
C
H
 
H
P
 
P
F
 
F
Y
 
Y
T
 
T
G
 
G
K
 
K
Q
 
Q
K
 
K
T
 
V
L
 
L
D
 
D
T
 
T
G
 
G
G
 
G
R
 
R
V
 
I
Q
 
D
K
x
R
F
 
F
A
 
K
D
 
Q
R
|
R
F
 
F
G
 
G
A
 
V
F
 
F
G
 
G

5akaZ Em structure of ribosome-srp-ftsy complex in closed state (see paper)
54% identity, 95% coverage: 1:69/73 of query aligns to 1:69/70 of 5akaZ

query
sites
5akaZ
M
|
M
K
 
K
T
 
K
D
 
D
I
 
I
H
 
H
P
 
P
E
x
K
Y
|
Y
P
x
E
V
x
E
V
x
I
A
x
T
V
x
A
T
 
S
C
 
C
S
|
S
C
 
C
G
 
G
N
|
N
K
x
V
F
 
M
E
 
K
T
x
I
R
|
R
S
 
S
T
|
T
Y
x
V
G
|
G
K
x
H
A
 
D
L
 
L
A
x
N
I
x
L
D
 
D
V
 
V
C
 
C
N
 
S
E
 
K
C
 
C
H
 
H
P
 
P
F
 
F
Y
x
F
T
 
T
G
 
G
K
 
K
Q
 
Q
K
x
R
T
 
D
L
 
V
D
 
A
T
|
T
G
 
G
G
 
G
R
 
R
V
 
V
Q
 
D
K
 
R
F
 
F
A
 
N
D
 
K
R
 
R
F
 
F
G
 
N
A
 
I
F
 
P
G
 
G
A
 
S

P0A7M9 Large ribosomal subunit protein bL31; 50S ribosomal protein L31 from Escherichia coli (strain K12) (see 2 papers)
54% identity, 95% coverage: 1:69/73 of query aligns to 1:69/70 of P0A7M9

query
sites
P0A7M9
M
 
M
K
 
K
T
 
K
D
 
D
I
 
I
H
 
H
P
 
P
E
x
K
Y
 
Y
P
 
E
V
 
E
V
 
I
A
 
T
V
 
A
T
 
S
C
|
C
S
 
S
C
|
C
G
 
G
N
 
N
K
 
V
F
 
M
E
 
K
T
 
I
R
 
R
S
 
S
T
 
T
Y
 
V
G
 
G
K
 
H
A
 
D
L
 
L
A
 
N
I
 
L
D
 
D
V
 
V
C
|
C
N
x
S
E
x
K
C
|
C
H
 
H
P
 
P
F
 
F
Y
 
F
T
 
T
G
 
G
K
 
K
Q
 
Q
K
 
R
T
 
D
L
 
V
D
 
A
T
 
T
G
 
G
G
 
G
R
 
R
V
 
V
Q
 
D
K
 
R
F
 
F
A
 
N
D
 
K
R
 
R
F
 
F
G
 
N
A
 
I
F
 
P
G
 
G
A
 
S

6yst6 of the P+9 ArfB-ribosome complex with P/E hybrid tRNA in the post-hydrolysis state (see paper)
55% identity, 89% coverage: 1:65/73 of query aligns to 1:65/66 of 6yst6

