Job name:

4DJK chain A

1a219783-c11b-4ddc-b9ca-4559622bfee1
Finished
Models Number of gaps:3 Gap lengths: 25, 13, 4
Model Entanglement Average DOPE-HR (by gap length)
DOPE-HR 1st gap2nd gap3rd gap
Model 1 Non-trivial -52842
Model 2 Non-trivial -53083
Model 3 Non-trivial -51397
Model 4 Non-trivial -50369
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Warning: All models are renumbered - the first residue in the structure has index 1.
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EntanglementHelpKnotProtLassoProtLinkProt
Model Type Knot core Slipknot Lasso Piercing Show
range loop range loop position in JSmol
Model 1 Slipknot S 4131 32-300 300-489 -- --
Model 2 Knot S 4131 30-209 -- -- --
Model 3 Slipknot S 4131 207-475 475-489 -- --
Model 4 Slipknot S 824131 208-474 474-489 -- --
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.
Model 1
Model 2
Model 3
Model 4
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.
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PDB
code		 Chain Entanglement
type		 Seq
identity		 Total gap
coverage		 Total gap
identity		 RMSD [Å] Pairwise alignment to the target: gap


4DJI
A
S +31,41,+31
97.97%
260.92%
260.92%
0.86

..Target: --QLTLLGFFAITASMVMAVYEYPTFATSGFSLVFFLLLGGILWFIPVGLCAAEMATVDGWEEGGVFAWVSNTLGPRWGFAAISFGYLQIAIGFIPMLYFVLGALSYILKWPALNEDPITKTIAALIILWALALTQFGGTKYTARIAKVGFFAGILLPAFILIALAAIYLHSGAPVAIEMDSKTFFPDFSKVGTLVVFVAFILSYMGVEASATHVNEMSNPGRDYPLAMLLLMVAAICLSSVGGLSIAMVIPGNEINLSAGVMQTFTVLMSHVAPEIEWTVRVISALLLLGVLAEIASWIVGPSRGMYVTAQKNLLPAAFAKMNKNGVPVTLVISQLVITSIALIILTNTGGGNNMSFLIALALTVVIYLCAYFMLFIGYIVLVLKHPDLKRTFNIPGGKGVKLVVAIVGLLTSIMAFIVSFLPPDNIQGDSTDMYVELLVVSFLVVLALPFILYAVHDRKGKANTGVTLEPINSQNAPKGHFFLHPRARSP--------
Template: AKQLTLLGFFAITASMVMAVYEYPTFATSGFSLVFFLLLGGILWFIPVGLCAAEMATVDGWEEGGVFAWVSNTLGPRWGFAAISFGYLQIAIGFIPMLYFVLGALSYILKWPALNEDPITKTIAALIILWALALTQFGGTKYTARIAKVGFFAGILLPAFILIALAAIYLHSGA---IEMDSKTFFPDFSKVGTLVVFVAFILSYMGVEASATHVNEMSNPGRDYPLAMLLLMVAAICLSSVGGLSIAMVIPGNEINLSAGVMQTFTVLMSHVAPEIEWTVRVISALLLLGVLAEIASWIVGPSRGMYVTAQKNLLPAAFAKMNKNGVPVTLVISQLVITSIALIILTNTGGGNNMSFLIALALTVVIYLCAYFMLFIGYIVLVLKHPDLKRTFNIPGGKGVKLVVAIVGLLTSIMAFIVSFLPPDNIQGDSTDMYVELLVVSFLVVLALPFILYAVHD----ANTGVTLEPINSQNAPKGHFFLHPRARSPHYIVMNDK

