Streptomyces roseosporus NRRL 11379 β-glucosidase Download PDB file

Protein: Beta-glucosidase

Organism: Streptomyces roseosporus NRRL 11379

Lenght: 485

UniprotID: W9FP75 (Download sequence)

Template: 1GNX:A (69.36%) | [φ,ψ] plot

Amino acid:

Local position¹:

Global position²:

Conserved > 80%:

Conserved 50-79%:

Secondary structure:

Co-evoluted network:

Mutation predicted:

Co-evolution network³

Residue	Community	Network

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.

									

						                        
Loop | bend | hydrogen bonded turn', 
                            'default', 
                            '', 
                            '1', 
                            '316',
                            'methionine');" 
                            onmouseout="hideAminoAcid('M', 'M1')"  
                            onmouseover="showAminoAcid('M1'); selectID(glviewer,1)" 
                            class="btn btn-default
A PHP Error was encounteredSeverity: Warning
Message:  Uninitialized string offset 1
Filename: views/view.php
Line Number: 255
Backtrace:

			File: /scratch/html/glutantbase/application/views/view.php

			Line: 255

			Function: _error_handler			

			File: /scratch/html/glutantbase/application/libraries/Template.php

			Line: 13

			Function: view			

			File: /scratch/html/glutantbase/application/controllers/Protein.php

			Line: 188

			Function: show			

			File: /scratch/html/glutantbase/index.php

			Line: 315

			Function: require_once			
 ss_loop_inactive" 
                            style=""
                            title="M
Local position: 1
Global position: 316"
                        >
                            M                            
                        					                        						                        
Loop | bend | hydrogen bonded turn', 
                            'default', 
                            '', 
                            '2', 
                            '317',
                            'threonine');" 
                            onmouseout="hideAminoAcid('T', 'T2')"  
                            onmouseover="showAminoAcid('T2'); selectID(glviewer,2)" 
                            class="btn btn-default
A PHP Error was encounteredSeverity: Warning
Message:  Uninitialized string offset 2
Filename: views/view.php
Line Number: 255
Backtrace:

			File: /scratch/html/glutantbase/application/views/view.php

			Line: 255

			Function: _error_handler			

			File: /scratch/html/glutantbase/application/libraries/Template.php

			Line: 13

			Function: view			

			File: /scratch/html/glutantbase/application/controllers/Protein.php

			Line: 188

			Function: show			

			File: /scratch/html/glutantbase/index.php

			Line: 315

			Function: require_once			
 ss_loop_inactive" 
                            style=""
                            title="T
Local position: 2
Global position: 317"
                        >
                            T                            
                        					                        						                        
Loop | bend | hydrogen bonded turn', 
                            'default', 
                            '', 
                            '3', 
                            '318',
                            'alanine');" 
                            onmouseout="hideAminoAcid('A', 'A3')"  
                            onmouseover="showAminoAcid('A3'); selectID(glviewer,3)" 
                            class="btn btn-default
A PHP Error was encounteredSeverity: Warning
Message:  Uninitialized string offset 3
Filename: views/view.php
Line Number: 255
Backtrace:

			File: /scratch/html/glutantbase/application/views/view.php

			Line: 255

			Function: _error_handler			

			File: /scratch/html/glutantbase/application/libraries/Template.php

			Line: 13

			Function: view			

			File: /scratch/html/glutantbase/application/controllers/Protein.php

			Line: 188

			Function: show			

			File: /scratch/html/glutantbase/index.php

			Line: 315

			Function: require_once			
 ss_loop_inactive" 
                            style=""
                            title="A
Local position: 3
Global position: 318"
                        >
                            A                            
                        					                        						                        

Loop | bend | hydrogen bonded turn', 'default', '', '4', '319', 'valine');" onmouseout="hideAminoAcid('V', 'V4')" onmouseover="showAminoAcid('V4'); selectID(glviewer,4)" class="btn btn-default

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 4

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
Function: _error_handler

File: /scratch/html/glutantbase/application/libraries/Template.php
Line: 13
Function: view

File: /scratch/html/glutantbase/application/controllers/Protein.php
Line: 188
Function: show

