SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing N515DRAFT_2697 FitnessBrowser__Dyella79:N515DRAFT_2697 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 5 hits to proteins with known functional sites (download)

Q8GAI3 4-methylaminobutanoate oxidase (formaldehyde-forming); MABO; Demethylating gamma-N-methylaminobutyrate oxidase; Gamma-N-methylaminobutyrate oxidase 1; EC 1.5.3.19 from Paenarthrobacter nicotinovorans (Arthrobacter nicotinovorans) (see paper)
27% identity, 53% coverage: 13:238/429 of query aligns to 15:225/824 of Q8GAI3

query
sites
Q8GAI3

T

T

A

A

S

T

A

S

Y

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Y

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W66 (≠ G69) mutation W->F,S: Contains a non-covalently bound FAD. Loss of enzyme activity.
H67 (≠ R70) mutation to A: Contains a non-covalently bound FAD. Exhibits about 10% of the wild-type enzyme activity.

O31616 Glycine oxidase; GO; EC 1.4.3.19 from Bacillus subtilis (strain 168) (see 3 papers)
22% identity, 73% coverage: 76:390/429 of query aligns to 62:355/369 of O31616

query
sites
O31616

F

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W

V174 (≠ A209) binding
H244 (≠ F286) mutation to A: 2-fold decrease in catalytic efficiency on glycine and similar catalytic efficiency on glyphosate. 60-fold decrease in catalytic efficiency on glycine and 210-fold increase in that on glyphosate; when associated with S-51 and R-54.
R302 (≠ M341) binding
327:333 (vs. 364:370, 14% identical) binding
R329 (≠ G366) binding

Sites not aligning to the query:

14:15 binding
34:35 binding
42:43 binding
47:49 binding
51 G→R: 130-fold decrease in catalytic efficiency on glycine and 28-fold increase in that on glyphosate.; G→S: 60-fold decrease in catalytic efficiency on glycine and 210-fold increase in that on glyphosate; when associated with R-54 and A-244.
54 A→R: 20-fold decrease in catalytic efficiency on glycine and 34-fold increase in that on glyphosate. 60-fold decrease in catalytic efficiency on glycine and 210-fold increase in that on glyphosate; when associated with S-51 and A-244.

3if9A Crystal structure of glycine oxidase g51s/a54r/h244a mutant in complex with inhibitor glycolate (see paper)
22% identity, 73% coverage: 76:390/429 of query aligns to 62:355/364 of 3if9A

query
sites
3if9A

F

F

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Q

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L

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E

R

-

A

-

R

-

A

-

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L

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Y

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A

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E

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R

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A

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I

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binding flavin-adenine dinucleotide: P173 (≠ D208), V174 (≠ A209), S202 (≠ C237), G203 (= G238), W205 (≠ Y240), F209 (≠ L244), G300 (= G339), R302 (≠ M341), H327 (≠ F364), F328 (≠ G365), R329 (≠ G366), N330 (≠ H367), G331 (= G368), I332 (≠ L369)
binding glycolic acid: Y246 (= Y288), R302 (≠ M341), R329 (≠ G366)

Sites not aligning to the query:

active site: 47, 48, 49
binding flavin-adenine dinucleotide: 11, 13, 15, 34, 35, 42, 43, 46, 47, 48, 49

1ng3A Complex of thio (glycine oxidase) with acetyl-glycine (see paper)
22% identity, 73% coverage: 76:390/429 of query aligns to 62:355/364 of 1ng3A

query
sites
1ng3A

F

F

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A

D

A

L

I

I

-

M

-

N

A

K

E

E

R

V

D

N

Q

Q

R

D

W

W

binding acetylamino-acetic acid: Y246 (= Y288), R302 (≠ M341), R329 (≠ G366)
binding flavin-adenine dinucleotide: V174 (≠ A209), S202 (≠ C237), G203 (= G238), W205 (≠ Y240), F209 (≠ L244), G300 (= G339), R302 (≠ M341), H327 (≠ F364), R329 (≠ G366), N330 (≠ H367), G331 (= G368), I332 (≠ L369)
binding phosphate ion: R89 (≠ E107), R254 (= R296)

Sites not aligning to the query:

active site: 47, 48, 49
binding flavin-adenine dinucleotide: 11, 13, 15, 33, 34, 35, 41, 42, 43, 46, 47, 48, 49

