Job name:

noname(4UF5 chain A)

4f12c601-eb56-4c9a-a0da-05678f865274
Finished
Warning: Knot detection did not finish.
Models Number of gaps:2 Gap lengths: 13, 11
Model Entanglement Average DOPE-HR (by gap length)
DOPE-HR 1st gap2nd gap
Model 1 Err -35168
Model 2 Err -35396
Model 3 Err -34076
Model 4 Err -34084
Model 5 Non-trivial -34001
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.
Warning: JSmol may at times display gaps where there are none - due to some overlaps in models. This does not indicate presence of gaps in downloaded structure!
EntanglementHelpKnotProtLassoProtLinkProt
Model Type Knot core Slipknot Lasso Piercing Show
range loop range loop position in JSmol
Model 1 Lasso SL 2--C -- -- 22-95
Model 2 Lasso SL 2--C -- -- 22-95
Model 3 Lasso SL 2--C -- -- 22-95
Model 4 Lasso SL 2--C -- -- 22-95
Model 5 Lasso SL 2--C -- -- 22-95
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
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.
PDB
code
Chain Entanglement
type
Seq
identity
Total gap
coverage
Total gap
identity
RMSD [Å] Pairwise alignment to the target: gap


4UEL

A

K -52,-31,-31

100.00%

90.21%

90.21%

1.22

..Target: GEWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSFARQQMFEFDTKTSAKEEDAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLMAIVSDRKMIYEQKIAELQRQLAEEPMDTDQGNSMLSAIQSEVAKNQMLIEEEVQKLKRYKIENIRRKHNYLPFIMELLKTLAEHQQLIPLVEKAKEKQN
Template: GEWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSFARQQMFEFDT------EDAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLMAIVSDRKMIYEQKIAELQRQLAEE-------NSMLSAIQSEVAKNQMLIEEEVQKLKRYKIENIRRKHNYLPFIMELLKTLAEHQQLIPLVEKAKEKQN


4WLQ

A

K -52,-31,-31

97.26%

68.53%

59.44%

1.00

..Target: GEWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSFARQQMFEFDTKTSAKEEDAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLMAIVSDRKMIYEQKIAELQRQLAEEPMDTDQGNSMLSAIQSEVAKNQMLIEEEVQKLKRYKIENIRRKHNYLPFIMELLKTLAEHQQLIPLVEKAKEKQN
Template: GEWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPESFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLETIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSFARQQMFE-----------AFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWITAVRPVIEKRIQKYSEGEIRFNLMAIVSDRKMIYEQKIAELQRQLAEEPM------TVLSAIQSEVARNQMLIEEEVQKLKRYKIENIRRKHNYLPFIMELLKTLAEHQQLIPLV------EK


3IHR

A

K -52,-31,-31

97.16%

45.45%

36.36%

1.04

..Target: GEWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSFARQQMFEFDTKTSAKEEDAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLMAIVSDRKMIYEQKIAELQRQLAEEPMDTDQGNSMLSAIQSEVAKNQMLIEEEVQKLKRYKIENIRRKHNYLPFIMELLKTLAEHQQLIPLVEKAKEKQN
Template: -EWCLXESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAXKGLALSNSDVIRQVHNSFA-----------------AFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLXAIVSDRKXIYEQKIAELQRQLAEEPXD------XLSAIQSEVAKNQXLIEEEVQKLKRYKIENIRRKHNYLPFIXELLKTLAEHQQLIPL---------


4IG7

A

K -52,-31,-31

52.38%

107.69%

16.78%

1.24

..Target: GEWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSFARQQMFEFDTKTSAKEEDAFHFVSYVPVNGRLYELDGLREGPIDLGACNQD-DWISAVRPVIEKRIQKYSEGEIRFNLMAIVSDRKMIYEQKIAELQRQLAEEPMDTDQGNSMLSAIQSEVAKNQMLIEEEVQKLKRYKIENIRRKHNYLPFIMELLKTLAEHQQLIPLVEKAKEKQN
Template: GNWCLIESDPGIFTEMIHGFGCTGLQVEELVVLD-ESIEHLKPIHGFIFLFRWLK--------------TDVYFSQQVIQNACASQALINLLLNCDHPDVDLGPTLKEFKDFTYDLDSASRGLCLTNSEKIRAVHNSFG---------------EDVFHFVTYVPVNDGVYELDGLRAAPLRLGTVASDGDWTEVAIKAIKEKIKNYGESEVRFNLMAVISDQKLKYE---REMEK--FAQAGDSAEVDRLVALIAAEDAK--------------------------------------------------RERYA


3RIS

A

K -52,-31,-31

98.68%

53.85%

53.85%

1.00

..Target: GEWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSFARQQMFEFDTKTSAKEEDAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLMAIVSDRKMIYEQKIAELQRQLAEEPMDTDQGNSMLSAIQSEVAKNQMLIEEEVQKLKRYKIENIRRKHNYLPFIMELLKTLAEHQQLIPLVEKAKEKQN
Template: -EWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSFARQQMFEFDTK------DAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLMAIVSDRKMIYEQ--------------------------------------------------------------------------------KIAELQ-