File: /scratch/html/glutantbase/index.php
Line: 315
Function: require_once

ss_loop_inactive" style="" title="V Local position: 4 Global position: 319" > V

									

						                        
Loop | bend | hydrogen bonded turn', 
                            'danger', 
                            ' coevo_1_inactive', 
                            '36', 
                            '448',
                            'glutamic acid');" 
                            onmouseout="hideAminoAcid('E', 'E36')"  
                            onmouseover="showAminoAcid('E36'); selectID(glviewer,36)" 
                            class="btn btn-danger coevo_1_inactive conserved80_active
A PHP Error was encounteredSeverity: Warning
Message:  Uninitialized string offset 36
Filename: views/view.php
Line Number: 255
Backtrace:

			File: /scratch/html/glutantbase/application/views/view.php

			Line: 255

			Function: _error_handler			

			File: /scratch/html/glutantbase/application/libraries/Template.php

			Line: 13

			Function: view			

			File: /scratch/html/glutantbase/application/controllers/Protein.php

			Line: 188

			Function: show			

			File: /scratch/html/glutantbase/index.php

			Line: 315

			Function: require_once			
 ss_loop_inactive" 
                            style=""
                            title="E
Local position: 36
Global position: 448"
                        >
                            E                            
                        					                        						                        

Loop | bend | hydrogen bonded turn', 'danger', ' coevo_1_inactive', '37', '449', 'glycine');" onmouseout="hideAminoAcid('G', 'G37')" onmouseover="showAminoAcid('G37'); selectID(glviewer,37)" class="btn btn-danger coevo_1_inactive conserved80_active

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 37

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
Function: _error_handler

File: /scratch/html/glutantbase/application/libraries/Template.php
Line: 13
Function: view

File: /scratch/html/glutantbase/application/controllers/Protein.php
Line: 188
Function: show

File: /scratch/html/glutantbase/index.php
Line: 315
Function: require_once

ss_loop_inactive" style="" title="G Local position: 37 Global position: 449" > G

									

						                        
Loop | bend | hydrogen bonded turn', 
                            'info', 
                            '', 
                            '71', 
                            '537',
                            'histidine');" 
                            onmouseout="hideAminoAcid('H', 'H71')"  
                            onmouseover="showAminoAcid('H71'); selectID(glviewer,71)" 
                            class="btn btn-info conserved50_active
A PHP Error was encounteredSeverity: Warning
Message:  Uninitialized string offset 71
Filename: views/view.php
Line Number: 255
Backtrace:

			File: /scratch/html/glutantbase/application/views/view.php

			Line: 255

			Function: _error_handler			

			File: /scratch/html/glutantbase/application/libraries/Template.php

			Line: 13

			Function: view			

			File: /scratch/html/glutantbase/application/controllers/Protein.php

			Line: 188

			Function: show			

			File: /scratch/html/glutantbase/index.php

			Line: 315

			Function: require_once			
 ss_loop_inactive" 
                            style=""
                            title="H
Local position: 71
Global position: 537"
                        >
                            H                            
                        					                        						                        

Loop | bend | hydrogen bonded turn', 'danger', ' coevo_1_inactive', '72', '538', 'phenylalanine');" onmouseout="hideAminoAcid('F', 'F72')" onmouseover="showAminoAcid('F72'); selectID(glviewer,72)" class="btn btn-danger coevo_1_inactive conserved80_active

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 72

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
Function: _error_handler

File: /scratch/html/glutantbase/application/libraries/Template.php
Line: 13
Function: view

File: /scratch/html/glutantbase/application/controllers/Protein.php
Line: 188
Function: show

File: /scratch/html/glutantbase/index.php
Line: 315
Function: require_once

ss_loop_inactive" style="" title="F Local position: 72 Global position: 538" > F

									

						                        
Loop | bend | hydrogen bonded turn', 
                            'default', 
                            '', 
                            '106', 
                            '590',
                            'proline');" 
                            onmouseout="hideAminoAcid('P', 'P106')"  
                            onmouseover="showAminoAcid('P106'); selectID(glviewer,106)" 
                            class="btn btn-default
A PHP Error was encounteredSeverity: Warning
Message:  Uninitialized string offset 106
Filename: views/view.php
Line Number: 255
Backtrace:

			File: /scratch/html/glutantbase/application/views/view.php

			Line: 255

			Function: _error_handler			

			File: /scratch/html/glutantbase/application/libraries/Template.php

			Line: 13

			Function: view			

			File: /scratch/html/glutantbase/application/controllers/Protein.php

			Line: 188

			Function: show			

			File: /scratch/html/glutantbase/index.php

			Line: 315

			Function: require_once			
 ss_loop_inactive" 
                            style=""
                            title="P
Local position: 106
Global position: 590"
                        >
                            P                            
                        					                        						                        

Loop | bend | hydrogen bonded turn', 'default', '', '107', '591', 'alanine');" onmouseout="hideAminoAcid('A', 'A107')" onmouseover="showAminoAcid('A107'); selectID(glviewer,107)" class="btn btn-default

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 107

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
Function: _error_handler

File: /scratch/html/glutantbase/application/libraries/Template.php
Line: 13
Function: view

File: /scratch/html/glutantbase/application/controllers/Protein.php
Line: 188
Function: show

File: /scratch/html/glutantbase/index.php
Line: 315
Function: require_once

ss_loop_inactive" style="" title="A Local position: 107 Global position: 591" > A

									

						                        
Loop | bend | hydrogen bonded turn', 
                            'default', 
                            '', 
                            '141', 
                            '662',
                            'glutamic acid');" 
                            onmouseout="hideAminoAcid('E', 'E141')"  
                            onmouseover="showAminoAcid('E141'); selectID(glviewer,141)" 
                            class="btn btn-default
A PHP Error was encounteredSeverity: Warning
Message:  Uninitialized string offset 141
Filename: views/view.php
Line Number: 255
Backtrace:

			File: /scratch/html/glutantbase/application/views/view.php

			Line: 255

			Function: _error_handler			

			File: /scratch/html/glutantbase/application/libraries/Template.php

			Line: 13

			Function: view			

			File: /scratch/html/glutantbase/application/controllers/Protein.php

			Line: 188

			Function: show			

			File: /scratch/html/glutantbase/index.php

			Line: 315

			Function: require_once			
 ss_loop_inactive" 
                            style=""
                            title="E
Local position: 141
Global position: 662"
                        >
                            E                            
                        					                        						                        

Loop | bend | hydrogen bonded turn', 'danger', ' coevo_1_inactive', '142', '663', 'leucine');" onmouseout="hideAminoAcid('L', 'L142')" onmouseover="showAminoAcid('L142'); selectID(glviewer,142)" class="btn btn-danger coevo_1_inactive conserved80_active

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 142

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
Function: _error_handler

File: /scratch/html/glutantbase/application/libraries/Template.php
Line: 13
Function: view

File: /scratch/html/glutantbase/application/controllers/Protein.php
Line: 188
Function: show

File: /scratch/html/glutantbase/index.php
Line: 315
Function: require_once

ss_loop_inactive" style="" title="L Local position: 142 Global position: 663" > L

									

						                        
Loop | bend | hydrogen bonded turn', 
                            'default', 
                            '', 
                            '176', 
                            '741',
                            'threonine');" 
                            onmouseout="hideAminoAcid('T', 'T176')"  
                            onmouseover="showAminoAcid('T176'); selectID(glviewer,176)" 
                            class="btn btn-default
A PHP Error was encounteredSeverity: Warning
Message:  Uninitialized string offset 176
Filename: views/view.php
Line Number: 255
Backtrace:

			File: /scratch/html/glutantbase/application/views/view.php

			Line: 255

			Function: _error_handler			

			File: /scratch/html/glutantbase/application/libraries/Template.php

			Line: 13

			Function: view			

			File: /scratch/html/glutantbase/application/controllers/Protein.php

			Line: 188

			Function: show			

			File: /scratch/html/glutantbase/index.php

			Line: 315

			Function: require_once			
 ss_loop_inactive" 
                            style=""
                            title="T
Local position: 176
Global position: 741"
                        >
                            T                            
                        					                        						                        

Loop | bend | hydrogen bonded turn', 'danger', '', '177', '742', 'threonine');" onmouseout="hideAminoAcid('T', 'T177')" onmouseover="showAminoAcid('T177'); selectID(glviewer,177)" class="btn btn-danger conserved80_active

