Job name:

noname(PROT chain A)

677c4caf-cc67-4ae0-9e79-8c184b13bc23
Finished
Models Number of gaps:1 Gap lengths: 10
Model Entanglement Average DOPE-HR (by gap length)
DOPE-HR 1st gap
Model 1 Non-trivial -41827
Model 2 Non-trivial -40088
Model 3 Non-trivial -39220
Model 4 Non-trivial -38765
Reload
Warning: All models are renumbered - the first residue in the structure has index 1.
Mix & match
Provided protein had only one gap - thus there are no gap-filling combinations to be made.

Warning: JSmol may at times display gaps where there are none - due to some overlaps in models. This does not indicate presence of gaps in downloaded structure!
EntanglementHelpKnotProtLassoProtLinkProt
Model Type Knot core Slipknot Lasso Piercing Show
range loop range loop position in JSmol
Model 1 Knot K +31 139-251 -- -- --
Model 2 Knot K +31 138-251 -- -- --
Model 3 Slipknot S 31 139-252 252-411 -- --
Model 4 Slipknot S 31 139-252 252-411 -- --
None
Topologies marked by an OK sign () are in accordance with the template topology.
Warning: Entanglement type is assigned automatically - for more complicated topologies there may be some disagreements with manually curated databases.
Model 1
Model 2
Model 3
Model 4
DOPE (Discrete Optimized Protein Energy) score per residue. The lower the score, the better.
Since DOPE is calculated against the neighbours of a given amino acid, the scores
can vary between unmoved segments of different models. See here for more information.
PDB
code
Chain Entanglement
type
Seq
identity
Total gap
coverage
Total gap
identity
RMSD [Å] Pairwise alignment to the target: gap


2KGW

A

Unknot

32.56%

80.00%

30.00%

1.18

..Target: AVHTDAVQDWKNGTINAQLTLDLARARMRLPADRTAASQFLRYKAPAQLKDVYLSVLVDSQNRVGDCLAHEKIRLADITALVDAGHHAVTTLSPSVRSLQLSHQTPLTALARLFVTHETAYVPAIPPTSAVSRPYTGILIDARGSLPVHGEYVSEPLSACLFPKIWSTDMDLIYEKNMVHPDRAKAWGVVRYGSVWDEKMYRDRIGTTPLKIIARGVFGQQRTDPIIASKDAAQILARPENLRLLAEGNVIILCDEAALRVHVPYPLVDEHFYFAYHDVKRFLTDERSPGVGVRSGINTLKITVYDVRFVANSPEILASEKDRVDVIATALKKMGPYTRFLIEGHTADLHRPQEEAALSVARAQRMAQELSRRGIEMTRITTAGHGATKPIAPSDTHANKAKNRRVEITILR
Template: ----------------------------------------------------------------------------------------------------------------------------APPGPPASGP----CADLQSAI--------------------------------------------------------------------NAVTG----GPIAFGND---------------------------------------------------------------------------------GASLIPADYEILNRVADKLKAC-PDARVTINGYTDNTGSEGINIPLSAQRAKIVADYLVARGVAGDHIATVGLGSVNPIASNATPEGRAKNRRVEI-VVN


2L26

A

Unknot

29.37%

80.00%

20.00%

1.38

..Target: AVHTDAVQDWKNGTINAQLTLDLARARMRLPADRTAASQFLRYKAPAQLKDVYLSVLVDSQNRVGDCLAHEKIRLADITALVDAGHHAVTTLSPSVRSLQLSHQTPLTALARLFVTHETAYVPAIPPTSAVSRPYTGILIDARGSLPVHGEYVSEPLSACLFPKIWSTDMDLIYEKNMV----------HPDRAKAWGVVRYGSVWDEKMYRDRIGTTPLKIIAR-GVFGQQRTDPIIASKDAAQILARPENLRLLAEGNVIILCDEAALRVHVPYPLVDEHFYFAYHDVKRFLTDERSPGVGVRSGINTLKITVYDVRFVANSPEILASEKDRVDVIATALKKMGPYTRFLIEGHTADLHRPQEEAALSVARAQRMAQELSRRGIEMTRITTAGHGATKPIAPSDTHANKAKNRRVEITILR
Template: --------------------------------------------SALSLSLLSISRSGNTVTLIGD-FPDEAAKAALMTAL-------NGLLAPGVNVIDQIHVDP--------------VVRSLDFSSA------------------------EPVFTASVP---IPDFGLKVERDTVTLTGTAPSSEHKDAVKR----AATSTW-----------PDMKIVNNIEVTGQAPPGP------------------------------------PASGPCAD-----------------------LQSAINA--VTGGPIAFGNDGASLIPADYEILNRVADKLKAC-PDARVTINGYTDNTGSEGINIPLSAQRAKIVADYLVARGVAGDHIATVGLGSVNPIASNATPEGRAKNRRVEI-VVN

