Job name:

noname(1CMX chain A)

1b366f46-b785-469f-9990-f519979c7f38
Finished
Models Number of gaps:1 Gap lengths: 16
Model Entanglement Average DOPE-HR (by gap length)
DOPE-HR 1st gap
Model 1 Non-trivial -26370
Model 2 Non-trivial -26359
Model 3 Non-trivial -26196
Model 4 Non-trivial -26120
Model 5 Non-trivial -25955
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 5231 6-166 -- -- --
Model 2 Knot K 5231 5-165 -- -- --
Model 3 Knot K 5231 6-165 -- -- --
Model 4 Knot K 5231 6-182 -- -- --
Model 5 Slipknot S 31 6-182 182-224 -- --
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


1UCH

A

K -52,-31,-31

36.89%

87.50%

37.50%

1.21

..Target: RAVVPIESNPEVFTNFAHKLGLKNEWAYFDIYSLTEPELLAFLPRPVKAIVLLFPI----------NEDRKSSTSQQITSSYDVIWFKQSVKNACGLYAILHSLSNNQSLL--EPGSDLDNFLKSQSDTSSSKNRFDDVTTDQFVLNVIKENVQTFSTGQSEAPEATA-----------DTNLHYITYVEENGGIFELDGRNLSGPLYLGKSDPTATDLIEQELVRVRVASYMENANEEDVLNFAMLGLGPN
Template: R-WLPLEANPEVTNQFLKQLGLHPNWQFVDVYGM-DPELLSMVPRPVCAVLLLFPITEKYEVFRTEEEEKIKSQGQDVTSS--VYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFL--------------------------EESV-------SMSPEERARYLENYDAIRVD--LHFIALVHVDGHLYELDGR---KPFPINHGE-TSDETLLEDAIEV-CKKFME--RDPDELRFNAIALSAA


4DM9

A

K -52,-31,-31

29.15%

100.00%

12.50%

1.26

..Target: RAVVPIESNPEVFTNFAHKLGLKNEWAYFDIYSLTEPELLAFLPRPVKAIVLLFPINEDRKSSTSQQI--TSSYDV---IWF-KQSVKNACGLYAILHSLSNNQSLL--EPGSDLDNFLKSQSDTSSSKNRFDDVTTDQFVLNVIKENVQTFSTGQSEAPEATADTNL--HYITYVEENGGIFELDGRNLSGPLYLGKSDPTATDLIEQELVRVRVASYME-NANEEDVLNFAMLGL-GPN
Template: MQLKPMEINPEMLNKVLSRLGVAGQWRFVDVLGL-EEESLGSVPAPACALLLLFPLTAQHENFRKKQIEELKGQEVSPKVYFMKQTIGNSCGTIGLIHAVANNQDKLGFEDGSVLKQFL-SETEKMSPEDR-----AKCFEKN---EAIQAAHDAVAQEGQCRVDDKVNFHFILFNNVDGHLYELDGR-MPFPVNHGAS-------SEDTLLKDAAKVCREFTEREQGEVRFSAVALCKAA

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

PI----------NEDRKSSTSQQITSSYDVIW

1UCH A K -52,-31,-31 37.50% 87.50%

PITEKYEVFRTEEEEKIKSQGQDVTSS--VYF

4DM9 A K -52,-31,-31 12.50% 100.00%

PLTAQHENFRKKQIEELKGQEVSPKVY


Wed Sep 13 10:44:34 2017	JOB CREATED : 1b366f46-b785-469f-9990-f519979c7f38
Wed Sep 13 10:45:02 2017	STATUS CHANGED : N -> R
Wed Sep 13 10:45:02 2017	INFO : JOB STARTED AT: 2017-09-13 10:45:02.714045
Wed Sep 13 10:45:02 2017	INFO : METHOD: 1
Wed Sep 13 10:45:03 2017	INFO : Precalculated profile found...
Wed Sep 13 10:45:03 2017	INFO : Homologue pool found...
Wed Sep 13 10:45:03 2017	INFO : Verifying structure sequences of homologues...
Wed Sep 13 10:45:48 2017	INFO : Starting homologue filtering...
Wed Sep 13 10:46:16 2017	INFO : Getting structures from PDB...
Wed Sep 13 10:46:21 2017	INFO : Creating modelling alignment...
Wed Sep 13 10:46:21 2017	INFO : Modelling...
Wed Sep 13 10:48:09 2017	INFO : Model 1 built
Wed Sep 13 10:48:09 2017	INFO : Validating Calpha distances...
Wed Sep 13 10:48:09 2017	INFO : Model 1 distances correct: True
Wed Sep 13 10:48:09 2017	INFO : Modelling...
Wed Sep 13 10:49:55 2017	INFO : Model 2 built
Wed Sep 13 10:49:55 2017	INFO : Validating Calpha distances...
Wed Sep 13 10:49:55 2017	INFO : Model 2 distances correct: True
Wed Sep 13 10:49:55 2017	INFO : Modelling...
Wed Sep 13 10:51:41 2017	INFO : Model 3 built
Wed Sep 13 10:51:41 2017	INFO : Validating Calpha distances...
Wed Sep 13 10:51:41 2017	INFO : Model 3 distances correct: True
Wed Sep 13 10:51:41 2017	INFO : Modelling...
Wed Sep 13 10:54:28 2017	INFO : Model 4 built
Wed Sep 13 10:54:28 2017	INFO : Validating Calpha distances...
Wed Sep 13 10:54:28 2017	INFO : Model 4 distances correct: True
Wed Sep 13 10:54:28 2017	INFO : Modelling...
Wed Sep 13 10:56:13 2017	INFO : Model 5 built
Wed Sep 13 10:56:13 2017	INFO : Validating Calpha distances...
Wed Sep 13 10:56:13 2017	INFO : Model 5 distances correct: True
Wed Sep 13 10:56:32 2017	INFO : Finished modelling
Wed Sep 13 10:56:32 2017	STATUS CHANGED : R -> P
Wed Sep 13 10:56:32 2017	INFO : Checking topology...
Wed Sep 13 10:57:11 2017	INFO : Knot matrices done...
Wed Sep 13 10:57:44 2017	INFO : Some knots found!
Wed Sep 13 10:57:44 2017	INFO : No lassos found...
Wed Sep 13 10:57:44 2017	INFO : Finishing...
Wed Sep 13 10:57:44 2017	INFO : Job done
Wed Sep 13 10:57:44 2017	STATUS CHANGED : P -> F
Wed Sep 13 10:57:44 2017	STATUS CHANGED : F -> F

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