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 177

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
Function: _error_handler

File: /scratch/html/glutantbase/application/libraries/Template.php
Line: 13
Function: view

File: /scratch/html/glutantbase/application/controllers/Protein.php
Line: 188
Function: show

File: /scratch/html/glutantbase/index.php
Line: 315
Function: require_once

ss_loop_inactive" style="" title="T Local position: 177 Global position: 742" > T

									

						                        
Loop | bend | hydrogen bonded turn', 
                            'default', 
                            '', 
                            '211', 
                            '871',
                            'leucine');" 
                            onmouseout="hideAminoAcid('L', 'L211')"  
                            onmouseover="showAminoAcid('L211'); selectID(glviewer,211)" 
                            class="btn btn-default
A PHP Error was encounteredSeverity: Warning
Message:  Uninitialized string offset 211
Filename: views/view.php
Line Number: 255
Backtrace:

			File: /scratch/html/glutantbase/application/views/view.php

			Line: 255

			Function: _error_handler			

			File: /scratch/html/glutantbase/application/libraries/Template.php

			Line: 13

			Function: view			

			File: /scratch/html/glutantbase/application/controllers/Protein.php

			Line: 188

			Function: show			

			File: /scratch/html/glutantbase/index.php

			Line: 315

			Function: require_once			
 ss_loop_inactive" 
                            style=""
                            title="L
Local position: 211
Global position: 871"
                        >
                            L                            
                        					                        						                        

Loop | bend | hydrogen bonded turn', 'default', '', '212', '872', 'asparagine');" onmouseout="hideAminoAcid('N', 'N212')" onmouseover="showAminoAcid('N212'); selectID(glviewer,212)" class="btn btn-default

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 212

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
Function: _error_handler

File: /scratch/html/glutantbase/application/libraries/Template.php
Line: 13
Function: view

File: /scratch/html/glutantbase/application/controllers/Protein.php
Line: 188
Function: show

File: /scratch/html/glutantbase/index.php
Line: 315
Function: require_once

ss_loop_inactive" style="" title="N Local position: 212 Global position: 872" > N

									

						                        
Loop | bend | hydrogen bonded turn', 
                            'default', 
                            '', 
                            '246', 
                            '981',
                            'aspartic acid');" 
                            onmouseout="hideAminoAcid('D', 'D246')"  
                            onmouseover="showAminoAcid('D246'); selectID(glviewer,246)" 
                            class="btn btn-default
A PHP Error was encounteredSeverity: Warning
Message:  Uninitialized string offset 246
Filename: views/view.php
Line Number: 255
Backtrace:

			File: /scratch/html/glutantbase/application/views/view.php

			Line: 255

			Function: _error_handler			

			File: /scratch/html/glutantbase/application/libraries/Template.php

			Line: 13

			Function: view			

			File: /scratch/html/glutantbase/application/controllers/Protein.php

			Line: 188

			Function: show			

			File: /scratch/html/glutantbase/index.php

			Line: 315

			Function: require_once			
 ss_loop_inactive" 
                            style=""
                            title="D
Local position: 246
Global position: 981"
                        >
                            D                            
                        					                        						                        

Loop | bend | hydrogen bonded turn', 'default', '', '247', '1089', 'serine');" onmouseout="hideAminoAcid('S', 'S247')" onmouseover="showAminoAcid('S247'); selectID(glviewer,247)" class="btn btn-default

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 247

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
Function: _error_handler

File: /scratch/html/glutantbase/application/libraries/Template.php
Line: 13
Function: view

File: /scratch/html/glutantbase/application/controllers/Protein.php
Line: 188
Function: show

File: /scratch/html/glutantbase/index.php
Line: 315
Function: require_once

ss_loop_inactive" style="" title="S Local position: 247 Global position: 1089" > S

									

						                        
Loop | bend | hydrogen bonded turn', 
                            'default', 
                            '', 
                            '281', 
                            '1276',
                            'aspartic acid');" 
                            onmouseout="hideAminoAcid('D', 'D281')"  
                            onmouseover="showAminoAcid('D281'); selectID(glviewer,281)" 
                            class="btn btn-default
A PHP Error was encounteredSeverity: Warning
Message:  Uninitialized string offset 281
Filename: views/view.php
Line Number: 255
Backtrace:

			File: /scratch/html/glutantbase/application/views/view.php

			Line: 255

			Function: _error_handler			

			File: /scratch/html/glutantbase/application/libraries/Template.php

			Line: 13

			Function: view			

			File: /scratch/html/glutantbase/application/controllers/Protein.php

			Line: 188

			Function: show			

			File: /scratch/html/glutantbase/index.php

			Line: 315

			Function: require_once			
 ss_loop_inactive" 
                            style=""
                            title="D
Local position: 281
Global position: 1276"
                        >
                            D                            
                        					                        						                        

Loop | bend | hydrogen bonded turn', 'default', '', '282', '1277', 'threonine');" onmouseout="hideAminoAcid('T', 'T282')" onmouseover="showAminoAcid('T282'); selectID(glviewer,282)" class="btn btn-default

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 282

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
Function: _error_handler

File: /scratch/html/glutantbase/application/libraries/Template.php
Line: 13
Function: view

File: /scratch/html/glutantbase/application/controllers/Protein.php
Line: 188
Function: show

File: /scratch/html/glutantbase/index.php
Line: 315
Function: require_once

ss_loop_inactive" style="" title="T Local position: 282 Global position: 1277" > T

									

						                        
Loop | bend | hydrogen bonded turn', 
                            'default', 
                            '', 
                            '316', 
                            '1410',
                            'isoleucine');" 
                            onmouseout="hideAminoAcid('I', 'I316')"  
                            onmouseover="showAminoAcid('I316'); selectID(glviewer,316)" 
                            class="btn btn-default
A PHP Error was encounteredSeverity: Warning
Message:  Uninitialized string offset 316
Filename: views/view.php
Line Number: 255
Backtrace:

			File: /scratch/html/glutantbase/application/views/view.php

			Line: 255

			Function: _error_handler			

			File: /scratch/html/glutantbase/application/libraries/Template.php

			Line: 13

			Function: view			

			File: /scratch/html/glutantbase/application/controllers/Protein.php

			Line: 188

			Function: show			

			File: /scratch/html/glutantbase/index.php

			Line: 315

			Function: require_once			
 ss_loop_inactive" 
                            style=""
                            title="I
Local position: 316
Global position: 1410"
                        >
                            I                            
                        					                        						                        

Loop | bend | hydrogen bonded turn', 'info', '', '317', '1411', 'valine');" onmouseout="hideAminoAcid('V', 'V317')" onmouseover="showAminoAcid('V317'); selectID(glviewer,317)" class="btn btn-info conserved50_active

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 317

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
Function: _error_handler

File: /scratch/html/glutantbase/application/libraries/Template.php
Line: 13
Function: view

File: /scratch/html/glutantbase/application/controllers/Protein.php
Line: 188
Function: show

File: /scratch/html/glutantbase/index.php
Line: 315
Function: require_once

ss_loop_inactive" style="" title="V Local position: 317 Global position: 1411" > V

									

						                        
Loop | bend | hydrogen bonded turn', 
                            'default', 
                            '', 
                            '351', 
                            '1494',
                            'alanine');" 
                            onmouseout="hideAminoAcid('A', 'A351')"  
                            onmouseover="showAminoAcid('A351'); selectID(glviewer,351)" 
                            class="btn btn-default
A PHP Error was encounteredSeverity: Warning
Message:  Uninitialized string offset 351
Filename: views/view.php
Line Number: 255
Backtrace:

			File: /scratch/html/glutantbase/application/views/view.php

			Line: 255

			Function: _error_handler			

			File: /scratch/html/glutantbase/application/libraries/Template.php

			Line: 13

			Function: view			

			File: /scratch/html/glutantbase/application/controllers/Protein.php

			Line: 188

			Function: show			

			File: /scratch/html/glutantbase/index.php

			Line: 315

			Function: require_once			
 ss_loop_inactive" 
                            style=""
                            title="A
Local position: 351
Global position: 1494"
                        >
                            A                            
                        					                        						                        

