GapRepairer

Models

Number of gaps:6

Gap lengths: 64, 36, 11, 7, 5, 4

Model	Entanglement	Average	DOPE-HR (by gap length)			Smaller
		DOPE-HR	1st gap	2nd gap	3rd gap	gaps
Model 1	Non-trivial	-78084	-2301	400	-3296
Model 2	Non-trivial	-77776	-2210	587	-3089
						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.

Pro Tip: Since you provided a structure that contains some crystallographic information you can verify our models using the wwPDB service.
Validity report for the RCSB PDB structure you were repairing can be accessed here

EntanglementHelpKnotProtLassoProtLinkProt

Model	Type		Knot core	Slipknot	Lasso	Piercing	Show
			range	loop range	loop	position	in JSmol
Model 1	Knot	K 8₂3₁	147-622	--	--	--
	Lasso	LL_-1,-1	--	--	569-686	-162
Model 2	Knot	K 8₂3₁	148-690	--	--	--
	Lasso	LL_-1,-1	--	--	569-686	-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
Lasso thumbnails

Knot help

Lasso help

Model 1

Model 2

Model 1

Model 2

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
3NAF	A	Unknot	95.22%	442.19%	417.19%	0.97	..Target: ------------KHIVVCGHITLESVSNFLKDFLHKDRDDVNVEIVFLHNISPNLELEALFKRHFTQVEFYQGSVLNPHDLARVKIESADACLILANKYCADPDAEDASNIMRVISIKNYHPKIRIITQMLQYHNKAHLLNIPSWNWKEGDDAICLAELKLGFIAQSCLAQGLSTMLANLFSMRSFIKIEEDTWQKYYLEGVSNEMYTEYLSSAFVGLSFPTVCELCFVKLKLLMIAIEYKSANRESRILINPGNHLKIQEGTLGFFIASDAKEVKRAFFYCKACHDDITDPKRIKKCGCKRLEDEQPSTLSPKKKQRNGGMRNSPNTSPKLMRHDPLLIPGNDQIDNMDSNVKKYDSTGMFHWCAPKEIEKVILTRSEAAMTVLSGHVVVCIFGDVSSALIGLRNLVMPLRASNFHYHELKHIVFVGSIEYLKREWETLHNFPKVSILPGTPLSRADLRAVNINLCDMCVILSANQNNIDDTSLQDKECILASLNIKSMQFDDSIGVLQANSQGFTPPGMDRSSPDNSPVHGMLRQPSITTGVNIPIITELVNDTNVQFLDQDDDDDPDTELYLTQPFACGTAFAVSVLDSLMSATYFNDNILTLIRTLVTGGATPELEALIAEENALRGGYSTPQTLANRDRCRVAQLALLDGPFADLGDGGCYGDLFCKALKTYNMLCFGIYRLRDAHLSTPSQCTKRYVITNPPYEFELVPTDLIFCLMQFD--- Template: KYGGSYSAVSGRKHIVVCGHITLESVSNFLKDFLHKDRDDVNVEIVFLHNISPNLELEALFKRHFTQVEFYQGSVLNPHDLARVKIESADACLILANKYCADPDAEDASNIMRVISIKNYHPKIRIITQMLQYHNKAHLLNIPSWNWKEGDDAICLAELKLGFIAQSCLAQGLSTMLANLFSMRSFIKIEEDTWQKYYLEGVSNEMYTEYLSSAFVGLSFPTVCELCFVKLKLLMIAIEYKSANRESRILINPGNHLKIQEGTLGFFIASDAKEVKRAFFYCKACH--------------------------XXXXXXXXXXXXXXXXSPKLMRHD-----------------KKYDSTGMFHWCAPKEIEKVILTRSEAAMTVLSGHVVVCIFGDVSSALIGLRNLVMPLRASNFHYHELKHIVFVGSIEYLKREWETLHNFPKVSILPGTPLSRADLRAVNINLCDMCVILSANQNNIDDTSLQDKECILASLNIKSMQFD--------------------------------------TGVNIPIITELVNDTNVQFLDQDDDDDPDTELYLTQPFACGTAFAVSVLDSLMSATYFNDNILTLIRTLVTGGATPELEALIAEENALRGGYSTPQTLANRDRCRVAQLALLDGPFADLGDGGCYGDLFCKALKTYNMLCFGIYRLRDAHLSTPSQCTKRYVITNPPYEFELVPTDLIFCLMQFDHNA

Templates (similarity to the largest gap - 64 aa) Help

PDB code	Chain	Knot type	Gap coverage	Gap identity	>Target_Sequence: gap	YCKACHDDITDPKRIKKCGCKRLEDEQPSTLSPKKKQRNGGMRNSPNTSPKLMRHDPLLIPGNDQIDNMD
3NAF	A	Unknot	17.19%	42.19%	YCKACH--------------------------XXXXXXXXXXXXXXXXSPKLMRHD--------------

Templates (similarity to the 2nd largest gap - 36 aa)

