Job name:

1MQS chain A

dbf8fc6c-5c0d-49f7-b878-96576bc462d5
Finished
Models Number of gaps:4 Gap lengths: 21, 19, 16, 13
Model Entanglement Average DOPE-HR (by gap length) Smaller
DOPE-HR 1st gap2nd gap3rd gapgaps
Model 1 Non-trivial -55788

Model 2 Unknot -63440

Model 3 Non-trivial -53734

Model 4 Unknot -54242

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 1 Slipknot S 41+31 325-518 518-547 -- --
Model 3 Slipknot S +31 325-518 518-545 -- --
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 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


3C98

A

Unknot

22.12%

365.66%

39.76%

1.35

..Target: KDISLRDXQISAILKXLFLNKDLNNNDNITTITDDIFNQQEIIWKVLILDIKSTATISSVLRVNDLLKAGITVHSLIKQDRSPLPDVPAIYFVSPTKENIDIIVNDLK---SDKYSEFYINFTSSLPRNLLEDLAQQVSITGKSDK-IKQVYDQYLDFIVTEPELFSLEISNAYLTLNDPKTTEEEITGLCANIADGLFNTVLTINSIPIIRAAKGGPAEIIAEKLGTKLRDFVINTNSSSTSTLQGNDSLERGVLIILDRNIDFASXFSHSWIYQCXVFDIFKLSRNTVTIPLESKENGTDNTTAKPLATKKYDIEPNDFFWXENSHLPFPEAAENVEAALNTYKEEAAEITRKTGVTNISDLDPNSN-NDTVQIQEVVKKLPELTAKKNTIDTHXNIFAALLSQLESKSLDTFFEVEQDPGSTKTRSRFLDILKDGKTNNLEDKLRSFIVLYLTSTTGLPKDFVQNVENYFKENDYD-IN-ALKYVYKLREFXQLS-NXSLQNKSLEDGSDSAFKPSNLTLSGIYGLTEGKLQGGVGSLISGIKKLLPEKKTIPITNVVDAIXDPLNSSQKNLETTDSYLYIDPKITRGSHTRKPKRQSYNKSLVFVVGGGNYLEYQNLQEWAHSQLHNPKKVXYGSTAITTPAEFLNEISRLGASNSS-
Template: ----------------IGL-KAVVGEKIMHDVIKKVKKKGE--WKVLVVDQLSMRMLSSCCKMTDIMTEGITIVEDINKRREPLPSLEAVYLITPSEKSVHSLISDFKDPPTAKYRAAHVFFTDSCPDALFNEL-----VKSRAAKVIKTLTEINIAFLPYESQVYSLDSADSFQSFYSPHKAQMK-NPILERLAEQIATLCATLKEYPAVR----YRGEYKDNALLAQLIQDKLDAYKADDPTMGEGPDKARSQLLILDRGFDPSSPVLHELTFQAMSYD---------LLPIENDVYKYETSGIGEARVKEVLLDEDDDLWIALRH--------------KHIAEVSQEVTR-----SLKDFSSSKRM--MRDLSQMLKKMPQYQKELSKYSTHLHLAEDCMKHYQG-TVDKLCRVEQD----------LAMGTDAEGEKIKDPMRAIVPILLDANV----------------STYDKIRIILLYIFLKNGITEENLNKLIQHAQIPP-EDSEI-ITNMAHLGVPIVTDSTLR----RRSKPERKERISEQTYQLSRWTPIIKDIMEDTIEDKLDTKHYPYISTR------------RSGPRLIIFILGGVSLNEMRCAYE--VTQANGKWEVLIGSTHILTPQKLLDTLKKLNKTDEEI


2XHE

A

Unknot

24.69%

345.43%

55.05%

1.37

..Target: KDISLRDXQISAILKXLFLNKDLNNNDNITTITDDIFNQQEIIWKVLILDIKSTATISSVLRVNDLLKAGITVHSLIKQDRSPLPDVPAIYFVSPTKENIDIIVNDL--KSDKYSEFYINFTSSLPRNLLEDLAQQVSITGKSDK-IKQVYDQYLDFIVTEPELFSLEISNAYLTLNDPKTTEEEITGLCANIADGLFNTVLTINSIPIIRAAKGGPAEIIAEKLGTKLRDFVINTNSSSTSTLQGNDSLERGVLIILDRNIDFASXFSHSWIYQCXVFDIFKLSRNTVTIPLESKENGTDNTTAKPLATKKYDIEPNDFFWXENSHLPFPEAAENVEAALNTYKEEAAEITRKTGVTNISDLDPNSNNDTVQIQEVVKKLPELTAKKNTIDTHXNIFAALLSQLESKSLDTFFEVEQ------DPGSTKTRS---RFLDILKDGKTNNLEDKLRSFIVLYLTSTTGLPKDFVQNVENYFKENDYDINALKYVYKLREFXQLSNXSLQNKSLEDGSDSAFKPSNLTLSGIYGLTEGKLQGGVGSLISGIKKLLPEKKTIPITNVVDAIXDPLNSSQKNLET----TDSYLYIDPKITRGSHTRKPKRQSYNKSLVFVVGGGNYLEYQNLQEWAHSQLHNPKKVXYGSTAITTPAEFLNEISRLGASNSS
Template: -HMSLK----SAV-KTVLTN-------SLRSVADG------GDWKVLVVDKPALRMISECARMSEILDLGVTVVEDVSKQRKVLPQFHGVYFIEPTEENLDYVIRDFADRTPTYEAAHLFFLSPVPDALMAKLA-----SAKAVKYVKTLKEINTLFIPKEHRVFTLNEPHGLVQYYGSRSSSYNIDHLVRRLS----TLCTTMNVAPIVRYSSTSTPG--TERMAMQLQK-EIDM-SVSQGLINAREGKLKSQFLILDRAVDLKSPLVHELTYQAAAYDLLNI-ENDI------YSYSTVDAGGRE-QQRQVVLGEDDDIWLQMRHLHISEVFRKVK---SSFDEFCVSARRLQG---LRD-SQQGEGGAGALKQMLKDLPQHREQMQKYSLHLDMSNA-INMAFSSTIDSCTKAEQNIVTEEEQDGNKVRDFIGEVASVVVDRRVST-EDKLRC-LMLCVLAKNG-----------------------------TSSHELNNL-LDNANIATPSRSAI--YNLEMLGATVVAD--RRGRKPKTMKRIERDMPYVLS-RWTPIVKDLMEYIATGQLDLESYPAVRDGPSVVQPK-----ESAKPK------LFVFINGTVSYNEIRCAYE--VSQ-SSGYEVYIGAHNIATPAEFVELVSLL---DKA


