Job name:

4WVM chain B

85e1207e-7bef-4030-8a72-1e2cc49f0f53
Finished
Models Number of gaps:9 Gap lengths: 21, 17, 15, 11, 6, 5, 5, 4, 4
Model Entanglement Average DOPE-HR (by gap length) Smaller
DOPE-HR 1st gap2nd gap3rd gapgaps
Model 1 Unknot -55347

Model 2 Non-trivial -54254

Model 3 Non-trivial -54068

Model 4 Unknot -52096

None
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 2 Slipknot S 31 121-236 236-696 -- --
Model 3 Slipknot S +31 119-236 236-696 -- --
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
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


4B3N

A

Unknot

21.18%

727.92%

219.65%

1.09

..Target: DILVVAALGRPFTLGMLYDARNDKLIPGFTLWEDEVIEESTLESSQPSSAFEIIASDSTDDKSSLMDIEASLKASFLGGLVEVGGSAKYLNNQKKFKNQSRVTLQYKATTSFKQLMTNLGTKHVE-YSELFENIQATHVVIGILYGANAFFVFDS--NKVDSTNVQEIQGQMEAVIKKIP----SVEISGKASVQLTGEETDITNSFSCEFHGDFFLTTNPTTFEDAVKTYQQLPQMMGKDNAVPMTVWLVPMVNFYSEAPQLMADSSTPILRKVRNTLEAIVQVQMRCNDALDDPTVNLFTEVQKKLSDFQKI-CDDHMSKLQATIAKKLFAIR--SGDEDESALLNLFEENLQSPFNIESLNMWMEFEEREINVLRSCMDILTKAKPKVIFNQGVLFKGLYDSKVKHALCYVF-TNVTKNDVFLNVLNEFLDSP------QSRPKKLRPSPKDYWYSYDDIPETM--REKAYLFRNLAKEMNNRCVHFFVTAIHNPKQEGAGI-------------HYYRESIQIIDEFTKPYMPGVESIKDRRELQWYDCELTLDPETAHQVLTLSEGNKKAVSGNTKSPTDHLEKFSHFQQVMCTKGL-SGRHYWELEWSGYVGAGVTYKGIGRKTS------TSDSSLGKNEKSWLFEYSTKSGYQQIHNSKKTRVTVSSTG------------------FKLLGVYLDWPAGTLSFYMVNKAWVTHLHTFHTKFNEAVY--PAFLIGDAQQKVNGQIKLL
Template: -----------------------------------------------------------------------------------GKLVIWINGDKGYNGLAEVGKKFEKDTGIK-----VTVEHPDKLEEKFPQVAATGDGPDII-----FWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGK----LIAYPIAV-EALSLIYNKD--LLPNP------PKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGG-------------------------------YAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKG-ETAMTINGPWAWSNIDTSKVNYGVTVLPTF-KGQPSKPF-VGVLSAGIDAASPNKELAKEFLENYLLTDEGLEAVNK--DKPLGAVALKSYEEELAKDPR--------IAATMENAQKGEIMPNI--PQMSAFWYAVRTAVINAASGRQTVDEALKDAQTRITRRVFR-----LDMF--------RELTDARR-YWVDVTLATN-NISHAVIA---EDKRQVS--SRNP--------YCTGVLGSQSITSGKHYWEVD-------------VSKKSAWILGVCAGFQSDAMYNIEQNENYQPKYGYWVIGLQEGVKYSVFQDGSSHTPFAPFIVPLSVIICPDRVGVFVDYEACTVSFFNITN----HGFLIY-KFSQCSFSKPVFPYLN-PRKCTVPMTLC


4N7I

A

Unknot

34.76%

200.00%

20.00%

1.10

..Target: DILVVAALGRPFTLGMLYDARNDKLIPGFTLWEDEVIEESTLESSQPSSAFEIIASDSTDDKSSLMDIEASLKASFLGGLVEVGGSAKYLNNQKKFKNQSRVTLQYKATTSFKQLMTNLGTKHVEYSELFENIQATHVVIGILYGANAFFVFDSNKVDSTNVQEIQGQMEAVIKKIPSVEISGKASVQLTGEETDITNSFSCEFHGDFFLTTNPTTFEDAVKTYQQLPQMMGKDNAVPMTVWLVPMVNFYSEAPQLMADSSTPILRKVRNTLEAIVQVQMRCNDALDDPTVNLFTEVQKKLSDFQKICDDHMSKLQATIAKKLFAIRSGDEDESALLNLFEENLQSPFNIESLNMWMEFEEREINVLRSCMDILTKAKPKVIFNQGVLFKGLYDSKVKHALCYVFTNVTKNDVFLNVLNEFLDSPQSRPKKLRPSPKDYWYSYDDIPETMREKAYLFRNLAKEMNNRCVHFFVTAIHNPKQEGAGIHYYRESIQIIDEFTKPYMPGVESIKDRRELQWYDCELTLDPETAHQVLTLSEGNKKAVSGNTKSPTD---HLEKFS-HFQQVMCTKGLSGRHYWELE------WSGYVGAGVTYKGIGRKTSTSDSSLGKNEKSWLFEYSTKSGY--QQIHNSKKTR-VTVSSTGFKL------LGVYLDWPAGTLSFYMVNKAWVTHLHTF-HTKFNEAVYPAFLIGDAQQKVNGQIKLL
Template: -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAYNEW--------KKALFKPAD------------------------------------------------------------------------------------VILDPKTADPILLVSE-DQRSVE-RAKEPQDLPDNPERFNWHYCVLGCESFISGRHYWEVEVGDRKEW----HIGVCSKNVQRK-------------GWV-KMTPENGFWTMGLTDGNKYRTLTEPRTNLKLPKPPKKVGVFLDYETGDISFY--NAVDGSHIHTFLDVSFSEALYPVFRILTLEPTAL-TICPA

