Parageobacillus caldoxylosilyticus β-glucosidase Download PDB file Protein:
Beta-glucosidase Organism:
Parageobacillus caldoxylosilyticus Lenght:
490 UniprotID:
A0A150LGF5 Download sequence )Template:
3AHX:A 40.72% ) | [φ,ψ] plot
Show:
Conserved 50-79%
Conserved >80%
Catalytic AA
Mutations
Co-evoluted networks
Secondary structures
Amino acid:
Local position¹:
Global position²:
Conserved > 80%:
Conserved 50-79%:
Secondary structure:
Co-evoluted network:
Mutation predicted:
Co-evolution network³
Residue
Community
Network
F25 1 Y73 G28 Q35 E37 G38 G44 D51 G28 1 F25 Q35 E37 G38 G44 D51 A30 1 W362 Q35 1 F25 G28 E37 G38 G44 D51 E37 1 F25 G28 Q35 G38 G44 D51 G38 1 F25 G28 Q35 E37 G44 D51 G44 1 F25 G28 Q35 E37 G38 D51 N109 L143 G112 D51 1 F25 G28 Q35 E37 G38 G44 N109 A69 1 G148 G112 G448 L82 H211 D71 1 R92 G234 G112 H211 Y73 1 F25 L82 1 A69 R92 1 D71 P102 1 G112 H211 N109 1 G44 D51 G112 G112 1 G44 D71 N109 G448 P102 H211 Y413 T133 A69 V458 T133 1 G112 G448 H211 Y413 V458 L143 1 G44 G148 1 A69 H211 1 D71 G112 G448 P102 Y413 G370 T133 A69 V458 G234 1 D71 Y275 1 W362 1 A30 R452 G370 1 H211 E390 1 W437 N391 1 Y434 R452 N459 Y413 1 G112 H211 T133 Y434 1 N391 W437 1 E390 R470 G448 1 G112 H211 T133 A69 R452 1 N391 W362 N459 G454 1 V458 N459 R470 K473 S475 V458 1 G112 H211 T133 G454 N459 1 N391 R452 G454 R470 1 W437 G454 S475 K473 1 G454 S475 S475 1 G454 R470 K473 W50 2 N311 T389 Y453 N217 Y91 2 P198 Y453 N217 F93 2 P198 S438 S444 Y449 N311 T389 Y453 N217 D138 2 G309 A254 N311 Q183 2 P198 S444 N311 P198 2 S438 Q183 S444 G309 F93 Y449 N311 T389 Y453 N217 Y91 N217 2 P198 S444 F93 Y449 N311 W50 T389 W445 Y453 Y91 L442 A254 2 D138 V269 2 G309 N311 G309 2 P198 D138 S444 V269 N311 N311 2 P198 D138 Q183 S444 G309 F93 V269 W50 T389 N217 T389 2 P198 S438 F93 N311 W50 Y453 N217 S438 2 P198 F93 T389 L442 2 W445 Y453 N217 S444 2 P198 Q183 G309 F93 Y449 N311 Y453 N217 W445 2 Y453 N217 L442 Y449 2 P198 S444 F93 Y453 N217 Y453 2 P198 S444 F93 Y449 W50 T389 W445 N217 Y91 L442
¹ Residue Corresponding position in the amino acids sequence.
² We performed multiple alignment between all GH1 beta-glucosidases sequences using Clustal omega (default parameters). We collected the amino acids that appear in more than 50% of the sequences and more than 80% of the sequences.
³ Co-evolution network was generated using PFSTATS and family GH1 sequences obtained from PFAM. Amino acid residues edges represent correlation links between them.