query
sites
6yst6
M
|
M
K
|
K
T
 
K
D
 
D
I
 
I
H
|
H
P
 
P
E
 
K
Y
 
Y
P
 
E
V
 
E
V
 
I
A
 
T
V
 
A
T
 
S
C
 
C
S
 
S
C
|
C
G
 
G
N
 
N
K
 
V
F
 
M
E
 
K
T
 
I
R
 
R
S
 
S
T
 
T
Y
 
V
G
 
G
K
 
H
A
 
D
L
 
L
A
 
N
I
 
L
D
 
D
V
 
V
C
 
C
N
 
S
E
x
K
C
|
C
H
 
H
P
 
P
F
 
F
Y
 
F
T
 
T
G
 
G
K
 
K
Q
 
Q
K
 
R
T
 
D
L
 
V
D
 
A
T
 
T
G
 
G
G
 
G
R
 
R
V
 
V
Q
 
D
K
 
R
F
 
F
A
 
N
D
 
K
R
 
R
F
 
F
G
 
N

5afi6 Structure of E. coli ribosome-EF-TU complex by cs-corrected cryo-EM (see paper)
55% identity, 89% coverage: 1:65/73 of query aligns to 1:65/66 of 5afi6

query
sites
5afi6
M
|
M
K
|
K
T
 
K
D
 
D
I
 
I
H
|
H
P
 
P
E
 
K
Y
 
Y
P
 
E
V
 
E
V
 
I
A
 
T
V
 
A
T
 
S
C
|
C
S
 
S
C
|
C
G
 
G
N
 
N
K
 
V
F
 
M
E
 
K
T
 
I
R
 
R
S
 
S
T
 
T
Y
 
V
G
 
G
K
 
H
A
 
D
L
 
L
A
 
N
I
 
L
D
 
D
V
 
V
C
|
C
N
 
S
E
 
K
C
 
C
H
 
H
P
 
P
F
 
F
Y
 
F
T
 
T
G
 
G
K
 
K
Q
 
Q
K
 
R
T
 
D
L
 
V
D
 
A
T
 
T
G
 
G
G
 
G
R
 
R
V
 
V
Q
 
D
K
 
R
F
 
F
A
 
N
D
 
K
R
 
R
F
 
F
G
 
N

5zeb2 50S ribosomal protein L33 1 (see paper)
58% identity, 89% coverage: 1:65/73 of query aligns to 1:66/66 of 5zeb2

query
sites
5zeb2
M
|
M
K
|
K
T
 
T
D
 
G
I
 
I
H
|
H
P
 
P
E
 
E
Y
 
Y
P
 
V
V
 
D
V
 
T
A
 
T
V
 
V
T
 
Q
C
 
C
S
 
G
C
 
C
G
 
G
N
 
H
K
 
S
F
 
F
E
 
T
T
 
T
R
 
R
S
 
S
T
 
T
-
 
K
Y
 
Q
G
 
S
K
 
G
A
 
T
L
 
I
A
 
V
I
 
V
D
 
E
V
 
V
C
 
C
N
 
S
E
 
Q
C
 
C
H
 
H
P
 
P
F
 
F
Y
 
Y
T
 
T
G
 
G
K
 
K
Q
 
Q
K
 
K
T
 
I
L
 
L
D
 
D
T
 
S
G
 
G
G
 
G
R
 
R
V
 
V
Q
 
A
K
 
R
F
 
F
A
 
E
D
 
K
R
 
R
F
 
Y
G
 
G

9c4g4 Cutibacterium acnes 50s ribosomal subunit with clindamycin bound (see paper)
59% identity, 89% coverage: 1:65/73 of query aligns to 1:66/66 of 9c4g4

query
sites
9c4g4
M
 
M
K
 
K
T
 
Q
D
 
G
I
 
I
H
 
H
P
 
P
E
 
D
Y
 
Y
P
 
R
V
 
E
V
 
T
A
 
T
V
 
V
T
 
V
C
|
C
S
 
T
C
 
C
G
 
G
N
 
N
K
 
T
F
 
F
E
 
T
T
 
T
R
 
R
S
 
S
T
 
T
Y
 
S
G
 
Q
K
 
S
A
 
G
-
 
T
L
 
L
A
 
N
I
 
A
D
 
D
V
|
V
C
|
C
N
 
S
E
 
K
C
|
C
H
 
H
P
 
P
F
 
F
Y
 
Y
T
 
T
G
 
G
K
 
K
Q
 
Q
K
 
K
T
 
I
L
 
L
D
 
D
T
 
A
G
 
G
G
 
G
R
 
R
V
 
V
Q
 
A
K
 
R
F
 
F
A
 
E
D
 
R
R
 
R
F
 
Y
G
 
G

8crx4 30S ribosomal protein S17 (see paper)
59% identity, 89% coverage: 1:65/73 of query aligns to 1:66/66 of 8crx4

