SWISS-MODEL Repository
Uniprot features:
SWISS-MODEL Repository - Model Details
Model Overview
Sequence
| UniProt | Q8K2I9 |
Database: TrEMBL (Unreviewed)  |
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Domain
Model 3D Structure
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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 ]
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Alignment
TARGET 1 KT SIQLTHEQQL ILNHKMEPLQ VVKIMAFAGT
3oiyA 58 aefwneyedf rsffkk--kf gkdltgyqrl wakrivqgk- sftmvaptgv
TARGET hhhhh hhhhh
3oiyA hhhhhhh hhhhhh hh hhhhh hhhhhhh sss
TARGET 33 GKTSTLVKYA E--KWSQSRF LYVTFNKSIA KQAELVF -- ----------
3oiyA 105 gkttfgmmta lwlarkgkks alvfptvtlv kqtlerlqkl adekvkifgf
TARGET hhhhhhhhh hhh hhhhhhh
3oiyA hhhhhhhhh hhhhh ss ssss hhhh hhhhhhhhhh sssss
TARGET ---------- ---------- ---------- ---------- ----------
3oiyA 155 yssmkkeeke kfeksfeedd yhilvfstqf vsknreklsq krfdfvfvdd
TARGET
3oiyA hhhhh hhhhhhhh ssssssshh hh hhhh ssssss
TARGET ---------- ---------- ---------- ---------- ----------
3oiyA 205 vdavlkasrn idtllmmvgi peeiirkafs tikqgkiyer pknlkpgilv
TARGET
3oiyA hhhh hh hhhhhhh hhhhhhhhh hhh sss
TARGET ---------- ---------- ---------- ---------- ----------
3oiyA 255 vssatakprg irpllfrdll nftvgrlvsv arnithvris srskeklvel
TARGET
3oiyA ss hhhhh sssssss hhhhhhh
TARGET ---------- ---------- ---------- ---------- ----------
3oiyA 305 leifrdgili faqteeegke lyeylkrfkf nvgetwsefe knfedfkvgk
TARGET
3oiyA hhhh ssss ss hhhhhh hhhhhhh sssss hh hhhhhhhh
TARGET ---------- ---------- ---------- ---------- ----------
3oiyA 355 iniligvqay ygkltrgvdl perikyvifw gtpsgpdvyt yiqasgrssr
TARGET
3oiyA sssssss ssssss s hhh hhhhhhh s
TARGET ---------- ---------- ---------- ---------- ----------
3oiyA 475 ilngvlvkgv svifeedeei feslktrlll iaeeeiieea eanwkelvhe
TARGET
3oiyA ss sss ss sssss hhh hhhhhhhhhh hh sss hhhhhhh
TARGET ----------
3oiyA 525 veesrrrser
TARGET
3oiyA hhhhhhhhh
Template's ligands section
Ligands in the template:POP : 1.
The template contains ligands that are not yet part of the pipeline. Ligands which are currently assessed are listed in the help page.
No ligands were included in the model.
Quaternary Structure Annotation of the Template
3oiy 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: 3oiy.pdb1.gz
Quaternary Structure Modelling of the Target Protein
The target and template sequences are too diverse (seqid: 20.290) to infer a conservation of the oligomeric state
Please use the advancend features of the SwissModel Project Mode
The target structure was calculated as SINGLE CHAIN
Template Selection
- Start SMR-Pipeline for:61bd3fb46afd86a1ec2afa7f3a410a8e on BC2-cluster at Sat Feb 23 06:15:06
2013
- Analyze BLAST summary ...
- No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH
- Run HHSearch to detect more templates...
- Generate new template library
- Run template selection against modfied template library
- Summarize templates:
- Warning: Oligomer Prediction was not successfull!
- 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 3oiyA (435-501) 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:61bd3fb46afd86a1ec2afa7f3a410a8e on BC2-cluster at Sat Feb 23 06:16:39
2013
Template Search
| Template Description |
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3p4y: HELICASE DOMAIN OF REVERSE GYRASE FROM THERMOTOGA MARITIMA Solved by: X-RAY, Resolution: 3.20A, Identified by HHSEARCH |
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3p4x: HELICASE DOMAIN OF REVERSE GYRASE FROM THERMOTOGA MARITIMA Solved by: X-RAY, Resolution: 2.41A, Identified by HHSEARCH |
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3oiy: HELICASE DOMAIN OF REVERSE GYRASE FROM THERMOTOGA MARITIMA Solved by: X-RAY, Resolution: 2.35A, Identified by HHSEARCH |
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3b85: CRYSTAL STRUCTURE OF PREDICTED PHOSPHATE STARVATION-INDUCEATPASE PHOH2 FROM CORYNEBACTERIUM GLUTAMICUM Solved by: X-RAY, Resolution: 2.35A, Identified by HHSEARCH |
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4ddw: THERMOTOGA MARITIMA REVERSE GYRASE, C-CENTERED ORTHORHOMBI Solved by: X-RAY, Resolution: 4.17A, Identified by HHSEARCH |
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4ddx: THERMOTOGA MARITIMA REVERSE GYRASE, PRIMITIVE MONOCLINIC F Solved by: X-RAY, Resolution: 4.17A, Identified by HHSEARCH |
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4ddv: THERMOTOGA MARITIMA REVERSE GYRASE, TRICLINIC FORM Solved by: X-RAY, Resolution: 4.17A, Identified by HHSEARCH |
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4ddu: THERMOTOGA MARITIMA REVERSE GYRASE, C2 FORM 1 Solved by: X-RAY, Resolution: 4.17A, Identified by HHSEARCH |
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4ddt: THERMOTOGA MARITIMA REVERSE GYRASE, C2 FORM 2 Solved by: X-RAY, Resolution: 4.17A, Identified by HHSEARCH |
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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.