1
M
K
K
N
N
E
E
K
E
E
K
E
M
E
H
K
Q
L
R
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F
P
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G
F
L
W
G
S
A
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A
A
Y
Q
35
36
V
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G
A
W
N
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D
G
K
G
P
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V
W
D
V
F
A
K
Q
P
G
R
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K
G
T
N
G
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A
V
70
71
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Y
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A
L
M
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L
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A
W
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N
G
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105
106
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140
141
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A
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D
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F
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A
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K
175
176
Y
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N
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F
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G
Y
R
L
G
L
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K
R
M
Y
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A
N
210
211
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Y
V
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245
246
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W
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Y
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A
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W
280
281
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Y
L
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I
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G
D
M
E
L
L
K
A
G
K
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D
F
M
G
V
N
Y
Y
Q
T
315
316
K
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Y
N
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G
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G
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G
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N
T
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G
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G
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G
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350
351
T
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N
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W
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G
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385
386
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N
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420
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File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
ss_loop_inactive"
style=""
title="N
Local position: 459
Global position: 1789"
>
N
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 460
Filename: views/view.php
Line Number: 225
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
Loop | bend | hydrogen bonded turn',
'info',
'',
'460',
'1790',
'arginine');"
onmouseout="hideAminoAcid('R', 'R460')"
onmouseover="showAminoAcid('R460'); selectID(glviewer,460)"
class="btn btn-info conserved50_active
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 460
Filename: views/view.php
Line Number: 255
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
ss_loop_inactive"
style=""
title="R
Local position: 460
Global position: 1790"
>
R
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 461
Filename: views/view.php
Line Number: 225
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
Loop | bend | hydrogen bonded turn',
'default',
'',
'461',
'1791',
'aspartic acid');"
onmouseout="hideAminoAcid('D', 'D461')"
onmouseover="showAminoAcid('D461'); selectID(glviewer,461)"
class="btn btn-default
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 461
Filename: views/view.php
Line Number: 255
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
ss_loop_inactive"
style=""
title="D
Local position: 461
Global position: 1791"
>
D
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 462
Filename: views/view.php
Line Number: 225
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
Loop | bend | hydrogen bonded turn',
'default',
'',
'462',
'1792',
'aspartic acid');"
onmouseout="hideAminoAcid('D', 'D462')"
onmouseover="showAminoAcid('D462'); selectID(glviewer,462)"
class="btn btn-default
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 462
Filename: views/view.php
Line Number: 255
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
ss_loop_inactive"
style=""
title="D
Local position: 462
Global position: 1792"
>
D
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 463
Filename: views/view.php
Line Number: 225
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
Loop | bend | hydrogen bonded turn',
'default',
'',
'463',
'1793',
'glutamic acid');"
onmouseout="hideAminoAcid('E', 'E463')"
onmouseover="showAminoAcid('E463'); selectID(glviewer,463)"
class="btn btn-default
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 463
Filename: views/view.php
Line Number: 255
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
ss_loop_inactive"
style=""
title="E
Local position: 463
Global position: 1793"
>
E
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 464
Filename: views/view.php
Line Number: 225
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
Loop | bend | hydrogen bonded turn',
'default',
'',
'464',
'1794',
'serine');"
onmouseout="hideAminoAcid('S', 'S464')"
onmouseover="showAminoAcid('S464'); selectID(glviewer,464)"
class="btn btn-default
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 464
Filename: views/view.php
Line Number: 255
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
ss_loop_inactive"
style=""
title="S
Local position: 464
Global position: 1794"
>
S
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 465