PDB
code
Chain Knot
type
Gap
coverage
Gap
identity
>Target_Sequence: gap

AYVPAIPPTSAVSRPY

2KGW A Unknot 30.00% 80.00%

-----APPGPPASGP-

2L26 A Unknot 20.00% 80.00%

-VVRSLDFSSA-----


Models
Similarity profile
Modelling alignment
Raw knot fingerprint matrices:
Model_1
Model_2
Model_3
Model_4

Tue Jul 25 15:15:01 2017	JOB CREATED : 677c4caf-cc67-4ae0-9e79-8c184b13bc23
Tue Jul 25 15:15:01 2017	STATUS CHANGED : N -> R
Tue Jul 25 15:15:01 2017	INFO : JOB STARTED AT: 2017-07-25 15:15:01.516202
Tue Jul 25 15:15:01 2017	INFO : METHOD: 1
Tue Jul 25 15:15:01 2017	INFO : Building Profile...
Tue Jul 25 15:15:01 2017	INFO : --E-value set to 0.001--
Tue Jul 25 15:26:06 2017	INFO : Homologue pool found...
Tue Jul 25 15:26:06 2017	INFO : Verifying structure sequences of homologues...
Tue Jul 25 15:29:52 2017	INFO : Excluding specified templates...
Tue Jul 25 15:29:52 2017	INFO : Excluded: 5JIR
Tue Jul 25 15:29:52 2017	INFO : Starting homologue filtering...
Tue Jul 25 15:30:23 2017	INFO : Getting structures from PDB...
Tue Jul 25 15:30:27 2017	INFO : Creating modelling alignment...
Tue Jul 25 15:30:27 2017	INFO : Modelling...
Tue Jul 25 15:33:18 2017	INFO : Model 1 built
Tue Jul 25 15:33:18 2017	INFO : 1/1 gaps will be remodelled
Tue Jul 25 15:44:15 2017	INFO : Validating Calpha distances...
Tue Jul 25 15:44:15 2017	INFO : Model 1 distances correct: True
Tue Jul 25 15:44:15 2017	INFO : Modelling...
Tue Jul 25 15:49:41 2017	INFO : Model 2 built
Tue Jul 25 15:49:41 2017	INFO : 1/1 gaps will be remodelled
Tue Jul 25 16:00:25 2017	INFO : Validating Calpha distances...
Tue Jul 25 16:00:25 2017	INFO : Model 2 distances correct: False
Tue Jul 25 16:00:25 2017	INFO : Modelling...
Tue Jul 25 16:04:22 2017	INFO : Model 3 built
Tue Jul 25 16:04:22 2017	INFO : 1/1 gaps will be remodelled
Tue Jul 25 16:15:25 2017	INFO : Validating Calpha distances...
Tue Jul 25 16:15:25 2017	INFO : Model 3 distances correct: True
Tue Jul 25 16:15:25 2017	INFO : Modelling...
Tue Jul 25 16:18:09 2017	INFO : Model 4 built
Tue Jul 25 16:18:09 2017	INFO : 1/1 gaps will be remodelled
Tue Jul 25 16:28:28 2017	INFO : Validating Calpha distances...
Tue Jul 25 16:28:28 2017	INFO : Model 4 distances correct: True
Tue Jul 25 16:28:28 2017	INFO : Modelling...
Tue Jul 25 16:31:05 2017	INFO : Model 5 built
Tue Jul 25 16:31:05 2017	INFO : 1/1 gaps will be remodelled
Tue Jul 25 16:41:25 2017	INFO : Validating Calpha distances...
Tue Jul 25 16:41:25 2017	INFO : Model 5 distances correct: True
Tue Jul 25 16:41:45 2017	INFO : Finished modelling
Tue Jul 25 16:41:45 2017	STATUS CHANGED : R -> P
Tue Jul 25 16:41:45 2017	INFO : Checking topology...
Tue Jul 25 16:54:11 2017	INFO : Knot matrices done...
Tue Jul 25 16:56:54 2017	INFO : Some knots found!
Tue Jul 25 16:56:54 2017	INFO : No lassos found...
Tue Jul 25 16:56:54 2017	INFO : Finishing...
Tue Jul 25 16:56:54 2017	INFO : Job done
Tue Jul 25 16:56:54 2017	STATUS CHANGED : P -> F
Tue Jul 25 16:56:54 2017	STATUS CHANGED : F -> F

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