3RII

B

K -52,-31,-31

96.73%

61.54%

61.54%

1.01

..Target: GEWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSFARQQMFEFDTKTSAKEEDAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLMAIVSDRKMIYEQKIAELQRQLAEEPMDTDQGNSMLSAIQSEVAKNQMLIEEEVQKLKRYKIENIRRKHNYLPFIMELLKTLAEHQQLIPLVEKAKEKQN
Template: -EWCLXESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQVINNASATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAXKGLALSNSDVIRQVHNSFAR-------TKTSAKEEDAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLXAIV---------------------------------------------------------------------------------------------SDR

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

RQQMFEFDTKTSAKEEDAF

4UEL A K -52,-31,-31 53.85% 53.85%

RQQMFEFDT------EDAF

4WLQ A K -52,-31,-31 23.08% 23.08%

RQQMFE-----------AF

3IHR A K -52,-31,-31 0.00% 0.00%

-----------------AF

4IG7 A K -52,-31,-31 7.69% 7.69%

---------------EDVF

3RIS A K -52,-31,-31 53.85% 53.85%

RQQMFEFDTK------DAF

3RII B K -52,-31,-31 61.54% 61.54%

R-------TKTSAKEEDAF

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

QLAEEPMDTDQGNSMLS

4UEL A K -52,-31,-31 36.36% 36.36%

QLAEE-------NSMLS

4WLQ A K -52,-31,-31 36.36% 45.45%

QLAEEPM------TVLS

3IHR A K -52,-31,-31 36.36% 45.45%

QLAEEPXD------XLS

4IG7 A K -52,-31,-31 9.09% 100.00%

--FAQAGDSAEVDRLVA

3RIS A K -52,-31,-31 0.00% 0.00%

-----------------

3RII B K -52,-31,-31 0.00% 0.00%

-----------------


Mon Sep 11 11:27:49 2017	JOB CREATED : 4f12c601-eb56-4c9a-a0da-05678f865274
Mon Sep 11 11:28:01 2017	STATUS CHANGED : N -> R
Mon Sep 11 11:28:01 2017	INFO : JOB STARTED AT: 2017-09-11 11:28:01.929407
Mon Sep 11 11:28:01 2017	INFO : METHOD: 1
Mon Sep 11 11:28:02 2017	INFO : Building Profile...
Mon Sep 11 11:28:02 2017	INFO : --E-value set to 0.001--
Mon Sep 11 11:36:41 2017	INFO : Homologue pool found...
Mon Sep 11 11:36:41 2017	INFO : Verifying structure sequences of homologues...
Mon Sep 11 11:37:42 2017	INFO : Starting homologue filtering...
Mon Sep 11 11:38:16 2017	INFO : Getting structures from PDB...
Mon Sep 11 11:38:37 2017	INFO : Creating modelling alignment...
Mon Sep 11 11:38:37 2017	INFO : Modelling...
Mon Sep 11 11:42:15 2017	INFO : Model 1 built
Mon Sep 11 11:42:15 2017	INFO : Validating Calpha distances...
Mon Sep 11 11:42:15 2017	INFO : Model 1 distances correct: True
Mon Sep 11 11:42:15 2017	INFO : Modelling...
Mon Sep 11 11:50:10 2017	INFO : Model 2 built
Mon Sep 11 11:50:10 2017	INFO : Validating Calpha distances...
Mon Sep 11 11:50:10 2017	INFO : Model 2 distances correct: True
Mon Sep 11 11:50:10 2017	INFO : Modelling...
Mon Sep 11 11:53:50 2017	INFO : Model 3 built
Mon Sep 11 11:53:50 2017	INFO : Validating Calpha distances...
Mon Sep 11 11:53:50 2017	INFO : Model 3 distances correct: True
Mon Sep 11 11:53:50 2017	INFO : Modelling...
Mon Sep 11 11:59:57 2017	INFO : Model 4 built
Mon Sep 11 11:59:57 2017	INFO : Validating Calpha distances...
Mon Sep 11 11:59:57 2017	INFO : Model 4 distances correct: True
Mon Sep 11 11:59:57 2017	INFO : Modelling...
Mon Sep 11 12:03:34 2017	INFO : Model 5 built
Mon Sep 11 12:03:34 2017	INFO : Validating Calpha distances...
Mon Sep 11 12:03:34 2017	INFO : Model 5 distances correct: True
Mon Sep 11 12:03:57 2017	INFO : Finished modelling
Mon Sep 11 12:03:57 2017	STATUS CHANGED : R -> P
Mon Sep 11 12:03:57 2017	INFO : Checking topology...
Mon Sep 11 12:03:58 2017	INFO : Knot matrices done...
Mon Sep 11 12:03:58 2017	INFO : No knots found...
Mon Sep 11 12:04:02 2017	INFO : Some lassos found!
Mon Sep 11 12:04:02 2017	INFO : Finishing...
Mon Sep 11 12:04:02 2017	INFO : Job done
Mon Sep 11 12:04:02 2017	STATUS CHANGED : P -> F
Mon Sep 11 12:04:02 2017	STATUS CHANGED : F -> F

GapRepairer | Interdisciplinary Laboratory of Biological Systems Modelling