query
sites
8crx4
M
|
M
K
|
K
T
 
Q
D
 
G
I
 
I
H
|
H
P
 
P
E
 
D
Y
 
Y
P
 
R
V
 
E
V
 
T
A
 
T
V
 
V
T
 
V
C
 
C
S
 
T
C
|
C
G
 
G
N
 
N
K
 
T
F
 
F
E
 
T
T
 
T
R
 
R
S
 
S
T
 
T
Y
 
S
G
 
Q
K
 
S
A
 
G
-
 
T
L
 
L
A
 
N
I
 
A
D
 
D
V
|
V
C
|
C
N
 
S
E
 
K
C
|
C
H
 
H
P
 
P
F
 
F
Y
 
Y
T
 
T
G
 
G
K
 
K
Q
 
Q
K
 
K
T
 
I
L
 
L
D
 
D
T
 
A
G
 
G
G
 
G
R
 
R
V
 
V
Q
 
A
K
x
R
F
 
F
A
 
E
D
 
R
R
|
R
F
 
Y
G
 
G

7unr3 30S ribosomal protein S6
64% identity, 64% coverage: 1:47/73 of query aligns to 1:47/47 of 7unr3

query
sites
7unr3
M
|
M
K
|
K
T
 
A
D
 
D
I
 
I
H
|
H
P
 
P
E
 
T
Y
 
Y
P
 
E
V
 
A
V
 
I
A
 
E
V
 
A
T
 
T
C
|
C
S
 
S
C
|
C
G
 
G
N
 
N
K
 
V
F
 
I
E
 
K
T
 
T
R
 
R
S
 
S
T
 
T
Y
 
L
G
 
C
K
 
K
A
 
P
L
 
I
A
 
H
I
 
L
D
 
D
V
 
V
C
|
C
N
 
S
E
 
E
C
|
C
H
 
H
P
 
P
F
 
F
Y
 
Y
T
 
T
G
 
G
K
 
K

Q03223 Large ribosomal subunit protein bL31; 50S ribosomal protein L31 from Bacillus subtilis (strain 168) (see paper)
46% identity, 89% coverage: 1:65/73 of query aligns to 1:64/66 of Q03223

query
sites
Q03223
M
 
M
K
 
K
T
 
A
D
 
G
I
 
I
H
 
H
P
 
P
E
 
N
Y
 
F
P
 
K
V
 
K
V
 
A
A
 
T
V
 
V
T
 
K
C
 
C
S
 
A
C
 
C
G
 
G
N
 
N
K
 
E
F
 
F
E
 
E
T
 
T
R
 
G
S
 
S
T
 
V
Y
 
-
G
 
K
K
 
E
A
 
E
L
 
V
A
 
R
I
 
V
D
 
E
V
 
I
C
|
C
N
 
S
E
 
E
C
|
C
H
 
H
P
 
P
F
 
F
Y
 
Y
T
 
T
G
 
G
K
 
R
Q
 
Q
K
 
K
T
 
F
L
 
A
D
 
S
T
 
A
G
 
D
G
 
G
R
 
R
V
 
V
Q
 
D
K
 
R
F
 
F
A
 
N
D
 
K
R
 
K
F
 
Y
G
 
G

3j9wB3 30S ribosomal protein uS9 (see paper)
46% identity, 89% coverage: 1:65/73 of query aligns to 1:64/64 of 3j9wB3

