GapRepairer

Models

Number of gaps:7

Gap lengths: 96, 29, 22, 15, 9, 7, 4

Model	Entanglement	Average	DOPE-HR (by gap length)			Smaller
		DOPE-HR	1st gap	2nd gap	3rd gap	gaps
Model 1	Non-trivial	-111006	-2784	-3546	-2270
Model 2	Non-trivial	-111531	-2635	-4108	-2327
Model 3	Non-trivial	-110612	-2622	-3711	-2123
Model 4	Non-trivial	-111159	-2581	-3854	-2300
Model 5	Non-trivial	-110407	-2517	-4160	-2276
						None
Colour the base model according to the B-factor (lowest to highest)						Reload

Warning: All models are renumbered - the first residue in the structure has index 1.

Mix & match

None of the models is perfect? By clicking the button below you can download a .pdb file with the currently shown mix of models - for each gap at most one model can be selected. If none of them is checked, the gap will be left as is. Fourth and further gaps (sorted by size) can only come from one of the models.

EntanglementHelpKnotProtLassoProtLinkProt

Model	Type		Knot core	Slipknot	Lasso	Piercing	Show
			range	loop range	loop	position	in JSmol
Model 1	Slipknot	S +3₁	755-1116	1116-1131	--	--
	Lasso	L_-3N	--	--	149-228	-110,+124,-134
Model 2	Slipknot	S +3₁	755-1116	1116-1131	--	--
	Lasso	L_-3N	--	--	149-228	-110,+124,-134
Model 3	Slipknot	S +3₁	755-1116	1116-1131	--	--
	Lasso	L_-3N	--	--	149-228	-110,+124,-134
Model 4	Slipknot	S +3₁	755-1116	1116-1131	--	--
	Lasso	L_-3N	--	--	149-228	-110,+124,-134
Model 5	Slipknot	S +3₁	755-1116	1116-1131	--	--
	Lasso	L_-3N	--	--	149-228	-110,+124,-134
							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.

Knotting fingerprint thumbnails
Lasso thumbnails

Knot help

Lasso help

Model 1

Model 2

Model 3

Model 4

Model 5

Model 1

Model 2

Model 3

Model 4

Model 5

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.

Warning: No templates were used. Models were generated using de novo prediction. Possible reasons include: no homologues similar enough; homologues do not cover the gaps in the target; all gaps at most 2 amino acids long.

Download Files Models Similarity profile Modelling alignment Raw knot fingerprint matrices: Model_1 Model_2 Model_3 Model_4 Model_5

Job Log

Sun Jul 23 14:59:10 2017	JOB CREATED : a3462928-615e-4652-9962-79c18fd577f1
Sun Jul 23 22:35:01 2017	STATUS CHANGED : N -> R
Sun Jul 23 22:35:01 2017	INFO : JOB STARTED AT: 2017-07-23 22:35:01.812820
Sun Jul 23 22:35:01 2017	INFO : METHOD: 1
Sun Jul 23 22:35:01 2017	INFO : Precalculated profile found...
Sun Jul 23 22:35:01 2017	INFO : Homologue pool found...
Sun Jul 23 22:35:01 2017	INFO : Verifying structure sequences of homologues...
Sun Jul 23 22:36:26 2017	INFO : Starting homologue filtering...
Sun Jul 23 22:37:17 2017	INFO : Getting structures from PDB...
Sun Jul 23 22:37:18 2017	INFO : Creating modelling alignment...
Sun Jul 23 22:37:18 2017	INFO : Modelling...
Mon Jul 24 02:37:57 2017	INFO : Model 1 built
Mon Jul 24 02:37:57 2017	INFO : Validating Calpha distances...
Mon Jul 24 02:37:57 2017	INFO : Model 1 distances correct: True
Mon Jul 24 02:37:57 2017	INFO : Modelling...
Mon Jul 24 05:53:45 2017	INFO : Model 2 built
Mon Jul 24 05:53:45 2017	INFO : Validating Calpha distances...
Mon Jul 24 05:53:45 2017	INFO : Model 2 distances correct: True
Mon Jul 24 05:53:45 2017	INFO : Modelling...
Mon Jul 24 09:11:46 2017	INFO : Model 3 built
Mon Jul 24 09:11:46 2017	INFO : Validating Calpha distances...
Mon Jul 24 09:11:46 2017	INFO : Model 3 distances correct: True
Mon Jul 24 09:11:46 2017	INFO : Modelling...
Mon Jul 24 11:45:13 2017	INFO : Model 4 built
Mon Jul 24 11:45:13 2017	INFO : Validating Calpha distances...
Mon Jul 24 11:45:13 2017	INFO : Model 4 distances correct: True
Mon Jul 24 11:45:13 2017	INFO : Modelling...
Mon Jul 24 13:39:46 2017	INFO : Model 5 built
Mon Jul 24 13:39:46 2017	INFO : Validating Calpha distances...
Mon Jul 24 13:39:46 2017	INFO : Model 5 distances correct: True
Mon Jul 24 13:40:53 2017	INFO : Finished modelling
Mon Jul 24 13:40:53 2017	STATUS CHANGED : R -> P
Mon Jul 24 13:40:53 2017	INFO : Checking topology...
Mon Jul 24 16:48:20 2017	INFO : Knot matrices done...
Mon Jul 24 17:05:28 2017	INFO : Some knots found!
Mon Jul 24 17:05:44 2017	INFO : Some lassos found!
Mon Jul 24 17:05:44 2017	INFO : Finishing...
Mon Jul 24 17:05:45 2017	INFO : Job done
Mon Jul 24 17:05:45 2017	STATUS CHANGED : P -> F
Mon Jul 24 17:05:45 2017	STATUS CHANGED : F -> F

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