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

FKQLMTNLGTKHVE-YSELFENIQATHV

4B3N A Unknot 19.05% 80.95%

IK-----VTVEHPDKLEEKFPQVAATGD

4N7I A Unknot 0.00% 0.00%

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

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

KLIPGFTLWEDEVIEESTLESSQ

4B3N A Unknot 0.00% 0.00%

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

4N7I A Unknot 0.00% 0.00%

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

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

VPMVNFYSEAPQLMADSSTPI

4B3N A Unknot 26.67% 100.00%

FNLQEPYFTWPLIAADGG---

4N7I A Unknot 0.00% 0.00%

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

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

P----SVEISGKASVQLTGEE

4B3N A Unknot 27.27% 63.64%

PFTWDAVRYNGK----LIAYP

4N7I A Unknot 0.00% 0.00%

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

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

LIGDAQQKVNGQ

4B3N A Unknot 16.67% 83.33%

PYLN-PRKCTVP

4N7I A Unknot 0.00% 100.00%

RILTLEPTAL-T

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

QMMGKDNAVPM

4B3N A Unknot 20.00% 100.00%

ALDKELKAKGK

4N7I A Unknot 0.00% 0.00%

-----------

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

EYSTKSGYQQI

4B3N A Unknot 60.00% 100.00%

NYQPKYGYWVI

4N7I A Unknot 20.00% 100.00%

KMTPENGFWTMGL

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

FAIR--SGDEDE

4B3N A Unknot 25.00% 100.00%

IKNKHMNADTDY

4N7I A Unknot 0.00% 0.00%

----------

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

DSP------QSRPKKL

4B3N A Unknot 25.00% 100.00%

DKPLGAVALKSYEEEL

4N7I A Unknot 0.00% 0.00%

-------KKA


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

Sun Jul 23 14:57:10 2017	JOB CREATED : 85e1207e-7bef-4030-8a72-1e2cc49f0f53
Sun Jul 23 19:29:01 2017	STATUS CHANGED : N -> R
Sun Jul 23 19:29:01 2017	INFO : JOB STARTED AT: 2017-07-23 19:29:01.798804
Sun Jul 23 19:29:01 2017	INFO : METHOD: 1
Sun Jul 23 19:29:01 2017	INFO : Precalculated profile found...
Sun Jul 23 19:29:01 2017	INFO : Homologue pool found...
Sun Jul 23 19:29:01 2017	INFO : Verifying structure sequences of homologues...
Sun Jul 23 19:29:26 2017	INFO : Starting homologue filtering...
Sun Jul 23 19:30:01 2017	INFO : Getting structures from PDB...
Sun Jul 23 19:30:09 2017	INFO : Creating modelling alignment...
Sun Jul 23 19:30:09 2017	INFO : Modelling...
Sun Jul 23 22:06:50 2017	INFO : Model 1 built
Sun Jul 23 22:06:50 2017	INFO : 2 gaps will be remodelled
Sun Jul 23 22:38:50 2017	INFO : Validating Calpha distances...
Sun Jul 23 22:38:50 2017	INFO : Model 1 distances correct: True
Sun Jul 23 22:38:50 2017	INFO : Modelling...
Mon Jul 24 00:00:06 2017	INFO : Model 2 built
Mon Jul 24 00:00:06 2017	INFO : 1 gaps will be remodelled
Mon Jul 24 00:21:04 2017	INFO : Validating Calpha distances...
Mon Jul 24 00:21:04 2017	INFO : Model 2 distances correct: True
Mon Jul 24 00:21:04 2017	INFO : Modelling...
Mon Jul 24 02:31:22 2017	INFO : Model 3 built
Mon Jul 24 02:31:22 2017	INFO : 1 gaps will be remodelled
Mon Jul 24 02:50:14 2017	INFO : Validating Calpha distances...
Mon Jul 24 02:50:14 2017	INFO : Model 3 distances correct: True
Mon Jul 24 02:50:14 2017	INFO : Modelling...
Mon Jul 24 05:04:10 2017	INFO : Model 4 built
Mon Jul 24 05:04:10 2017	INFO : 3 gaps will be remodelled
Mon Jul 24 05:41:32 2017	INFO : Validating Calpha distances...
Mon Jul 24 05:41:33 2017	INFO : Model 4 distances correct: False
Mon Jul 24 05:41:33 2017	INFO : Modelling...
Mon Jul 24 07:22:17 2017	INFO : Model 5 built
Mon Jul 24 07:22:17 2017	INFO : 2 gaps will be remodelled
Mon Jul 24 07:46:34 2017	INFO : Validating Calpha distances...
Mon Jul 24 07:46:34 2017	INFO : Model 5 distances correct: True
Mon Jul 24 07:47:20 2017	INFO : Finished modelling
Mon Jul 24 07:47:20 2017	STATUS CHANGED : R -> P
Mon Jul 24 07:47:20 2017	INFO : Checking topology...
Mon Jul 24 08:43:23 2017	INFO : Knot matrices done...
Mon Jul 24 08:50:24 2017	INFO : Some knots found!
Mon Jul 24 08:50:24 2017	INFO : No lassos found...
Mon Jul 24 08:50:24 2017	INFO : Finishing...
Mon Jul 24 08:50:25 2017	INFO : Job done
Mon Jul 24 08:50:25 2017	STATUS CHANGED : P -> F
Mon Jul 24 08:50:25 2017	STATUS CHANGED : F -> F

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