query
sites
3j9wB3
M
|
M
K
|
K
T
 
A
D
 
G
I
 
I
H
|
H
P
 
P
E
 
N
Y
 
F
P
 
K
V
 
K
V
 
A
A
 
T
V
 
V
T
 
K
C
 
C
S
 
A
C
 
C
G
 
G
N
 
N
K
 
E
F
 
F
E
 
E
T
 
T
R
 
G
S
 
S
T
 
V
Y
 
-
G
 
K
K
 
E
A
 
E
L
 
V
A
 
R
I
 
V
D
 
E
V
 
I
C
 
C
N
 
S
E
 
E
C
 
C
H
 
H
P
 
P
F
 
F
Y
 
Y
T
 
T
G
 
G
K
 
R
Q
 
Q
K
 
K
T
 
F
L
 
A
D
 
S
T
 
A
G
 
D
G
 
G
R
 
R
V
 
V
Q
 
D
K
 
R
F
 
F
A
 
N
D
 
K
R
 
K
F
 
Y
G
 
G

5a9zAa of Thermous thermophilus ribosome bound to BipA-GDPCP (see paper)
48% identity, 89% coverage: 1:65/73 of query aligns to 1:64/71 of 5a9zAa

query
sites
5a9zAa
M
|
M
K
|
K
T
x
E
D
 
G
I
 
I
H
 
H
P
 
P
E
 
K
Y
 
L
P
x
V
V
 
P
V
 
A
A
x
R
V
 
I
T
x
I
C
|
C
S
 
G
C
 
C
G
 
G
N
 
N
K
 
V
F
 
I
E
|
E
T
|
T
R
 
Y
S
|
S
T
|
T
Y
 
-
G
x
K
K
x
P
A
x
E
L
x
I
A
x
Y
I
 
V
D
x
E
V
|
V
C
 
C
N
 
S
E
 
K
C
|
C
H
|
H
P
|
P
F
|
F
Y
 
Y
T
|
T
G
 
G
K
 
Q
Q
 
Q
K
 
R
T
 
F
L
 
V
D
 
D
T
 
T
G
 
E
G
 
G
R
 
R
V
 
V
Q
 
E
K
x
R
F
|
F
A
 
Q
D
 
R
R
 
R
F
x
Y
G
 
G

Sites not aligning to the query:

1vy4B4 50S ribosomal protein L36 (see paper)
48% identity, 89% coverage: 1:65/73 of query aligns to 1:64/69 of 1vy4B4

query
sites
1vy4B4
M
|
M
K
|
K
T
 
E
D
 
G
I
 
I
H
|
H
P
 
P
E
 
K
Y
 
L
P
 
V
V
 
P
V
 
A
A
 
R
V
 
I
T
 
I
C
|
C
S
 
G
C
|
C
G
 
G
N
 
N
K
 
V
F
 
I
E
 
E
T
 
T
R
 
Y
S
 
S
T
 
T
Y
 
-
G
 
K
K
 
P
A
 
E
L
 
I
A
 
Y
I
 
V
D
 
E
V
 
V
C
|
C
N
 
S
E
 
K
C
|
C
H
 
H
P
 
P
F
 
F
Y
 
Y
T
 
T
G
 
G
K
 
Q
Q
 
Q
K
 
R
T
 
F
L
 
V
D
 
D
T
 
T
G
 
E
G
 
G
R
 
R
V
 
V
Q
 
E
K
 
R
F
 
F
A
 
Q
D
 
R
R
 
R
F
 
Y
G
 
G

7msc6 70SIC in complex with MtbEttA at Pre_R0 state (see paper)
50% identity, 89% coverage: 1:65/73 of query aligns to 1:58/60 of 7msc6

