GapRepairer

Models

Number of gaps:3

Gap lengths: 9, 9, 4

Model	Entanglement	Average	DOPE-HR (by gap length)
		DOPE-HR	1st gap	2nd gap	3rd gap
Model 1	Non-trivial	-19354	4170	-1448	-671
Model 2	Non-trivial	-17575	4625	-1586	-194
Model 3	Non-trivial	-17860	5166	-1505	-333
Model 4	Non-trivial	-14826	7989	-1436	-513
Model 5	Non-trivial	-14437	8284	-1638	-782
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	25-85	85-162	--	--
Model 2	Slipknot	S -3₁	24-88	88-163	--	--
Model 3	Slipknot	S 3₁	24-86	86-163	--	--
Model 4	Slipknot	S +3₁	24-88	88-164	--	--
Model 5	Slipknot	S 3₁	23-88	88-162	--	--
							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

Knot help

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
1P35	A	Unknot	97.32%	300.00%	300.00%	0.97	..Target: ----PVEIDVSQTIIRDCQVDKQTRELVYINKIMNTQLTKPVLMMFNISGPIRSVTRKNNNLRDRIKSKPDEQFDQLEKDYSDQMDGFHDSIKYFKDEHYSVSCQNGSVLKSKFAKILKSHDYTDKKSIEAYEKYCLPKLVDERNDYYVAVCVLKPGFENGSNQVLSFEYNPIGNKVIVPFAHEINDTGLYEYDVVAYVDSVQFDGEQFEEFVQSLILPSSFKNSEKVLYYNEASKNKSMIYKALEFTTESSWGKSEKYNWKIFCNGFIYDKKSKVLYVKLHNVTSALNKNVILNTI-- Template: CVIFPVEIDVSQTIIRDCQVDKQTRELVYINKIMNTQLTKPVLMMFNISGPIRSVTRKNNNLRDRIKSKVDEQFDQLERDYSDQMDGFHDSIKYFKDEHYSVSCQNGSVLKSKFAKILKSHDYTDKKSIEAYEKYCLPKLVDERNDYYVAVCVLKPGFENGSNQVLSFEYNPIGNKVIVPFAHEINDTGLYEYDVVAYVDSVQFDGEQFEEFVQSLILPSSFKNSEKVLYYNEASKNKSMIYKALEFTTESSWGKSEKYNWKIFCNGFIYDKKSKVLYVKLHNVTSALNKNVILNTIKA

Templates (similarity to the largest gap - 9 aa) Help

PDB code	Chain	Knot type	Gap coverage	Gap identity	>Target_Sequence: gap	KDYSDQMDGFHDSIK
1P35	A	Unknot	100.00%	100.00%	RDYSDQMDGFHDSIK

Templates (similarity to the 2nd largest gap - 9 aa)

PDB code	Chain	Knot type	Gap coverage	Gap identity	>Target_Sequence: gap	FTTESSWGKSEKYNW
1P35	A	Unknot	100.00%	100.00%	FTTESSWGKSEKYNW

Templates (similarity to the 3rd largest gap - 4 aa)

PDB code	Chain	Knot type	Gap coverage	Gap identity	>Target_Sequence: gap	NEASKNKSMI
1P35	A	Unknot	100.00%	100.00%	NEASKNKSMI

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

Job Log

Tue Jul 11 17:34:32 2017	JOB CREATED : e39950ba-457a-4fb7-b399-0e410f4b1a8f
Wed Jul 12 07:48:03 2017	STATUS CHANGED : N -> R
Wed Jul 12 07:48:03 2017	INFO : JOB STARTED AT: 2017-07-12 07:48:03.259479
Wed Jul 12 07:48:03 2017	INFO : METHOD: 1
Wed Jul 12 07:48:03 2017	INFO : Precalculated profile found...
Wed Jul 12 07:48:03 2017	INFO : Homologue pool found...
Wed Jul 12 07:48:03 2017	INFO : Verifying structure sequences of homologues...
Wed Jul 12 07:48:13 2017	INFO : Starting homologue filtering...
Wed Jul 12 07:48:46 2017	INFO : Getting structures from PDB...
Wed Jul 12 07:48:53 2017	INFO : Creating modelling alignment...
Wed Jul 12 07:48:53 2017	INFO : Modelling...
Wed Jul 12 11:01:26 2017	INFO : Finished modelling
Wed Jul 12 11:01:26 2017	STATUS CHANGED : R -> P
Wed Jul 12 11:01:26 2017	INFO : Checking topology...
Wed Jul 12 11:12:35 2017	INFO : Knot matrices done...
Wed Jul 12 11:14:31 2017	INFO : Some knots found!
Wed Jul 12 11:14:31 2017	INFO : No lassos found...
Wed Jul 12 11:14:31 2017	INFO : Finishing...
Wed Jul 12 11:14:31 2017	INFO : Job done
Wed Jul 12 11:14:31 2017	STATUS CHANGED : P -> F
Wed Jul 12 11:14:31 2017	STATUS CHANGED : F -> F

1I3P chain A