Loop | bend | hydrogen bonded turn', 'default', '', '352', '1495', 'glutamic acid');" onmouseout="hideAminoAcid('E', 'E352')" onmouseover="showAminoAcid('E352'); selectID(glviewer,352)" class="btn btn-default

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 352

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
Function: _error_handler

File: /scratch/html/glutantbase/application/libraries/Template.php
Line: 13
Function: view

File: /scratch/html/glutantbase/application/controllers/Protein.php
Line: 188
Function: show

File: /scratch/html/glutantbase/index.php
Line: 315
Function: require_once

ss_loop_inactive" style="" title="E Local position: 352 Global position: 1495" > E

									

						                        
Loop | bend | hydrogen bonded turn', 
                            'info', 
                            '', 
                            '386', 
                            '1565',
                            'valine');" 
                            onmouseout="hideAminoAcid('V', 'V386')"  
                            onmouseover="showAminoAcid('V386'); selectID(glviewer,386)" 
                            class="btn btn-info conserved50_active
A PHP Error was encounteredSeverity: Warning
Message:  Uninitialized string offset 386
Filename: views/view.php
Line Number: 255
Backtrace:

			File: /scratch/html/glutantbase/application/views/view.php

			Line: 255

			Function: _error_handler			

			File: /scratch/html/glutantbase/application/libraries/Template.php

			Line: 13

			Function: view			

			File: /scratch/html/glutantbase/application/controllers/Protein.php

			Line: 188

			Function: show			

			File: /scratch/html/glutantbase/index.php

			Line: 315

			Function: require_once			
 ss_loop_inactive" 
                            style=""
                            title="V
Local position: 386
Global position: 1565"
                        >
                            V                            
                        					                        						                        

Loop | bend | hydrogen bonded turn', 'danger', ' coevo_2_inactive', '387', '1566', 'threonine');" onmouseout="hideAminoAcid('T', 'T387')" onmouseover="showAminoAcid('T387'); selectID(glviewer,387)" class="btn btn-danger coevo_2_inactive conserved80_active

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 387

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
Function: _error_handler

File: /scratch/html/glutantbase/application/libraries/Template.php
Line: 13
Function: view

File: /scratch/html/glutantbase/application/controllers/Protein.php
Line: 188
Function: show

File: /scratch/html/glutantbase/index.php
Line: 315
Function: require_once

ss_loop_inactive" style="" title="T Local position: 387 Global position: 1566" > T

									

						                        
Loop | bend | hydrogen bonded turn', 
                            'default', 
                            '', 
                            '421', 
                            '1660',
                            'arginine');" 
                            onmouseout="hideAminoAcid('R', 'R421')"  
                            onmouseover="showAminoAcid('R421'); selectID(glviewer,421)" 
                            class="btn btn-default
A PHP Error was encounteredSeverity: Warning
Message:  Uninitialized string offset 421
Filename: views/view.php
Line Number: 255
Backtrace:

			File: /scratch/html/glutantbase/application/views/view.php

			Line: 255

			Function: _error_handler			

			File: /scratch/html/glutantbase/application/libraries/Template.php

			Line: 13

			Function: view			

			File: /scratch/html/glutantbase/application/controllers/Protein.php

			Line: 188

			Function: show			

			File: /scratch/html/glutantbase/index.php

			Line: 315

			Function: require_once			
 ss_loop_inactive" 
                            style=""
                            title="R
Local position: 421
Global position: 1660"
                        >
                            R                            
                        					                        						                        

Loop | bend | hydrogen bonded turn', 'danger', '', '422', '1662', 'alanine');" onmouseout="hideAminoAcid('A', 'A422')" onmouseover="showAminoAcid('A422'); selectID(glviewer,422)" class="btn btn-danger conserved80_active

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 422

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
Function: _error_handler

File: /scratch/html/glutantbase/application/libraries/Template.php
Line: 13
Function: view

File: /scratch/html/glutantbase/application/controllers/Protein.php
Line: 188
Function: show

File: /scratch/html/glutantbase/index.php
Line: 315
Function: require_once

ss_loop_inactive" style="" title="A Local position: 422 Global position: 1662" > A

									