S5FMM4 Glycine oxidase; GO; BliGO; EC 1.4.3.19 from Bacillus licheniformis (see paper)
27% identity, 48% coverage: 176:383/429 of query aligns to 141:346/369 of S5FMM4

query
sites
S5FMM4

Y

F

E

I

R

R

N

D

A

D

F

V

H

H

L

V

H

E

P

P

L

A

N

A

F

V

A

C

I

R

G

A

L

F

A

A

A

R

A

G

A

A

A

R

G

M

Q

L

G

G

V

A

R

D

I

V

H

F

E

E

H

Y

T

T

D

P

A

V

W

L

Q

S

L

I

R

E

R

S

D

E

G

A

L

G

R

A

W

V

R

R

V

V

E

T

T

S

D

A

Q

S

G

G

T

T

V

A

L

E

A

A

E

E

H

H

V

A

V

V

L

I

A

A

C
x
S

G

G

G

V

Y

W

L

S

A

G

G

A

L

L

R

F

R

K

A

Q

I

I

-

G

-

L

D

D

R

K

A

R

I

F

L

Y

P

P

I

V

A

K

T

G

Y

E

V

C

M

L

T

S

T

V

E

W

P

N

L

D

G

G

D

I

R

S

L

L

R

-

A

-

C

-

L

-

D

-

T

T

R

R

A

T

A

L

I

Y

Y

H

D

D

T

-

R

-

F

-

A

-

F

H

D

C

Y

Y

Y

I

R

V

P

P

L

R

P

H

D

S

T

G

R

R

L

L

L

V

W

V

G

G

G

A

R

T

I

M

S

K

I

P

R

G

-

D

-

W

N

N

R

E

S

Q

P

P

Q

E

-

L

-

G

A

G

V

I

R

E

L

L

L

I

T

-

R

R

D

K

L

A

L

K

R

S

V

M

F

L

P

P

A

G

L

I

Q

E

G

S

V

M

R

K

I

I

D

D

H

Q

A

C

W

W

S

A

G

G

L

L

M

R

S

P

Y

E

A

T

R

G

H

D

Q

G

M

N

P

P

Q

Y

I

I

G

G

-

R

-

H

-

P

G

E

G

N

D

D

E

R

G

I

L

L

W

F

W

A

A

A

Q

G

A

H

F

F

-

R

G

N

G

G

H
x
I

G

L

L

L

A

A

P

P

T

-

C

-

A

A

A

T

G

G

E

E

L

M

L
x
M

A

A

A

D

A

M

I

I

S202 (≠ C237) mutation to C: Shows 7.1- and 8-fold increase of affinity and catalytic efficiency to glyphosate, respectively, while the substrate affinity to glycine decreases 235-fold and catalytic efficiency decreases 113-fold; when associated with S-51, R-54, R-81, V-332 and V-342.
I332 (≠ H367) mutation to V: Shows 7.1- and 8-fold increase of affinity and catalytic efficiency to glyphosate, respectively, while the substrate affinity to glycine decreases 235-fold and catalytic efficiency decreases 113-fold; when associated with S-51, R-54, R-81, C-202 and V-342.
M342 (≠ L379) mutation to V: Shows 7.1- and 8-fold increase of affinity and catalytic efficiency to glyphosate, respectively, while the substrate affinity to glycine decreases 235-fold and catalytic efficiency decreases 113-fold; when associated with S-51, R-54, R-81, C-202 and V-332.

Sites not aligning to the query:

51 G→S: Shows 4.3- and 107-fold increase of affinity to glyphosate and glycine, respectively. Shows 7.1- and 8-fold increase of affinity and catalytic efficiency to glyphosate, respectively, while the substrate affinity to glycine decreases 235-fold and catalytic efficiency decreases 113-fold; when associated with R-54, R-81, C-202, V-332 and V-342.
54 A→R: Shows 7.1- and 8-fold increase of affinity and catalytic efficiency to glyphosate, respectively, while the substrate affinity to glycine decreases 235-fold and catalytic efficiency decreases 113-fold; when associated with S-51, R-81, C-202, V-332 and V-342.
81 K→R: Shows 7.1- and 8-fold increase of affinity and catalytic efficiency to glyphosate, respectively, while the substrate affinity to glycine decreases 235-fold and catalytic efficiency decreases 113-fold; when associated with S-51, R-54, C-202, V-332 and V-342.

Query Sequence

>N515DRAFT_2697 FitnessBrowser__Dyella79:N515DRAFT_2697
MKQPPAPSYYRATASAYEPYAALRGRAEAKVVIVGGGFAGLHTALGLAERGVRDVVLLER
EQVGFGASGRNGGFVFAGYSLGEQSLLDQLGEERARALFGLTTAAVERIRAQVLRYGIAC
DLVDEGVLWANWFRDPAVLRRRQALLEKHYGVQWEWVAQDALRERVHTRRYFDGLYERNA
FHLHPLNFAIGLAAAAAGQGVRIHEHTDAWQLRRDGLRWRVETDQGTVLAEHVVLACGGY
LAGLRRAIDRAILPIATYVMTTEPLGDRLRACLDTRAAIYDTRFAFDYYRPLPDTRLLWG
GRISIRNRSPQAVRRLLTRDLLRVFPALQGVRIDHAWSGLMSYARHQMPQIGGGDEGLWW
AQAFGGHGLAPTCAAGELLAAAIAERDQRWKQFADYGLASAHRPAGYLAAQASYWWHQGR
DWFKTRLEA

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