Filename: views/view.php
Line Number: 225
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
Loop | bend | hydrogen bonded turn',
'default',
'',
'465',
'1796',
'glutamic acid');"
onmouseout="hideAminoAcid('E', 'E465')"
onmouseover="showAminoAcid('E465'); selectID(glviewer,465)"
class="btn btn-default
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 465
Filename: views/view.php
Line Number: 255
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
ss_loop_inactive"
style=""
title="E
Local position: 465
Global position: 1796"
>
E
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 466
Filename: views/view.php
Line Number: 225
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
Loop | bend | hydrogen bonded turn',
'default',
'',
'466',
'1797',
'lysine');"
onmouseout="hideAminoAcid('K', 'K466')"
onmouseover="showAminoAcid('K466'); selectID(glviewer,466)"
class="btn btn-default
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 466
Filename: views/view.php
Line Number: 255
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
ss_loop_inactive"
style=""
title="K
Local position: 466
Global position: 1797"
>
K
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 467
Filename: views/view.php
Line Number: 225
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
Loop | bend | hydrogen bonded turn',
'default',
'',
'467',
'1798',
'aspartic acid');"
onmouseout="hideAminoAcid('D', 'D467')"
onmouseover="showAminoAcid('D467'); selectID(glviewer,467)"
class="btn btn-default
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 467
Filename: views/view.php
Line Number: 255
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
ss_loop_inactive"
style=""
title="D
Local position: 467
Global position: 1798"
>
D
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 468
Filename: views/view.php
Line Number: 225
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
Loop | bend | hydrogen bonded turn',
'info',
'',
'468',
'1800',
'leucine');"
onmouseout="hideAminoAcid('L', 'L468')"
onmouseover="showAminoAcid('L468'); selectID(glviewer,468)"
class="btn btn-info conserved50_active
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 468
Filename: views/view.php
Line Number: 255
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
ss_loop_inactive"
style=""
title="L
Local position: 468
Global position: 1800"
>
L
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 469
Filename: views/view.php
Line Number: 225
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
Loop | bend | hydrogen bonded turn',
'default',
'',
'469',
'1802',
'arginine');"
onmouseout="hideAminoAcid('R', 'R469')"
onmouseover="showAminoAcid('R469'); selectID(glviewer,469)"
class="btn btn-default
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 469
Filename: views/view.php
Line Number: 255
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
ss_loop_inactive"
style=""
title="R
Local position: 469
Global position: 1802"
>
R
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 470
Filename: views/view.php
Line Number: 225
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
Loop | bend | hydrogen bonded turn',
'danger',
' coevo_1_inactive',
'470',
'1803',
'arginine');"
onmouseout="hideAminoAcid('R', 'R470')"
onmouseover="showAminoAcid('R470'); selectID(glviewer,470)"
class="btn btn-danger coevo_1_inactive conserved80_active
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 470
Filename: views/view.php
Line Number: 255
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
ss_loop_inactive"
style=""
title="R
Local position: 470
Global position: 1803"
>
R
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 471
Filename: views/view.php
Line Number: 225
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
Loop | bend | hydrogen bonded turn',
'info',
'',
'471',
'1804',
'isoleucine');"
onmouseout="hideAminoAcid('I', 'I471')"
onmouseover="showAminoAcid('I471'); selectID(glviewer,471)"
class="btn btn-info conserved50_active
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 471
Filename: views/view.php
Line Number: 255
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
ss_loop_inactive"
style=""
title="I
Local position: 471
Global position: 1804"
>
I
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 472
Filename: views/view.php
Line Number: 225
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
Loop | bend | hydrogen bonded turn',
'default',
'',
'472',
'1805',
'lysine');"
onmouseout="hideAminoAcid('K', 'K472')"
onmouseover="showAminoAcid('K472'); selectID(glviewer,472)"
class="btn btn-default
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 472
Filename: views/view.php
Line Number: 255
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
ss_loop_inactive"
style=""
title="K
Local position: 472
Global position: 1805"
>
K
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 473
Filename: views/view.php
Line Number: 225
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
Loop | bend | hydrogen bonded turn',
'danger',
' coevo_1_inactive',
'473',
'1809',
'lysine');"
onmouseout="hideAminoAcid('K', 'K473')"
onmouseover="showAminoAcid('K473'); selectID(glviewer,473)"
class="btn btn-danger coevo_1_inactive conserved80_active
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 473
Filename: views/view.php
Line Number: 255
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
ss_loop_inactive"
style=""
title="K
Local position: 473
Global position: 1809"
>
K
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 474
Filename: views/view.php
Line Number: 225
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
Loop | bend | hydrogen bonded turn',
'default',
'',
'474',
'1810',
'lysine');"
onmouseout="hideAminoAcid('K', 'K474')"
onmouseover="showAminoAcid('K474'); selectID(glviewer,474)"
class="btn btn-default
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 474
Filename: views/view.php
Line Number: 255
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
ss_loop_inactive"
style=""
title="K
Local position: 474
Global position: 1810"
>
K
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 475
Filename: views/view.php
Line Number: 225
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
Loop | bend | hydrogen bonded turn',
'danger',
' coevo_1_inactive',
'475',
'1811',
'serine');"