PDB code	Chain	Knot type	Gap coverage	Gap identity	>Target_Sequence: gap	QFDDSIGVLQANSQGFTPPGMDRSSPDNSPVHGMLRQPSITT
3NAF	A	Unknot	0.00%	0.00%	QFD--------------------------------------T

Templates (similarity to the 3rd largest gap - 11 aa)

PDB code	Chain	Knot type	Gap coverage	Gap identity	>Target_Sequence: gap	SANQNNIDDTSLQDKEC
3NAF	A	Unknot	100.00%	100.00%	SANQNNIDDTSLQDKEC

Templates (similarity to the 4th largest gap - 7 aa)

PDB code	Chain	Knot type	Gap coverage	Gap identity	>Target_Sequence: gap	IEYKSANRESRIL
3NAF	A	Unknot	100.00%	100.00%	IEYKSANRESRIL

Templates (similarity to the 5th largest gap - 5 aa)

PDB code	Chain	Knot type	Gap coverage	Gap identity	>Target_Sequence: gap	RDAHLSTPSQC
3NAF	A	Unknot	100.00%	100.00%	RDAHLSTPSQC

Templates (similarity to the 6th largest gap - 4 aa)

PDB code	Chain	Knot type	Gap coverage	Gap identity	>Target_Sequence: gap	GGATPELEAL
3NAF	A	Unknot	100.00%	100.00%	GGATPELEAL

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

Job Log

Fri Dec  1 09:49:33 2017	JOB CREATED : 40591e3f-4611-4050-8ce7-ac9d5c60dd86
Sat Dec  2 03:10:03 2017	STATUS CHANGED : N -> R
Sat Dec  2 03:10:03 2017	INFO : JOB STARTED AT: 2017-12-02 03:10:03.033258
Sat Dec  2 03:10:03 2017	INFO : METHOD: 1
Sat Dec  2 03:10:03 2017	INFO : Precalculated profile found...
Sat Dec  2 03:10:03 2017	INFO : Homologue pool found...
Sat Dec  2 03:10:03 2017	INFO : Verifying structure sequences of homologues...
Sat Dec  2 03:11:05 2017	INFO : Starting homologue filtering...
Sat Dec  2 03:11:51 2017	INFO : Getting structures from PDB...
Sat Dec  2 03:12:17 2017	INFO : Creating modelling alignment...
Sat Dec  2 03:12:17 2017	INFO : Modelling...
Sat Dec  2 05:29:15 2017	INFO : Model 1 built
Sat Dec  2 05:29:15 2017	INFO : 1/6 gaps will be remodelled
Sat Dec  2 07:41:51 2017	INFO : Validating Calpha distances...
Sat Dec  2 07:41:51 2017	INFO : Model 1 distances correct: False
Sat Dec  2 07:41:51 2017	INFO : Modelling...
Sat Dec  2 08:46:08 2017	INFO : Model 2 built
Sat Dec  2 08:46:08 2017	INFO : Validating Calpha distances...
Sat Dec  2 08:46:08 2017	INFO : Model 2 distances correct: True
Sat Dec  2 08:46:08 2017	INFO : Modelling...
Sat Dec  2 09:44:12 2017	INFO : Model 3 built
Sat Dec  2 09:44:12 2017	INFO : 1/6 gaps will be remodelled
Sat Dec  2 10:45:50 2017	INFO : Validating Calpha distances...
Sat Dec  2 10:45:50 2017	INFO : Model 3 distances correct: False
Sat Dec  2 10:45:50 2017	INFO : Modelling...
Sat Dec  2 11:26:18 2017	INFO : Model 4 built
Sat Dec  2 11:26:18 2017	INFO : Validating Calpha distances...
Sat Dec  2 11:26:18 2017	INFO : Model 4 distances correct: True
Sat Dec  2 11:26:18 2017	INFO : Modelling...
Sat Dec  2 12:25:41 2017	INFO : Model 5 built
Sat Dec  2 12:25:41 2017	INFO : 1/6 gaps will be remodelled
Sat Dec  2 13:28:14 2017	INFO : Validating Calpha distances...
Sat Dec  2 13:28:14 2017	INFO : Model 5 distances correct: False
Sat Dec  2 13:28:34 2017	INFO : Finished modelling
Sat Dec  2 13:28:34 2017	STATUS CHANGED : R -> P
Sat Dec  2 13:28:34 2017	INFO : Checking topology...
Sat Dec  2 16:16:19 2017	INFO : Knot matrices done...
Sat Dec  2 16:20:35 2017	INFO : Some knots found!
Sat Dec  2 16:20:37 2017	INFO : Some lassos found!
Sat Dec  2 16:20:37 2017	INFO : Finishing...
Sat Dec  2 16:20:37 2017	STATUS CHANGED : P -> E
Sat Dec  2 16:20:37 2017	ERROR : Error while finishing
Sat Dec  2 16:20:37 2017	STATUS CHANGED : E -> F

3MT5 chain A