Job name:

noname(1UAK chain A)

aa335ce0-6b1a-47af-8c70-fbb4ae4a096d
Finished
Models Number of gaps:1 Gap lengths: 10
Model Entanglement Average DOPE-HR (by gap length)
DOPE-HR 1st gap
Model 1 Non-trivial -28131
Model 2 Non-trivial -28144
Model 3 Non-trivial -28064
Model 4 Non-trivial -28122
Model 5 Non-trivial -27903
Reload
Warning: All models are renumbered - the first residue in the structure has index 1.
Mix & match
Provided protein had only one gap - thus there are no gap-filling combinations to be made.

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 Knot K +31 86-133 -- -- --
Model 2 Knot K +31 86-133 -- -- --
Model 3 Knot K +31 86-133 -- -- --
Model 4 Knot K +31 86-133 -- -- --
Model 5 Knot K +31 86-133 -- -- --
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


1UAM

A

K +31

100.00%

80.00%

80.00%

0.53

..Target: SHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGKQASAEEDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNSLEHH
Template: SHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGKQ--AEEDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNSLEHH


3IEF

A

K +31

43.75%

100.00%

40.00%

1.46

..Target: SHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGKQASAEEDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNSLEHH
Template: KFQ-ARVLTLYPEMFPGFLGCSLAGQALKQGIWSLETVQIRDFA-----SVDDTPAGGGAGMVMRA----DVLAAALDSCPNDSPRLLMSPRGRLLNQAYARSLARSSGVTLVCGRFEGVDERIIEARELEEVSIGDYILSGGETAALVLLDAIVRLLPGVMGNEISAKCESFENGLLEHPQYTRPAVFEGRGIPPVLTSGHHKAIANWRQQQAESLTRQRRPDLY-----------------ALYNK-NRQ

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

GVLGKQASAEEDSFAD

1UAM A K +31 80.00% 80.00%

GVLGKQ--AEEDSFAD

3IEF A K +31 40.00% 100.00%

GVMGNEISAKCESFEN


Tue Aug  8 23:13:15 2017	JOB CREATED : aa335ce0-6b1a-47af-8c70-fbb4ae4a096d
Tue Aug  8 23:14:01 2017	STATUS CHANGED : N -> R
Tue Aug  8 23:14:01 2017	INFO : JOB STARTED AT: 2017-08-08 23:14:01.584276
Tue Aug  8 23:14:01 2017	INFO : METHOD: 4
Tue Aug  8 23:15:00 2017	INFO : Homologue pool found...
Tue Aug  8 23:15:00 2017	INFO : Verifying structure sequences of homologues...
Tue Aug  8 23:15:54 2017	INFO : Starting homologue filtering...
Tue Aug  8 23:16:21 2017	INFO : Getting structures from PDB...
Tue Aug  8 23:16:26 2017	INFO : Creating modelling alignment...
Tue Aug  8 23:16:26 2017	INFO : Modelling...
Tue Aug  8 23:17:28 2017	INFO : Model 1 built
Tue Aug  8 23:17:28 2017	INFO : Validating Calpha distances...
Tue Aug  8 23:17:28 2017	INFO : Model 1 distances correct: True
Tue Aug  8 23:17:28 2017	INFO : Modelling...
Tue Aug  8 23:18:29 2017	INFO : Model 2 built
Tue Aug  8 23:18:29 2017	INFO : Validating Calpha distances...
Tue Aug  8 23:18:29 2017	INFO : Model 2 distances correct: True
Tue Aug  8 23:18:29 2017	INFO : Modelling...
Tue Aug  8 23:19:27 2017	INFO : Model 3 built
Tue Aug  8 23:19:27 2017	INFO : Validating Calpha distances...
Tue Aug  8 23:19:27 2017	INFO : Model 3 distances correct: True
Tue Aug  8 23:19:27 2017	INFO : Modelling...
Tue Aug  8 23:20:31 2017	INFO : Model 4 built
Tue Aug  8 23:20:31 2017	INFO : Validating Calpha distances...
Tue Aug  8 23:20:31 2017	INFO : Model 4 distances correct: True
Tue Aug  8 23:20:31 2017	INFO : Modelling...
Tue Aug  8 23:21:33 2017	INFO : Model 5 built
Tue Aug  8 23:21:33 2017	INFO : Validating Calpha distances...
Tue Aug  8 23:21:33 2017	INFO : Model 5 distances correct: True
Tue Aug  8 23:21:47 2017	INFO : Finished modelling
Tue Aug  8 23:21:47 2017	STATUS CHANGED : R -> P
Tue Aug  8 23:21:47 2017	INFO : Checking topology...
Tue Aug  8 23:23:49 2017	INFO : Knot matrices done...
Tue Aug  8 23:26:34 2017	INFO : Some knots found!
Tue Aug  8 23:26:34 2017	INFO : No lassos found...
Tue Aug  8 23:26:34 2017	INFO : Finishing...
Tue Aug  8 23:26:34 2017	INFO : Job done
Tue Aug  8 23:26:34 2017	STATUS CHANGED : P -> F
Tue Aug  8 23:26:34 2017	STATUS CHANGED : F -> F

GapRepairer | Interdisciplinary Laboratory of Biological Systems Modelling