4DJI
B
S +31,41,+31
99.38%
256.62%
256.62%
0.88

..Target: QLTLLGFFAITASMVMAVYEYPTFATSGFSLVFFLLLGGILWFIPVGLCAAEMATVDGWEEGGVFAWVSNTLGPRWGFAAISFGYLQIAIGFIPMLYFVLGALSYILKWPALNEDPITKTIAALIILWALALTQFGGTKYTARIAKVGFFAGILLPAFILIALAAIYLHSGAPVAIEMDSKTFFPDFSKVGTLVVFVAFILSYMGVEASATHVNEMSNPGRDYPLAMLLLMVAAICLSSVGGLSIAMVIPGNEINLSAGVMQTFTVLMSHVAPEIEWTVRVISALLLLGVLAEIASWIVGPSRGMYVTAQKNLLPAAFAKMNKNGVPVTLVISQLVITSIALIILTNTGGGNNMSFLIALALTVVIYLCAYFMLFIGYIVLVLKHPDLKRTFNIPGGKGVKLVVAIVGLLTSIMAFIVSFLPPDNIQGDSTDMYVELLVVSFLVVLALPFILYAVHDRKGKANTGVTLEPINSQNAPKGHFFLHPRARSP---
Template: QLTLLGFFAITASMVMAVYEYPTFATSGFSLVFFLLLGGILWFIPVGLCAAEMATVDGWEEGGVFAWVSNTLGPRWGFAAISFGYLQIAIGFIPMLYFVLGALSYILKWPALNEDPITKTIAALIILWALALTQFGGTKYTARIAKVGFFAGILLPAFILIALAAIYLHSGA--AIEMDSKTFFPDFSKVGTLVVFVAFILSYMGVEASATHVNEMSNPGRDYPLAMLLLMVAAICLSSVGGLSIAMVIPGNEINLSAGVMQTFTVLMSHVAPEIEWTVRVISALLLLGVLAEIASWIVGPSRGMYVTAQKNLLPAAFAKMNKNGVPVTLVISQLVITSIALIILTNTGGGNNMSFLIALALTVVIYLCAYFMLFIGYIVLVLKHP----TFNIPGGKGVKLVVAIVGLLTSIMAFIVSFLPPDNIQGDSTDMYVELLVVSFLVVLALPFILYAVH-------TGVTLEPINSQNAPKGHFFLHPRARSPHYI

3LRB
A
S +31,41,+31
25.12%
226.77%
89.38%
1.61

..Target: QLTLLGFFAIT-----ASMVMAVYEYPTFATSGFSLVFFLLLGGILWFIPVGLCAAEMATVDGWEEGGVFAWVSNTLGPRWGFAAISFGYLQIAIGFIPMLYFVLGALSYILKWPALNEDPITKTIAALIILWALALTQFGGTKYTARIAKVGFFAGILLPAFILIALAAIYLHSGAPVAIEMDSKTFFPDF--SKVGT----LVVFVAFILSYMGVEASATHVNEMSNPGRDYPLAMLLLMVAAICLSSVGGLSIAMVIPGNEINLSAGVMQTFTVLMSHVAPEIEWTVRVISALLLLGVLAEIASWIVGPSRGMYVTAQKNLLPAAFAKMNKNGVPVTLVISQLVITSIALIILTNTGGGNNMSFLIALALTVVIYLCAYFMLFIGYIVLVLKHPDLKRTFNIPGGKGVKLVVAIVGLLTSIMAFIVSFLPPDNIQGDSTDMYVELLVVSFLVVLALPFILYAVHDRKGK--ANTGVTLEPINSQNAPKGHFFLHPRARSP
Template: DAHKVGLIPVTLMVSGNIMGSGVFLLPANLASTGGIAIYGWLVTIIGALGLSMVYAKMSFLDP-SPGGSYAYARRCFGPFLGYQTNVLYWLACWIGNIAMVVIGVGYLSYFF--PIL-KDPLVLTITCVVVLWIFVLLNIVGPKMITRVQAVATVLA-LIP-IVGIAVFGWFWFRG---------ETYMAAWNVSGLGTFGAIQSTLNVTLWSFIGVESASVAAGVVKNPKRNVP------------IATIGGVLIAAVC---------YVLST-TAIMGMIPN---TAGAIVSFCAAAGCLGSLGGWTLLAGQTAKAAADDGLFPPIFARVNKAGTP----VAGLIIVGILMTIFQLSSISPNATKEFGLVSSVSVIFTLVPYLYTCAALLLLGH---------------------------------------GHFGKARPAYLAVTTIAF------LYCIWAVVGSGAKEVMWSFVTLMVITAMYA-LNYNRLH---KNP