query
sites
7msc6
M
|
M
K
|
K
T
 
S
D
 
D
I
 
I
H
|
H
P
 
P
E
 
A
Y
 
Y
P
 
E
V
 
E
V
 
T
A
 
T
V
 
V
T
 
V
C
|
C
S
 
G
C
 
C
G
 
G
N
 
N
K
 
T
F
 
F
E
 
Q
T
 
T
R
 
R
S
 
S
T
 
T
Y
 
K
-
 
P
G
 
G
K
 
G
A
 
R
L
 
I
A
 
V
I
 
V
D
 
E
V
 
V
C
 
C
N
 
S
E
 
Q
C
|
C
H
 
H
P
 
P
F
 
F
Y
 
Y
T
 
-
G
 
-
K
 
-
Q
 
-
K
 
-
T
 
-
L
 
-
D
 
-
T
 
T
G
 
G
G
 
G
R
 
R
V
 
V
Q
 
A
K
 
R
F
 
F
A
 
E
D
 
K
R
 
R
F
 
Y
G
 
G

5o61g complete structure of the Mycobacterium smegmatis 70S ribosome (see paper)
50% identity, 89% coverage: 1:65/73 of query aligns to 1:59/59 of 5o61g

query
sites
5o61g
M
|
M
K
|
K
T
 
T
D
 
G
I
 
I
H
|
H
P
 
P
E
 
E
Y
 
Y
P
 
V
V
 
D
V
 
T
A
 
T
V
 
V
T
 
Q
C
|
C
S
 
G
C
|
C
G
 
G
N
 
H
K
 
S
F
 
F
E
 
T
T
 
T
R
 
R
S
 
S
T
 
T
-
 
K
Y
 
Q
G
 
S
K
 
G
A
 
T
L
 
I
A
 
V
I
 
V
D
 
E
V
 
V
C
 
C
N
 
S
E
 
Q
C
|
C
H
 
H
P
 
P
F
 
F
Y
 
Y
T
 
T
G
 
G
K
 
K
Q
 
-
K
 
-
T
 
-
L
 
-
D
 
-
T
 
-
G
 
-
G
 
G
R
 
R
V
 
V
Q
 
A
K
 
R
F
 
F
A
 
E
D
 
K
R
 
R
F
 
Y
G
 
G

5o60g Structure of the 50s large ribosomal subunit from mycobacterium smegmatis (see paper)
56% identity, 64% coverage: 1:47/73 of query aligns to 1:48/48 of 5o60g

query
sites
5o60g
M
|
M
K
|
K
T
 
T
D
 
G
I
 
I
H
|
H
P
 
P
E
 
E
Y
 
Y
P
 
V
V
 
D
V
 
T
A
 
T
V
 
V
T
 
Q
C
|
C
S
 
G
C
|
C
G
 
G
N
 
H
K
 
S
F
 
F
E
 
T
T
 
T
R
 
R
S
 
S
T
 
T
-
 
K
Y
 
Q
G
 
S
K
 
G
A
 
T
L
 
I
A
 
V
I
 
V
D
 
E
V
 
V
C
 
C
N
 
S
E
 
Q
C
|
C
H
 
H
P
 
P
F
 
F
Y
 
Y
T
 
T
G
 
G
K
 
K

6o8z1 50S ribosomal protein L31 type B (see paper)
39% identity, 89% coverage: 1:65/73 of query aligns to 1:79/83 of 6o8z1

