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Model Overview
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1
965

Sequence
UniProt Q8GTR4
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

Domain
Link to: [ InterPro ]
Alpha-amylase
CBM_48
DUF3372

Model 3D Structure
Model information:
Modelled residue range: 88 to 963
Based on template: [ 4aio ]  
Sequence Identity [%]: 62%
Model date: 2013-02-15
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (4aio): MONOMER
Model: MONOMER

Ligand information: [details]
Ligands in the template: CA: 2, GOL: 4, IOD: 4.
Ligands in the model: CA: 1
Template Links: [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  
display model: in [ AstexViewer ]
download model: as [ pdb ] - as [ Deepview project ]

This model has not been updated since 2013-01-30. In the meantime, new template structures may have become available which would allow building a more reliable model. Would you like to submit the target protein to SWISS-MODEL Workspace and build a new model now? [ Submit ]



Alignment 

TARGET    1            SRA YWVTQGVIAW NVDVGEG-SC YFYASKSAGL SFS--EDGID
4aio_1#8  2     afmpd--ara ywvtsdliaw nvgeleaqsv clyasraaam slspsnggiq
                                                                      
TARGET                     sss  sssss          s sssss                
4aio_1#8                   sss  sssss         ss sssss                


TARGET    41    GYDLRIKLEA ESGSLPADVI EKFPHIRNYK SFKVPKDLDI RDLVKSQLAV
4aio_1#8  50    gydskvelqp esaglpetvt qkfpfissyr afrvpssvdv aslvkcqlvv
                                                                      
TARGET             sssssss s     hhhh hh       s ssss     h hhhh  ssss
4aio_1#8           sssssss s      hhh h        s ssss     h hhhh  ssss


TARGET    91    VCFDAEGRLI QGTGLQLPGV LDELFSYDGP LGAHFTPEGV SLHLWAPTAQ
4aio_1#8  100   asfgadgkhv dvtglqlpgv lddmfaytgp lgavfsedsv slhlwaptaq
                                                                      
TARGET          ssss   sss sss    hhh hhhh        sssss  ss ssssss    
4aio_1#8        sss        sss    hhh hhhh        sssss  ss ssssss    


TARGET    141   AVSVCIYKNP LDKSPMEICP LKEANGVWST EGACSWGGCY YVYKVSVYHP
4aio_1#8  150   gvsvcffdgp agpa-letvq lkesngvwsv tgprewenry ylyevdvyhp
                                                                      
TARGET          sssssss          ssss ssss sssss ss      ss ssssssssss
4aio_1#8        ssssssss     ss sssss ssss sssss ss      ss ssssssssss


TARGET    191   STMKLETCYA NDPYARGLSA DGRKTFLVNL DSDDLKPEGW DNLADKKPCL
4aio_1#8  199   tkaqvlkcla gdpyarslsa ngartwlvdi nnetlkpasw deladekpkl
                                                                      
TARGET            ssssssss       ssss   sssss                  hhh    
4aio_1#8          ssssssss       ssss   sssss                  hhh    


TARGET    241   RSFSDISIYE LHVRDFSAND ETVEPENRGG YLAFTSKDSA GVKHLQKLVD
4aio_1#8  249   dsfsditiye lhirdfsahd gtvdsdsrgg frafayqasa gmehlrklsd
                                                                      
TARGET                ssss s hhh                  hhh     h hhhhhhhhhh
4aio_1#8              ssss s hhh                  hhh     h hhhhhhhhhh


TARGET    291   AGLTHLHLLP TFQFGDVDDE KENWKSVDTS LLEGLRPDST EAQARITEIQ
4aio_1#8  299   aglthvhllp sfhfagvddi ksnwkfvdec elatfppgsd mqqaavvaiq
                                                                      
TARGET          h  ssssss  sssss              hh hhh        hhhhhhh   
4aio_1#8        h  ssssss  sssss              hh hhh        hhhhhhh   


TARGET    341   NDDGYNWGYN PVLWGVPKGS YASDPTGPCR IIEFRKMVQA LNCTGLNVVL
4aio_1#8  349   eedpynwgyn pvlwgvpkgs yasdpdgpsr iieyrqmvqa lnriglrvvm
                                                                      
TARGET                   s ss   sss           hh hhhhhhhhhh hhh   ssss
4aio_1#8                 s ss   sss           hh hhhhhhhhhh hhh   ssss


TARGET    391   DVVYNHLHAS GPHDKESVLD KIVPGYYLRR NSDGFIENST CVNNTASEHY
4aio_1#8  399   dvvynhldss gpcgissvld kivpgyyvrr dtngqiensa amnntasehf
                                                                      
TARGET          ss  sss            hh hh    ssss s   sss      ssss   h
4aio_1#8        ss  sss            hh hh    ssss s   sss      ssss   h


