GapRepairer

Models

Number of gaps:2

Gap lengths: 8, 5

Model	Entanglement	Average	DOPE-HR (by gap length)
		DOPE-HR	1st gap	2nd gap
Model 1	Non-trivial	-50002	-1064	-2624
Model 2	Non-trivial	-50172	-1005	-2785
Model 3	Non-trivial	-49664	-937	-2405
Model 4	Non-trivial	-49650	-882	-2483
Model 5	Non-trivial	-49751	-816	-2568
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	34-244	244-251	--	--
	Lasso	L_+1N	--	--	46-167	+37
Model 2	Slipknot	S 3₁	34-244	244-251	--	--
	Lasso	L_+1N	--	--	46-167	+37
Model 3	Slipknot	S 3₁	34-244	244-251	--	--
	Lasso	L_+1N	--	--	46-167	+38
Model 4	Slipknot	S 3₁	34-244	244-251	--	--
	Lasso	L_+1N	--	--	46-167	+36
Model 5	Slipknot	S 3₁	34-244	244-251	--	--
	Lasso	L_+1N	--	--	46-167	+37
							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.

Templates (similarity across the whole protein) Help

PDB code	Chain	Entanglement type	Seq identity	Total gap coverage	Total gap identity	RMSD [Å]	Pairwise alignment to the target: gap
4GIP	D	Unknot	30.67%	150.00%	37.50%	1.44	..Target: GILHYEKLSKIGLVKGITRKYKIKSNPLTKDIVIKMKPNVSNVSKCTGTVMENYKSRLTGILSPIKGAIELYNNNTHDLVGDVKLAGVVMAGIAIGIATAAQITAGVALYEAMKNADNINKLKSSIESTNEAVVKLQETAEKTVYVLTALQDYINTNLVPSIDQISCKQTELALDLALSKYLSDLLFVFGPNLQDPVSNSMTIQAISQAFGGNYETLLRTLGYATEDFDDLLESDSITGQIVYVDLSSYYIIVRVYFPILTEIQQAYVQELLPVSFNNDNSEWISIVPNFVLIRNTLISNIEVKYCLITKKSVICNQDYATPMTASVRECLTGSTDKCPRELVVSSHVPRFALSGGVLFANCISVTCQCQTTGRAISQSGEQTLLMIDNTTCTTVVLGNIIISLGKYLGSINYNS----ESIAVGPPVYTDKVDISSQISSMNQSL-------QQSKDYIKE- Template: ------------------------------------------------------------------------------------FAGVVIGLAALGVATAAQVTAAVALVKANENAAAILNLKNAIQKTNAAVADVVQATQSLGTAVQAVQDHINSVVSPAITAANCKAQDAIIGSILNLYLTELTTIFHNQITNPALSPITIQALRILLGSTLPTVVEKSFNTQISAAELLSSGLLTGQIVGLDLTYMQMVIKIELPTLTVQPATQIIDLATISAFINNQEVMAQLPTRVMVTGSLIQAYPASQCTITPNTVYCRYNDAQVLSDDTMACLQGNLTRCTFSPVVGSFLTRFVLFDGIVYANCRSMLCKCMQPAAVILQPSSSPVTVIDMYKCVSLQLDNLRFTITQ-LANVTYNSTIKLESSQI---LSIDPLDISQNLAAVNKSLSDALQHLAQSDTYLSAI

Templates (similarity to the largest gap - 8 aa) Help

PDB code	Chain	Knot type	Gap coverage	Gap identity	>Target_Sequence: gap	DLVGDVKLAGVVMA
4GIP	D	Unknot	37.50%	50.00%	-------FAGVVIG

Templates (similarity to the 2nd largest gap - 5 aa)

PDB code	Chain	Knot type	Gap coverage	Gap identity	>Target_Sequence: gap	TLGYATEDFDD
4GIP	D	Unknot	0.00%	100.00%	KSFNTQISAAE

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 14:56:46 2017	JOB CREATED : 3bcb7b79-b749-4eb2-acbb-92a4c73a601b
Sun Jul 23 18:44:02 2017	STATUS CHANGED : N -> R
Sun Jul 23 18:44:02 2017	INFO : JOB STARTED AT: 2017-07-23 18:44:02.568444
Sun Jul 23 18:44:02 2017	INFO : METHOD: 1
Sun Jul 23 18:44:02 2017	INFO : Precalculated profile found...
Sun Jul 23 18:44:02 2017	INFO : Homologue pool found...
Sun Jul 23 18:44:02 2017	INFO : Verifying structure sequences of homologues...
Sun Jul 23 18:46:10 2017	INFO : Starting homologue filtering...
Sun Jul 23 18:46:58 2017	INFO : Getting structures from PDB...
Sun Jul 23 18:47:03 2017	INFO : Creating modelling alignment...
Sun Jul 23 18:47:03 2017	INFO : Modelling...
Sun Jul 23 18:54:42 2017	INFO : Model 1 built
Sun Jul 23 18:54:42 2017	INFO : Validating Calpha distances...
Sun Jul 23 18:54:42 2017	INFO : Model 1 distances correct: True
Sun Jul 23 18:54:42 2017	INFO : Modelling...
Sun Jul 23 19:02:43 2017	INFO : Model 2 built
Sun Jul 23 19:02:43 2017	INFO : Validating Calpha distances...
Sun Jul 23 19:02:43 2017	INFO : Model 2 distances correct: True
Sun Jul 23 19:02:43 2017	INFO : Modelling...
Sun Jul 23 19:21:17 2017	INFO : Model 3 built
Sun Jul 23 19:21:17 2017	INFO : Validating Calpha distances...
Sun Jul 23 19:21:17 2017	INFO : Model 3 distances correct: True
Sun Jul 23 19:21:17 2017	INFO : Modelling...
Sun Jul 23 19:29:31 2017	INFO : Model 4 built
Sun Jul 23 19:29:31 2017	INFO : Validating Calpha distances...
Sun Jul 23 19:29:31 2017	INFO : Model 4 distances correct: True
Sun Jul 23 19:29:31 2017	INFO : Modelling...
Sun Jul 23 19:37:39 2017	INFO : Model 5 built
Sun Jul 23 19:37:39 2017	INFO : Validating Calpha distances...
Sun Jul 23 19:37:39 2017	INFO : Model 5 distances correct: True
Sun Jul 23 19:38:11 2017	INFO : Finished modelling
Sun Jul 23 19:38:11 2017	STATUS CHANGED : R -> P
Sun Jul 23 19:38:11 2017	INFO : Checking topology...
Sun Jul 23 19:55:05 2017	INFO : Knot matrices done...
Sun Jul 23 19:57:15 2017	INFO : Some knots found!
Sun Jul 23 19:57:21 2017	INFO : Some lassos found!
Sun Jul 23 19:57:21 2017	INFO : Finishing...
Sun Jul 23 19:57:21 2017	INFO : Job done
Sun Jul 23 19:57:21 2017	STATUS CHANGED : P -> F
Sun Jul 23 19:57:21 2017	STATUS CHANGED : F -> F

5EJB chain A