3NCY
C
S +31,41,+31
23.10%
228.00%
73.38%
1.62

..Target: QLTLLGFFAITASMVMAVYEYPTFATSGFSLVFFLLLGGILWFIPVGLCAAEMATVDGWEEGGVFAWVSNTLGPRWGFAAISFGYLQIAIGFIPMLYFVLGALSYILKWPALNEDPITKTIAALIILWALALTQFGGTKYTARIAKVGFFAGILLPAFILIALAAIYLHSGAPVAIEMDSKTFF----PDFSKVGTLVVFVAFIL-SYMGVEASATHVNEMSNPGRDYPLAML-LLMVAAICLSSVGGLSIAMVIPGNEINLSAGVMQTFTVLMSHVAPEIEWTVRVISALLLLGVLAEIASWIVGPSRGMYVTAQKNLLPAAFAKMNKNGVPVTLVISQLVITSIALIILTNTGGGNNMSFLIALALTVVIYLCAYFMLFIGYIVLVLKHPDLKRTFNIPGGKGVKLVVAIVGLLTSIMAFIVSFLPPDNIQGDSTDMYVELLVVSFLVVLALPFILYAVHDRKGKANTGVTLEPINSQNAPKGHFFLHPRARSP
Template: GLIPVTLMVSGNIMGSGVFLLPANLAATGGIAIYGWLVTIIGALALSMVYAKMSSLDP-SPGGSYAYARRCFGPFLGYQTNVLYWLACWIGNIAMVVIGVGYLSYFF--PIL-KDPLVLTLTCVAVLWIFVLLNIVGPKMITRVQAV-----------------ATVLALVPIVGIAVFGWFWFKWNVSGMNTFGAIQSTLNVTLWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIAAVCY-VLSTTAIMGMIPNAALRVSA---SPFGDAARMALGDTAGAI--VSFCAAAGCLGSLGGWTLLAGQTAKAAADDGLFPPIFAR----GTP----VAGLLIVGVLMTIFQFSSMSPNAAKEFGLVSSVSVIFTLVPYLYTCAALLLLGH------GHFGKARPLYLLITFVAFVYCIWAVIGSG--------------AKEVMWSFVTLMVIT-ALYA-------------------LNYNRIHKNPYP-LDAP
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PDB
code		 Chain Knot
type		 Gap
coverage		 Gap
identity		 >Target_Sequence: gap

YAVHDRKGKANTGVTLEPINSQNAPKGHFFL
4DJI A S +31,41,+31 84.00% 84.00%

YAVHD----ANTGVTLEPINSQNAPKGHFFL
4DJI B S +31,41,+31 72.00% 72.00%

YAVH-------TGVTLEPINSQNAPKGHFFL
3LRB A S +31,41,+31 24.00% 96.00%

WAVVGSGAKEVMWSFVTLMVITAMYA-LNYNRL
3NCY C S +31,41,+31 8.00% 28.00%

YA-------------------LNYNRIHKNP
PDB
code		 Chain Knot
type		 Gap
coverage		 Gap
identity		 >Target_Sequence: gap

YLHSGAPVAIEMDSKTFFP
4DJI A S +31,41,+31 76.92% 76.92%

YLHSGA---IEMDSKTFFP
4DJI B S +31,41,+31 84.62% 84.62%

YLHSGA--AIEMDSKTFFP
3LRB A S +31,41,+31 15.38% 30.77%

FWFRG---------ETYMA
3NCY C S +31,41,+31 15.38% 100.00%

VLALVPIVGIAVFGWFWFKWNVS
PDB
code		 Chain Knot
type		 Gap
coverage		 Gap
identity		 >Target_Sequence: gap