TARGET    441   MVDRLIRDDL LNWVVNYKVD GFRFDLMGHI MKATIVNAKS AIGSLRKETD
4aio_1#8  449   mvdrlivddl lnwavnykvd gfrfdlmghi mkrtmmraks alqslttdah
                                                                      
TARGET          hhhhhhhhhh hhhhhh     sssss    s sshhhhhhhh hhh sss   
4aio_1#8        hhhhhhhhhh hhhhhh     sssss    s sshhhhhhhh hhh sss   


TARGET    491   GVDGSRIYLY GEGWNFGEVA ENGRGINASQ FNLGGTGIGS FNDRIRDATL
4aio_1#8  499   gvdgskiyly gegwdfaeva rnqrgingsq lnmsgtgigs fndrirdain
                                                                      
TARGET           sss   sss ss              sss h hh      ss ss hhhhhhh
4aio_1#8         sss   sss ss              sss h hh      ss ss hhhhhhh


TARGET    541   GGSPFGHPLQ QGFITGLLLQ PNAHDHGSEA TQELMLSTAK NHIQTGMAAN
4aio_1#8  549   ggnpfgnplq qgfntglfle pngfyqgnea dtrrslatya dqiqiglagn
                                                                      
TARGET                                        hh hhhhhhhhhh hhhhhhh   
4aio_1#8                                      hh hhhhhhhhhh hhhhhhh   


TARGET    591   LKDYMLTNHE GKEVKGSEVL MHDATPVAYA SLPTETINYV SAHDNETLFD
4aio_1#8  599   lrdyvlisht geakkgseih tfdglpvgyt aspietinyv sahdnetlfd
                                                                      
TARGET             sssss    sssss  ss s   sss        ssss          hhh
4aio_1#8           sssss    sssss  ss s   sss        ssss          hhh


TARGET    641   IISLKTPMEI SVDERCRINH LASSMIALSQ GIPFFHAGDE ILRSKSLDRD
4aio_1#8  649   visvktpmil svdercrinh lassmmalsq gipffhagde ilrsksidrd
                                                                      
TARGET          hhhhh       hhhhhhhhh hhhhhhh     ssssss              
4aio_1#8        hhhhh       hhhhhhhhh hhhhhhh     ssssss              


TARGET    691   SYNSGDWFNR LDFSYSSNNW GVGLPPKGKN EHNWPLIKPR LQDPSFKPKS
4aio_1#8  699   synsgdwfnk ldftyetnnw gvglppsekn ednwplmkpr lenpsfkpak
                                                                      
TARGET                                               hhhhhh hh       h
4aio_1#8              hhh                            hhhhhh hh       h


TARGET    741   SHIVATLHNF LDLLRIRYSS PLFRLDTARA IQERVRFHNT GPSSIPGAIV
4aio_1#8  749   ghilaaldsf vdilkiryss plfrlstand ikqrvrfhnt gpslvpgviv
                                                                      
TARGET          hhhhhhhhhh hhhhhhhh          hhh hhhsssss         ssss
4aio_1#8        hhhhhhhhhh hhhhhhhh          hhh hhhsssss         ssss


TARGET    791   MSIEDGHRGI PSVSQIDPIY SLIVVIFNAR PSEFSYPSPA LKDRKLELHP
4aio_1#8  799   mgiedarges pemaqldtnf syvvtvfnvc phevsmdipa lasmgfelhp
                                                                      
TARGET          sssss              ss sssssssss     sssss         sssh
4aio_1#8        sssss              ss sssssssss     sssss         sssh


TARGET    841   VQVMSADEIV KKSVYDSFSG GFTVPARTTT VFVESR               
4aio_1#8  849   vqvnssdtlv rksayeaatg rftvpgrtvs vfvepr-              
                                                                      
TARGET          hhh     hh h  sss   s ssss   sss ssssss               
4aio_1#8        hhh     hh h  sss   s ssss   sss ssssss

Quality 


Template's ligands section 
Ligands in the template: CA: 2, GOL: 4, IOD: 4. 
Ligands in the template that will be assessed: CA5, CA6. 
Model's ligands section 
CA5 
All the residues interacting with the ligand are completely conserved between model and template. 
The RMSD between the interacting residues of model and template is smaller than 2 Angstrom: 0.010 
Given the properties calculated previously, the ligand z.CA5 will be included in the final model. 
CA5: conservation:True, RMSD:True, included: True 
 
CA6 
Not all the residues interacting with the ligand are completely conserved between model and template. 
No RMSD calculation will be performed. 
Given the properties calculated previously, the ligand z.CA6 will not be included in the final model. 
CA6: conservation:False, RMSD:False, included: False 
 
The new model with the included ligands was saved successfully.

