SitesBLAST – Find functional sites

 

SitesBLAST

Comparing YP_004139565.1 NCBI__GCF_000185905.1:YP_004139565.1 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 2 hits to proteins with known functional sites (download)

8b01B Cryo-em structure of the tripartite atp-independent periplasmic (trap) transporter siaqm from photobacterium profundum in a nanodisc (see paper)
30% identity, 32% coverage: 12:203/593 of query aligns to 1:180/427 of 8b01B

query
sites
8b01B
M
 
M
F
 
F
A
 
T
S
 
S
L
 
I
I
 
V
I
 
G
F
 
W
L
 
L
-
 
G
-
 
L
-
 
L
L
 
F
I
 
A
G
 
G
Y
 
M
P
 
P
V
 
V
A
 
G
F
 
F
S
 
S
L
 
L
A
 
I
A
 
F
N
 
V
G
 
G
L
 
L
M
 
A
F
 
F
F
 
-
F
 
-
I
 
-
G
 
-
V
 
L
L
 
V
L
 
L
S
 
T
P
 
E
Y
 
S
S
 
T
G
 
G
G
 
-
S
 
-
I
 
I
N
 
N
L
 
F
A
 
A
W
 
A
P
 
Q
L
 
Q
L
 
M
H
 
I
A
 
G
L
 
G
P
 
L
D
 
D
N
 
N
F
 
F
Y
 
-
G
 
-
S
 
-
R
 
-
V
 
-
M
 
-
S
 
-
N
 
-
D
 
-
T
 
T
L
 
L
L
 
L
A
 
A
I
 
V
P
 
P
F
 
F
F
 
F
T
 
V
F
 
L
M
 
T
G
 
G
I
 
H
V
 
L
L
 
M
E
 
N
R
 
S
S
 
A
G
 
G
M
 
I
A
 
T
E
 
E
D
 
R
L
 
I
L
 
F
D
 
N
T
 
F
I
 
A
G
 
K
Q
 
A
L
 
M
F
 
V
G
 
G
P
 
H
I
 
I
R
 
T
G
 
G
G
 
S
L
 
L
A
 
G
Y
 
H
A
 
V
V
 
N
I
 
I
F
 
L
V
 
A
G
 
S
A
 
L
L
 
L
L
 
F
A
x
S
A
 
G
T
 
M
T
x
S
G
|
G
V
 
S
V
 
A
A
 
L
A
 
A
S
 
D
V
 
A
I
 
G
A
 
G
M
 
L
G
 
G
L
 
Q
I
 
L
S
 
E
L
 
I
P
 
K
I
 
S
M
 
M
L
 
R
R
 
D
Y
 
A
G
 
K
Y
 
Y
D
 
D
R
 
D
R
 
D
L
 
F
A
 
A
S
 
G
G
 
G
V
 
L
I
 
T
A
 
A
A
 
A
S
 
S
G
 
C
T
 
I
L
 
I
A
x
G
Q
 
P
I
 
L
I
x
V
P
|
P
P
|
P
S
 
S
L
 
I
V
 
P
L
 
L
I
 
V
V
 
I
L
 
Y
A
 
G
D
 
V
Q
 
V
L
 
S
G
 
N
R
 
T
S
 
S
V
 
I
G
 
G
D
 
A
M
 
L
Y
 
F
A
 
L
G
 
A
A
 
G
L
 
A
I
 
I
P
 
P
G
 
G
L
 
L
V
 
L
L
 
C
T
 
C

Sites not aligning to the query:

8y4wA Sialic acid bound form of tripartite atp-independent periplasmic (trap) transporter from fusobacterium nucleatum.
24% identity, 35% coverage: 311:518/593 of query aligns to 415:608/612 of 8y4wA