query
sites
6o8z1
M
|
M
K
|
K
T
 
Q
D
 
D
I
 
I
H
|
H
P
 
P
E
 
N
Y
 
Y
-
 
Q
P
 
P
V
 
V
V
 
V
A
 
F
V
 
M
T
 
D
C
 
S
S
 
T
C
 
T
G
 
G
N
 
F
K
 
K
F
 
F
E
 
L
T
 
S
R
 
G
S
 
S
T
 
T
Y
 
K
G
 
G
K
 
S
A
 
S
-
 
E
-
 
T
-
 
V
-
 
E
-
 
W
-
 
E
-
 
D
-
 
G
-
 
N
-
 
T
-
 
Y
-
 
P
-
 
L
L
 
L
A
 
R
I
 
V
D
 
E
V
 
V
C
 
T
N
 
S
E
 
D
C
 
S
H
 
H
P
 
P
F
 
F
Y
 
Y
T
 
T
G
 
G
K
 
R
Q
 
Q
K
 
K
T
 
F
L
 
T
D
 
Q
T
 
A
G
 
D
G
 
G
R
 
R
V
 
V
Q
 
D
K
 
R
F
 
F
A
 
N
D
 
K
R
 
K
F
 
Y
G
 
G

7nhn4 50S ribosomal protein L31 type B (see paper)
41% identity, 89% coverage: 1:65/73 of query aligns to 1:79/79 of 7nhn4

query
sites
7nhn4
M
|
M
K
|
K
T
 
T
D
 
G
I
 
I
H
|
H
P
 
P
E
 
E
Y
 
Y
-
 
R
P
 
P
V
 
V
V
 
V
A
 
F
V
 
V
T
 
D
C
 
T
S
 
S
C
 
T
G
 
D
N
 
F
K
 
K
F
 
F
E
 
L
T
 
S
R
 
G
S
 
S
T
 
T
Y
 
K
G
 
S
K
 
S
A
 
S
-
 
E
-
 
T
-
 
I
-
 
K
-
 
W
-
 
E
-
 
D
-
 
G
-
 
N
-
 
E
-
 
Y
-
 
P
-
 
L
L
 
L
A
 
R
I
 
V
D
 
E
V
 
I
C
 
S
N
 
S
E
 
D
C
 
S
H
 
H
P
 
P
F
 
F
Y
 
Y
T
 
T
G
 
G
K
 
K
Q
 
Q
K
 
K
T
 
H
L
 
A
D
 
T
T
 
A
G
 
D
G
 
G
R
 
R
V
 
V
Q
 
D
K
 
R
F
 
F
A
 
N
D
 
K
R
 
K
F
 
Y
G
 
G

6ysiW Acinetobacter baumannii ribosome-tigecycline complex - 50s subunit (see paper)
56% identity, 58% coverage: 1:42/73 of query aligns to 1:43/43 of 6ysiW

query
sites
6ysiW
M
|
M
K
x
R
T
 
A
D
 
D
I
 
I
H
 
H
P
 
P
E
 
K
Y
 
Y
P
 
E
V
 
K
V
 
L
A
 
V
V
 
A
T
 
T
C
 
C
S
 
S
C
 
C
G
 
G
N
 
N
K
 
V
F
 
I
E
 
E
T
 
T
R
 
R
S
 
S
T
 
A
Y
 
L
G
 
G
K
 
K
-
 
E
A
 
T
L
 
I
A
 
Y
I
 
L
D
 
D
V
 
V
C
 
C
N
 
S
E
 
A
C
 
C
H
 
H
P
 
P

8qcq6 Large ribosomal subunit protein bL31-A (see paper)
49% identity, 64% coverage: 1:47/73 of query aligns to 1:46/46 of 8qcq6

query
sites
8qcq6
M
|
M
K
|
K
T
 
A
D
 
G
I
 
I
H
|
H
P
 
P
E
 
N
Y
 
F
P
 
K
V
 
K
V
 
A
A
 
T
V
 
V
T
 
K
C
|
C
S
 
A
C
 
C
G
 
G
N
 
N
K
 
E
F
 
F
E
 
E
T
 
T
R
 
G
S
 
S
T
 
V
Y
 
-
G
 
K
K
 
E
A
 
E
L
 
V
A
 
R
I
 
V
D
 
E
V
 
I
C
|
C
N
 
S
E
 
E
C
|
C
H
 
H
P
 
P
F
 
F
Y
 
Y
T
 
T
G
 
G
K
 
R

Query Sequence

>PFR28_05003
MKTDIHPEYPVVAVTCSCGNKFETRSTYGKALAIDVCNECHPFYTGKQKTLDTGGRVQKF
ADRFGAFGATKKA

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