onmouseout="hideAminoAcid('S', 'S475')"
onmouseover="showAminoAcid('S475'); selectID(glviewer,475)"
class="btn btn-danger coevo_1_inactive conserved80_active
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 475
Filename: views/view.php
Line Number: 255
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
ss_loop_inactive"
style=""
title="S
Local position: 475
Global position: 1811"
>
S
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 476
Filename: views/view.php
Line Number: 225
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
Loop | bend | hydrogen bonded turn',
'default',
'',
'476',
'1812',
'phenylalanine');"
onmouseout="hideAminoAcid('F', 'F476')"
onmouseover="showAminoAcid('F476'); selectID(glviewer,476)"
class="btn btn-default
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 476
Filename: views/view.php
Line Number: 255
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
ss_loop_inactive"
style=""
title="F
Local position: 476
Global position: 1812"
>
F
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 477
Filename: views/view.php
Line Number: 225
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
Loop | bend | hydrogen bonded turn',
'default',
'',
'477',
'1817',
'tyrosine');"
onmouseout="hideAminoAcid('Y', 'Y477')"
onmouseover="showAminoAcid('Y477'); selectID(glviewer,477)"
class="btn btn-default
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 477
Filename: views/view.php
Line Number: 255
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
ss_loop_inactive"
style=""
title="Y
Local position: 477
Global position: 1817"
>
Y
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 478
Filename: views/view.php
Line Number: 225
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
Loop | bend | hydrogen bonded turn',
'info',
'',
'478',
'1818',
'tryptophan');"
onmouseout="hideAminoAcid('W', 'W478')"
onmouseover="showAminoAcid('W478'); selectID(glviewer,478)"
class="btn btn-info conserved50_active
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 478
Filename: views/view.php
Line Number: 255
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
ss_loop_inactive"
style=""
title="W
Local position: 478
Global position: 1818"
>
W
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 479
Filename: views/view.php
Line Number: 225
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
Loop | bend | hydrogen bonded turn',
'info',
'',
'479',
'1829',
'tyrosine');"
onmouseout="hideAminoAcid('Y', 'Y479')"
onmouseover="showAminoAcid('Y479'); selectID(glviewer,479)"
class="btn btn-info conserved50_active
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 479
Filename: views/view.php
Line Number: 255
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
ss_loop_inactive"
style=""
title="Y
Local position: 479
Global position: 1829"
>
Y
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 480
Filename: views/view.php
Line Number: 225
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
Loop | bend | hydrogen bonded turn',
'default',
'',
'480',
'1834',
'lysine');"
onmouseout="hideAminoAcid('K', 'K480')"
onmouseover="showAminoAcid('K480'); selectID(glviewer,480)"
class="btn btn-default
A PHP Error was encountered
Severity: Warning
Message: Uninitialized string offset 480
Filename: views/view.php
Line Number: 255
Backtrace:
File: /scratch/html/glutantbase/application/views/view.php
File: /scratch/html/glutantbase/application/libraries/Template.php
File: /scratch/html/glutantbase/application/controllers/Protein.php
File: /scratch/html/glutantbase/index.php
ss_loop_inactive"
style=""
title="K
Local position: 480
Global position: 1834"
>
K
A PHP Error was encountered
Severity: Warning
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α-helix | 3-helix | π-helix β-bridge | β-ladder | β-strand Loop | bend | hydrogen bonded turn Community 1 Community 2
Extrapoled mutations
E110K | Cellobiose docking
Poses (avg)
Affinity (wild)
Affinity (mutant)
ΔAffinity
ΔAffinity expected
Status
1
-5.73
-5.87
-0.14
ΔAffinity < 0
✓
1-3
-4.74
-4.86
-0.12
ΔAffinity < 0
✓
1-10
-4.05
-3.99
0.06
ΔAffinity < 0
x
E110K | Glucose docking
Poses (avg)
Affinity (wild)
Affinity (mutant)
ΔAffinity
ΔAffinity expected
Status
1
-5.73
-5.80
-0.069999999999999
ΔAffinity > 0
x
1-3
-4.74
-5.51
-0.77
ΔAffinity > 0
x
1-10
-4.95
-4.98
-0.03
ΔAffinity > 0
x
H196F | Cellobiose docking
Poses (avg)
Affinity (wild)
Affinity (mutant)
ΔAffinity
ΔAffinity expected
Status
1
-5.73
-5.63
0.1
ΔAffinity < 0
x
1-3
-4.74
-4.62
0.12
ΔAffinity < 0
x
1-10
-4.05
-3.80
0.25
ΔAffinity < 0
x
H196F | Glucose docking
Poses (avg)
Affinity (wild)
Affinity (mutant)
ΔAffinity
ΔAffinity expected
Status
1
-5.73
-5.93
-0.2
ΔAffinity > 0
x
1-3
-4.74
-5.66
-0.92
ΔAffinity > 0
x
1-10
-4.95
-5.06
-0.11
ΔAffinity > 0
x
Methodology
Comparative modeling
Three-dimensional structures were modeled by homology using MODELLER . Sequences were collected in UniProt . We searched for the E.C. number of beta-glucosidases (3.2.1.21) and collected sequences of family GH1 (~3000). For each sequence, we selected the structure of highest identity using BLAST against the PDB database to be used as a template. Sequences with identity lower than 25% were discarded. 100 models were constructed for each sequence. The best model was selected using the lowest value of the DOPE score. Mutants were modeled using MODELLER's mutation script. The mutations were based on beneficial mutations described in the literature.
Minimization
PDB models were minimized using AMBER tools . We performed 1000 steps of minimization in the vacuum (parameters: imin=1, maxcyc=1000, ncyc=750, cut=10.0, ntb=0, igb=0).
Multiple alignment
We performed multiple alignment using Clustal Omega (default parameters). We used Python scripts to detect conservation.
Docking
We performed docking of glucose (product) and cellobiose (substrate) for wild and mutant beta-glucosidases using AutoDock Vina (parameters: exhaustiveness = 20; num_modes = 10). The box center was defined using the median coordinate of the last atom of the two catalytic glutamates. The experiment was performed in triplicate. We collected ten poses for each docking and analyzed the average of affinity energies predicted by the software for (i) pose 1, (ii) poses 1-3, and (iii) poses 1-10.
