GapRepairer

Models

Number of gaps:1

Gap lengths: 22

Model	Entanglement	Average	DOPE-HR (by gap length)
		DOPE-HR	1st gap
Model 1	Non-trivial	-35662	-2444
Model 2	Non-trivial	-35621	-2412
Model 3	Non-trivial	-35573	-2365
Model 4	Non-trivial	-35308	-2110
Model 5	Non-trivial	-35226	-2063
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

Provided protein had only one gap - thus there are no gap-filling combinations to be made.

EntanglementHelpKnotProtLassoProtLinkProt

Model	Type		Knot core	Slipknot	Lasso	Piercing	Show
			range	loop range	loop	position	in JSmol
Model 1	Slipknot	S +3₁	67-197	197-354	--	--
	Lasso	L_-1C	--	--	291-340
Model 2	Lasso	L_+1C	--	--	66-154
Model 3	Slipknot	S +3₁	69-175	175-362	--	--
	Lasso	L_-1C	--	--	291-340
Model 4	Slipknot	S 3₁	69-162	162-362	--	--
	Lasso	L_-1C	--	--	291-340
Model 5	Slipknot	S 3₁	66-242	242-249	--	--
	Lasso	L_+1C	--	--	66-154
							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 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_3 Model_4 Model_5

Job Log

Sun Jul 23 14:56:07 2017	JOB CREATED : eb7cacdf-1e0f-4d62-95a1-a0f1c735877b
Sun Jul 23 17:05:02 2017	STATUS CHANGED : N -> R
Sun Jul 23 17:05:02 2017	INFO : JOB STARTED AT: 2017-07-23 17:05:02.324328
Sun Jul 23 17:05:02 2017	INFO : METHOD: 1
Sun Jul 23 17:05:02 2017	INFO : Precalculated profile found...
Sun Jul 23 17:05:02 2017	INFO : Homologue pool found...
Sun Jul 23 17:05:02 2017	INFO : Verifying structure sequences of homologues...
Sun Jul 23 17:05:31 2017	INFO : Starting homologue filtering...
Sun Jul 23 17:05:59 2017	INFO : Getting structures from PDB...
Sun Jul 23 17:06:00 2017	INFO : Creating modelling alignment...
Sun Jul 23 17:06:00 2017	INFO : Modelling...
Sun Jul 23 17:12:19 2017	INFO : Model 1 built
Sun Jul 23 17:12:19 2017	INFO : Validating Calpha distances...
Sun Jul 23 17:12:19 2017	INFO : Model 1 distances correct: True
Sun Jul 23 17:12:19 2017	INFO : Modelling...
Sun Jul 23 17:18:40 2017	INFO : Model 2 built
Sun Jul 23 17:18:40 2017	INFO : Validating Calpha distances...
Sun Jul 23 17:18:40 2017	INFO : Model 2 distances correct: True
Sun Jul 23 17:18:40 2017	INFO : Modelling...
Sun Jul 23 17:22:21 2017	INFO : Model 3 built
Sun Jul 23 17:22:21 2017	INFO : Validating Calpha distances...
Sun Jul 23 17:22:21 2017	INFO : Model 3 distances correct: True
Sun Jul 23 17:22:21 2017	INFO : Modelling...
Sun Jul 23 17:26:13 2017	INFO : Model 4 built
Sun Jul 23 17:26:13 2017	INFO : Validating Calpha distances...
Sun Jul 23 17:26:13 2017	INFO : Model 4 distances correct: True
Sun Jul 23 17:26:13 2017	INFO : Modelling...
Sun Jul 23 17:30:05 2017	INFO : Model 5 built
Sun Jul 23 17:30:05 2017	INFO : Validating Calpha distances...
Sun Jul 23 17:30:05 2017	INFO : Model 5 distances correct: True
Sun Jul 23 17:30:38 2017	INFO : Finished modelling
Sun Jul 23 17:30:38 2017	STATUS CHANGED : R -> P
Sun Jul 23 17:30:38 2017	INFO : Checking topology...
Sun Jul 23 17:39:49 2017	INFO : Knot matrices done...
Sun Jul 23 17:41:34 2017	INFO : Some knots found!
Sun Jul 23 17:41:40 2017	INFO : Some lassos found!
Sun Jul 23 17:41:40 2017	INFO : Finishing...
Sun Jul 23 17:41:41 2017	INFO : Job done
Sun Jul 23 17:41:41 2017	STATUS CHANGED : P -> F
Sun Jul 23 17:41:41 2017	STATUS CHANGED : F -> F

4TPL chain A