query
sites
8y4wA
L
 
L
V
 
I
L
 
I
G
 
G
T
 
G
I
 
I
F
 
F
L
 
S
G
 
G
I
 
I
A
 
F
T
 
T
P
 
P
T
 
T
E
 
E
G
 
A
G
 
A
A
 
V
M
 
I
G
 
A
S
 
T
V
 
F
G
 
Y
A
 
S
L
 
I
F
 
I
M
 
L
A
 
G
A
 
G
-
 
F
A
 
I
K
 
Y
G
 
K
R
 
E
L
 
L
S
 
T
L
 
V
D
 
K
V
 
S
V
 
F
K
 
F
Q
 
K
A
 
H
L
 
C
A
 
V
S
 
E
T
 
A
T
 
V
R
 
A
L
 
I
S
 
S
S
 
G
F
 
V
V
 
T
L
 
V
F
 
L
I
 
M
L
 
I
I
 
M
G
 
T
A
 
V
R
 
T
V
 
F
F
 
F
S
 
G
L
 
D
T
 
I
F
 
I
Y
 
A
G
 
R
V
 
E
N
 
Q
G
 
V
H
 
A
I
 
M
W
 
R
V
 
V
E
 
A
H
 
E
L
 
I
L
 
F
T
 
I
S
 
K
L
 
Y
P
 
A
G
 
T
G
 
S
E
 
P
V
 
M
G
 
M
F
 
V
L
 
L
I
 
V
G
 
M
V
 
I
N
 
N
M
 
L
L
 
L
V
 
L
F
 
L
F
 
F
L
 
L
A
 
G
F
 
M
F
 
F
L
 
I
D
|
D
F
 
A
F
 
L
E
 
A
L
 
L
A
 
Q
F
 
F
I
 
L
I
 
V
V
 
L
P
 
P
L
 
M
L
 
L
A
 
I
P
 
P
A
 
I
A
 
A
D
 
E
K
 
Q
L
 
V
G
 
G
I
 
I
D
 
D
L
 
L
I
 
V
W
 
F
F
 
F
G
 
G
V
 
V
L
 
M
L
 
T
G
 
T
V
 
L
N
 
N
M
 
M
Q
 
M
T
 
I
S
 
G
F
 
I
M
 
L
H
 
T
P
 
P
P
 
P
F
 
M
G
 
G
F
x
M
A
 
A
L
 
L
F
 
F
Y
 
V
L
 
V
R
 
-
S
 
-
V
 
-
A
 
-
A
 
-
R
 
-
V
 
-
P
 
-
Y
 
-
L
 
-
D
 
-
R
 
-
L
 
-
T
 
-
G
 
-
K
 
A
Q
 
Q
I
 
V
A
 
G
P
 
K
V
 
M
T
 
S
T
 
V
G
 
S
Q
 
T
I
 
V
Y
 
A
W
 
K
G
 
G
A
 
V
V
 
L
P
 
P
F
 
F
V
 
L
C
 
L
I
 
P
Q
 
I
V
 
F
I
 
I
M
 
T
I
 
L
G
 
V
L
 
I
T
 
I
I
 
T
A
 
I
F
 
F
P
 
P
Q
 
Q
M
 
I
V
 
I
M
 
L

Sites not aligning to the query:

Query Sequence

>YP_004139565.1 NCBI__GCF_000185905.1:YP_004139565.1
MEFIAQNMAPIMFASLIIFLLIGYPVAFSLAANGLMFFFIGVLLSPYSGGSINLAWPLLH
ALPDNFYGSRVMSNDTLLAIPFFTFMGIVLERSGMAEDLLDTIGQLFGPIRGGLAYAVIF
VGALLAATTGVVAASVIAMGLISLPIMLRYGYDRRLASGVIAASGTLAQIIPPSLVLIVL
ADQLGRSVGDMYAGALIPGLVLTGLYMSYILIMSIIRPNSMPALPLEARTLGHGVMSLLV
ALLVTSAVSYAAYRYLAPAHGDNADILGATAGVLFIYIVAIADKRLNFNMMSRLAQQVII
VLIPPLALIFLVLGTIFLGIATPTEGGAMGSVGALFMAAAKGRLSLDVVKQALASTTRLS
SFVLFILIGARVFSLTFYGVNGHIWVEHLLTSLPGGEVGFLIGVNMLVFFLAFFLDFFEL
AFIIVPLLAPAADKLGIDLIWFGVLLGVNMQTSFMHPPFGFALFYLRSVAARVPYLDRLT
GKQIAPVTTGQIYWGAVPFVCIQVIMIGLTIAFPQMVMHYKGTTVDPGTIDYKVPEVPGL
SPLGTPPADGAAPAGGATAPAAPDLSQPPSFGDPTPAKPAAPQPDLSQPPSFN

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