						                        
Loop | bend | hydrogen bonded turn', 
                            'danger', 
                            ' coevo_1_inactive', 
                            '456', 
                            '1788',
                            'valine');" 
                            onmouseout="hideAminoAcid('V', 'V456')"  
                            onmouseover="showAminoAcid('V456'); selectID(glviewer,456)" 
                            class="btn btn-danger coevo_1_inactive conserved80_active
A PHP Error was encounteredSeverity: Warning
Message:  Uninitialized string offset 456
Filename: views/view.php
Line Number: 255
Backtrace:

			File: /scratch/html/glutantbase/application/views/view.php

			Line: 255

			Function: _error_handler			

			File: /scratch/html/glutantbase/application/libraries/Template.php

			Line: 13

			Function: view			

			File: /scratch/html/glutantbase/application/controllers/Protein.php

			Line: 188

			Function: show			

			File: /scratch/html/glutantbase/index.php

			Line: 315

			Function: require_once			
 ss_loop_inactive" 
                            style=""
                            title="V
Local position: 456
Global position: 1788"
                        >
                            V                            
                        					                        						                        

Loop | bend | hydrogen bonded turn', 'danger', ' coevo_1_inactive', '457', '1789', 'aspartic acid');" onmouseout="hideAminoAcid('D', 'D457')" onmouseover="showAminoAcid('D457'); selectID(glviewer,457)" class="btn btn-danger coevo_1_inactive conserved80_active

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 457

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
Function: _error_handler

File: /scratch/html/glutantbase/application/libraries/Template.php
Line: 13
Function: view

File: /scratch/html/glutantbase/application/controllers/Protein.php
Line: 188
Function: show

File: /scratch/html/glutantbase/index.php
Line: 315
Function: require_once

ss_loop_inactive" style="" title="D Local position: 457 Global position: 1789" > D

Acid/base catalytic
Conserved (50-79%)
Conserved (> 80%)
Extrapoled mutation
Catalytic pocket (0-6.5Å from ligand)

Extrapoled mutations

| Cellobiose docking

Poses (avg)	Affinity (wild)	Affinity (mutant)	ΔAffinity	ΔAffinity expected	Status
1	-7.00	-7.00	0	ΔAffinity < 0	x
1-3	-6.87	-6.80	0.07	ΔAffinity < 0	x
1-10	-6.33	-6.30	0.03	ΔAffinity < 0	x

| Glucose docking

Poses (avg)	Affinity (wild)	Affinity (mutant)	ΔAffinity	ΔAffinity expected	Status
1	-7.00	-5.80	1.2	ΔAffinity > 0	✓
1-3	-6.87	-5.68	1.19	ΔAffinity > 0	✓
1-10	-5.56	-5.44	0.12	ΔAffinity > 0	✓

| Cellobiose docking

Poses (avg)	Affinity (wild)	Affinity (mutant)	ΔAffinity	ΔAffinity expected	Status
1	-7.00	-7.00	0	ΔAffinity < 0	x
1-3	-6.87	-6.73	0.14	ΔAffinity < 0	x
1-10	-6.33	-6.19	0.14	ΔAffinity < 0	x

| Glucose docking

Poses (avg)	Affinity (wild)	Affinity (mutant)	ΔAffinity	ΔAffinity expected	Status
1	-7.00	-5.63	1.37	ΔAffinity > 0	✓
1-3	-6.87	-5.58	1.29	ΔAffinity > 0	✓
1-10	-5.56	-5.36	0.2	ΔAffinity > 0	✓

| Cellobiose docking

Poses (avg)	Affinity (wild)	Affinity (mutant)	ΔAffinity	ΔAffinity expected	Status
1	-7.00	-6.07	0.93	ΔAffinity < 0	x
1-3	-6.87	-5.72	1.15	ΔAffinity < 0	x
1-10	-6.33	-4.	2.33	ΔAffinity < 0	x

| Glucose docking

Poses (avg)	Affinity (wild)	Affinity (mutant)	ΔAffinity	ΔAffinity expected	Status
1	-7.00	-5.60	1.4	ΔAffinity > 0	✓
1-3	-6.87	-5.47	1.4	ΔAffinity > 0	✓
1-10			0	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.