DGWEEGGVFA
4DJI A S +31,41,+31 100.00% 100.00%

DGWEEGGVFA
4DJI B S +31,41,+31 100.00% 100.00%

DGWEEGGVFA
3LRB A S +31,41,+31 50.00% 100.00%

DP-SPGGSYA
3NCY C S +31,41,+31 50.00% 100.00%

DP-SPGGSYA

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

Fri Dec  1 09:37:53 2017	JOB CREATED : 1a219783-c11b-4ddc-b9ca-4559622bfee1
Fri Dec  1 12:37:02 2017	STATUS CHANGED : N -> R
Fri Dec  1 12:37:02 2017	INFO : JOB STARTED AT: 2017-12-01 12:37:02.855429
Fri Dec  1 12:37:02 2017	INFO : METHOD: 1
Fri Dec  1 12:37:02 2017	INFO : Precalculated profile found...
Fri Dec  1 12:37:02 2017	INFO : Homologue pool found...
Fri Dec  1 12:37:02 2017	INFO : Verifying structure sequences of homologues...
Fri Dec  1 12:37:48 2017	INFO : Starting homologue filtering...
Fri Dec  1 12:38:31 2017	INFO : Getting structures from PDB...
Fri Dec  1 12:39:08 2017	INFO : Creating modelling alignment...
Fri Dec  1 12:39:08 2017	INFO : Modelling...
Fri Dec  1 13:32:31 2017	INFO : Model 1 built
Fri Dec  1 13:32:31 2017	INFO : 1/3 gaps will be remodelled
Fri Dec  1 13:49:40 2017	INFO : Validating Calpha distances...
Fri Dec  1 13:49:40 2017	INFO : Model 1 distances correct: True
Fri Dec  1 13:49:40 2017	INFO : Modelling...
Fri Dec  1 14:24:21 2017	INFO : Model 2 built
Fri Dec  1 14:24:21 2017	INFO : 1/3 gaps will be remodelled
Fri Dec  1 14:40:30 2017	INFO : Validating Calpha distances...
Fri Dec  1 14:40:30 2017	INFO : Model 2 distances correct: True
Fri Dec  1 14:40:30 2017	INFO : Modelling...
Fri Dec  1 15:26:04 2017	INFO : Model 3 built
Fri Dec  1 15:26:04 2017	INFO : 1/3 gaps will be remodelled
Fri Dec  1 15:42:28 2017	INFO : Validating Calpha distances...
Fri Dec  1 15:42:28 2017	INFO : Model 3 distances correct: True
Fri Dec  1 15:42:28 2017	INFO : Modelling...
Fri Dec  1 16:27:58 2017	INFO : Model 4 built
Fri Dec  1 16:27:58 2017	INFO : 1/3 gaps will be remodelled
Fri Dec  1 16:48:50 2017	INFO : Validating Calpha distances...
Fri Dec  1 16:48:50 2017	INFO : Model 4 distances correct: False
Fri Dec  1 16:48:50 2017	INFO : Modelling...
Fri Dec  1 17:34:45 2017	INFO : Model 5 built
Fri Dec  1 17:34:45 2017	INFO : 1/3 gaps will be remodelled
Fri Dec  1 17:55:42 2017	INFO : Validating Calpha distances...
Fri Dec  1 17:55:42 2017	INFO : Model 5 distances correct: True
Fri Dec  1 17:56:38 2017	INFO : Finished modelling
Fri Dec  1 17:56:38 2017	STATUS CHANGED : R -> P
Fri Dec  1 17:56:38 2017	INFO : Checking topology...
Fri Dec  1 19:02:18 2017	INFO : Knot matrices done...
Fri Dec  1 19:04:38 2017	INFO : Some knots found!
Fri Dec  1 19:04:38 2017	INFO : No lassos found...
Fri Dec  1 19:04:38 2017	INFO : Finishing...
Fri Dec  1 19:04:38 2017	STATUS CHANGED : P -> E
Fri Dec  1 19:04:38 2017	ERROR : Error while finishing
Fri Dec  1 19:04:38 2017	STATUS CHANGED : E -> F
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