 
Quaternary Structure Annotation of the Template 
 4aio is annotated as MONOMER 
 The oligomeric state of the structure was assigned by the authors of the corresponding PDB entry 
 The following biological unit was used to build the template structure: 4aio.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 Analysis of evolutionary and family specific aspects revealed conservation of the oligomeric structure 
 Hence, the oligomeric structures of the target and the template can be assumed to be similar (=MONOMER) 
 The corresponding reliability score is 0.79 (>0.5 indicates similarity) 
 Model was succesfully built as MONOMER.

Template Selection 
 - Start SMR-Pipeline for:0f48a37b677fe6b07105a2a1c0e5cf3c on BC2-cluster at Fri Feb 15 20:58:48
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  1
 - But still uncovered regions of the target sequence detected, go for: HHSEARCH

FATAL - No A3m found

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modfied template library 
 - Summarize templates: 
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:1): model based on new templates
 - Send 1 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -        *************************************************************************
 - building model based on 4aioA (88-963) was successful 
 - Repository Pipeline parameter

   Cut-off parameters to model the target based on a BLAST target-template alignment
    Evalue :                                     0.0001
    Minimum Template size (aa) for ranking :     25
    Minimum Sequence identity :                  60

   Cut-off parameters to model the target based on a HHSearch target-template alignment
    Evalue :                                     0.0001
    Probability :                                50
    MAC :                                        0.3

   Parameters for model selection
    Minimal number of uncovered target
     residues after BLAST to run HHSEARCH :      50
    Minimal number of uncovered target
     residues to model an additional template :  25
    
 - Finish SMR-Pipeline for:0f48a37b677fe6b07105a2a1c0e5cf3c on BC2-cluster at Fri Feb 15 21:06:47
2013


Template Description
Match Chain SeqId

4aio: CRYSTAL STRUCTURE OF THE STARCH DEBRANCHING ENZYME BARLEY DEXTRINASE
Solved by: X-RAY, Resolution: 1.90A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

88-963 4aioA 63%
[Model]

2y5e: BARLEY LIMIT DEXTRINASE IN COMPLEX WITH ALPHA-CYCLODEXTRIN
Solved by: X-RAY, Resolution: 2.49A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

88-963 2y5eA 63%
[Model]

2y4s: BARLEY LIMIT DEXTRINASE IN COMPLEX WITH BETA-CYCLODEXTRIN
Solved by: X-RAY, Resolution: 2.10A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

88-963 2y4sA 62%
[Model]

4amc: CRYSTAL STRUCTURE OF LACTOBACILLUS REUTERI 121 N-TERMINALLTRUNCATED GLUCANSUCRASE GTFA
Solved by: X-RAY, Resolution: 3.60A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

330-485 4amcA 18%
[Model]
520-595 4amcA 13%
[Model]

3kll: CRYSTAL STRUCTURE OF LACTOBACILLUS REUTERI N-TERMINALLY TRGLUCANSUCRASE GTF180-MALTOSE COMPLEX
Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

330-485 3kllA 17%
[Model]
519-594 3kllA 12%
[Model]

3hz3: LACTOBACILLUS REUTERI N-TERMINALLY TRUNCATED GLUCANSUCRASEGTF180(D1025N)-SUCROSE COMPLEX
Solved by: X-RAY, Resolution: 2.22A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

330-485 3hz3A 17%
[Model]
519-594 3hz3A 10%
[Model]

3klk: CRYSTAL STRUCTURE OF LACTOBACILLUS REUTERI N-TERMINALLY TRGLUCANSUCRASE GTF180 IN TRICLINIC APO- FORM
Solved by: X-RAY, Resolution: 1.65A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

330-485 3klkA 17%
[Model]
519-594 3klkA 12%
[Model]

4aef: THE CRYSTAL STRUCTURE OF THERMOSTABLE AMYLASE FROM THE PYR
Solved by: X-RAY, Resolution: 2.34A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

214-917 4aefA 11%
[Model]
217-274 4aefA 8%
[Model]
214-917 4aefB 11%
[Model]
217-274 4aefB 8%
[Model]

Downloads
Reference

If you are using models from the SWISS-MODEL Repository, please cite the following articles:

- Kiefer F, Arnold K, Künzli M, Bordoli L, Schwede T (2009).
The SWISS-MODEL Repository and associated resources.
Nucleic Acids Res. 37, D387-D392.

- Jürgen Kopp and Torsten Schwede (2004)
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models.
Nucleic Acids Res. 32, D230-D234.
SWISS-MODEL is developed by the Protein Structure Bioinformatics group at the SIB - Swiss Institute of Bioinformatics & the Biozentrum University of Basel. © 2011.