Job name:

2NMV chain A

a4dfb0a2-ef66-4459-86ab-2ee2902013a7
Finished
Models Number of gaps:1 Gap lengths: 32
Model Entanglement Average DOPE-HR (by gap length)
DOPE-HR 1st gap
Model 1 Unknot -73564
Model 2 Non-trivial -71973
Model 3 Non-trivial -71774
Model 4 Non-trivial -72068
Model 5 Non-trivial -71523
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 2 Knot K 41 417-600 -- -- --
Model 3 Knot K 41 417-600 -- -- --
Model 4 Knot K 41 417-599 -- -- --
Model 5 Knot K 41 417-600 -- -- --
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 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


4BRU

A

Unknot

29.33%

59.38%

21.88%

1.44

..Target: DRFE--------LVSKYQPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKT--FTVSNLIKEVNKPTLVIAHNKTLAGQLYSEFKEFFPNNAVEYFVSYYDYYQPEAYVPQTDTFIEKDASINDEIDKLRHSATSALFERRDVIIIASVSCIYGLGSPEEYREMVVSLRTEMEIERNELLRKLVDIQYARNDIDFQRGTFRVRGDVVEIFPASRDEHCVRVEFFGDEIERIREVDALTGEILGDRDHVAIFPASHFVTRAEKMEKAIQNIEKELEEQLKVMHENGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLTLRPPGSTPYTLLDYFPDDFMIVVDESHVTIPQVRGMFNGDQARKQVLVDHGFRLPSALDNRPLRFEEFEKHMHNIVYVSATPGPYEIEHTDEMVEQIIRPTGLLDPLIDVRPIEGQIDDLIGEIQARIERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAEGRVIMYADKITKSMEIAINETKRRREQQERFNEEHGITPKTINKEIRDVIRATVAAEDKAEYKTKAAPKLSKMTKKERQKVVEQMEHEMKEAAKALDFERAAELRDLL
Template: NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTL--EKVKPKL----NK----------------------------IQALIMVPTRELAL----------------QTSQVV--RTLGKHCGISCMVTTGG--------TNLRDDI-LRLNETVHILV-------------GT---PGRVLDL---------------------------------ASRKVADLSDCSLF-----------------------IMDEADKML-----------------SRDFKTIIEQI---LSFLPP--THQSLL--FSATFPLTVDE-----------------------------------------FMDKHLH---------KPYEI----NLMEELTL-KGITQYYAFVE--ERQKLHCLNTLFSKLQINQAIIFCNSTNRV-ELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPK-----TAETYLHRIGRSGR-------------FGHLGLAIN--------LINWNDRFNL--YKIEQELGTEIAAIPATIDKSLY--------------------------------------------VA

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

TINKEIRDVIRATVAAEDKAEYKTKAAPKLSKMTKKER

4BRU A Unknot 21.88% 59.38%

KIEQELGTEIAAIPATIDKSLY----------------


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

Sun Jul 23 15:14:31 2017	JOB CREATED : a4dfb0a2-ef66-4459-86ab-2ee2902013a7
Mon Jul 24 03:41:02 2017	STATUS CHANGED : N -> R
Mon Jul 24 03:41:02 2017	INFO : JOB STARTED AT: 2017-07-24 03:41:02.194215
Mon Jul 24 03:41:02 2017	INFO : METHOD: 1
Mon Jul 24 03:41:02 2017	INFO : Precalculated profile found...
Mon Jul 24 03:41:02 2017	INFO : Homologue pool found...
Mon Jul 24 03:41:02 2017	INFO : Verifying structure sequences of homologues...
Mon Jul 24 03:51:52 2017	INFO : Starting homologue filtering...
Mon Jul 24 03:52:58 2017	INFO : Getting structures from PDB...
Mon Jul 24 03:53:01 2017	INFO : Creating modelling alignment...
Mon Jul 24 03:53:01 2017	INFO : Modelling...
Mon Jul 24 04:49:13 2017	INFO : Model 1 built
Mon Jul 24 04:49:13 2017	INFO : Validating Calpha distances...
Mon Jul 24 04:49:13 2017	INFO : Model 1 distances correct: True
Mon Jul 24 04:49:13 2017	INFO : Modelling...
Mon Jul 24 05:45:19 2017	INFO : Model 2 built
Mon Jul 24 05:45:19 2017	INFO : Validating Calpha distances...
Mon Jul 24 05:45:19 2017	INFO : Model 2 distances correct: True
Mon Jul 24 05:45:19 2017	INFO : Modelling...
Mon Jul 24 06:20:51 2017	INFO : Model 3 built
Mon Jul 24 06:20:51 2017	INFO : Validating Calpha distances...
Mon Jul 24 06:20:51 2017	INFO : Model 3 distances correct: True
Mon Jul 24 06:20:51 2017	INFO : Modelling...
Mon Jul 24 07:21:58 2017	INFO : Model 4 built
Mon Jul 24 07:21:58 2017	INFO : Validating Calpha distances...
Mon Jul 24 07:21:58 2017	INFO : Model 4 distances correct: True
Mon Jul 24 07:21:58 2017	INFO : Modelling...
Mon Jul 24 07:58:27 2017	INFO : Model 5 built
Mon Jul 24 07:58:27 2017	INFO : Validating Calpha distances...
Mon Jul 24 07:58:27 2017	INFO : Model 5 distances correct: True
Mon Jul 24 07:59:15 2017	INFO : Finished modelling
Mon Jul 24 07:59:15 2017	STATUS CHANGED : R -> P
Mon Jul 24 07:59:15 2017	INFO : Checking topology...
Mon Jul 24 08:54:28 2017	INFO : Knot matrices done...
Mon Jul 24 09:01:07 2017	INFO : Some knots found!
Mon Jul 24 09:01:07 2017	INFO : No lassos found...
Mon Jul 24 09:01:07 2017	INFO : Finishing...
Mon Jul 24 09:01:08 2017	INFO : Job done
Mon Jul 24 09:01:08 2017	STATUS CHANGED : P -> F
Mon Jul 24 09:01:08 2017	STATUS CHANGED : F -> F

GapRepairer | Interdisciplinary Laboratory of Biological Systems Modelling