4BX8

B

Unknot

23.86%

335.51%

70.12%

1.47

..Target: KDISLRDXQISAILKXLFLNKDLNNNDNITTITDDIFNQQEIIWKVLILDIKSTATISSVLRVNDLLKAGITVHSLIKQDRSPLPDVP-AIYFVSPTKENIDIIV-NDLKSDKY---SEFYINFTSSLPRNLL-EDLAQQVSITGKSDKIKQVYDQYLDFIVTEPELFSLEISNAYLTLNDPKTTEEEITGLCANIADGLFNTVLTINSIPIIRAAKGGPAEIIAEKLGTKLRDFVINTNSSSTSTLQGNDSLERGVLIILDRNIDFASXFSHSWIYQCXVFDIFKLSRNTVTIPLE---SKENGTDNTTAKPLATKKYDIEPNDFFWXENSHLPFPEAAENVEAALNTYKEEAAEITRKTGVTNISDLDPNSNNDTVQIQEVVKKLPELTAKKNTIDTHXNIFAALLSQLESKSLDTFFEVEQDPGSTKTRSRFLDILKDGKTNN-LED---------KLRSFIVLYLTSTTGLPKDFVQNVENYFK---------ENDYDINALKYVYKLR-EFXQLSNXSLQNKSLEDGSDSAFKPSNLTLSGIYGLTEGKLQGGVGSLISGIKKLLPEKKTIPITNVVDAIXDPLNSSQKNLETTDSYLYIDPKITRGSH--TRKP--KRQSYNK-SLVFVVGGGNYLEYQNLQEWAHSQLHNPKKVXYGSTAITTPAEFLNEISRLGA--SNSS
Template: ------AAHLSYGRVNLNVLREAVRRE-LREFLDKCAGSKAIVW-----DEYLTGPFGLIAQYSLLKEHEVEKMFTLKGNRLPAADVKNIIFFVRPRLELMDIIAENVLSEDRRGPTRDFHILFVPR--RSLLCEQRLKDLGVLG-SFIHREEY--SLDLIPFDGDLLSMESEGAF----KECYLEGDQTSL-YHAAKGLMTLQALYGTIPQI-FGKGECARQVANMMIRMKREF----TGSQNSIFPVFDN-----LLLLDRNVDLLTPLATQLTYEGLIDEIYGIQNSYVKLPPEKFAPKKQG-DGGKDLPTEAKKLQLNSAEELYAEIRDKNF--------------NAVGSVLSKKAKIISAAFEERHN--------------PHMQAARGSLANHTSI-AELIKDV--TTSEDFF------DKLTVEQEFMSGIDTDKVNNYIEDCIAQKHSLIKVLRLVCLQSVCNSGL----KQKVLDYYKREILQTYGYEHILTLHNLEKAGLLKPQTGGRNNYPTIRKTLRLWMDDVNEQNPTDISYVY--------SGYAPLSVRLAQLL---------------------SRPGWRSIEEVLRILP----GPHFEERQPLP-----NRVTLIFFLGGVTFAEIAALR--FLSQLED-----GGTEYVIATTKLMNGTSWIEALMEKPF

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

RKTGVTNISDLDPNSN-NDTVQIQEVVK

3C98 A Unknot 4.76% 76.19%

R-----SLKDFSSSKRM--MRDLSQMLK

2XHE A Unknot 9.52% 80.95%

RLQG---LRD-SQQGEGGAGALKQMLK

4BX8 B Unknot 0.00% 57.14%

KKAKIISAAFEERHN------------

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

KSLEDGSDSAFKPSNLTLSGIYGLT

3C98 A Unknot 21.05% 89.47%

AQIPP-EDSEI-ITNMAHLGVPIVT

2XHE A Unknot 31.58% 89.47%

ANIATPSRSAI--YNLEMLGATVVA

4BX8 B Unknot 15.79% 100.00%

KTLRLWMDDVNEQNPTDISYVY---

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

TIPLESKENGTDNTTAKPLATK

3C98 A Unknot 6.25% 100.00%

LLPIENDVYKYETSGIGEARVK

2XHE A Unknot 6.25% 75.00%

------YSYSTVDAGGRE-QQR

4BX8 B Unknot 31.25% 93.75%

KLPPEKFAPKKQG-DGGKDLPTEAK

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

TNSSSTSTLQGNDSLERGV

3C98 A Unknot 7.69% 100.00%

AYKADDPTMGEGPDKARSQ

2XHE A Unknot 7.69% 100.00%

M-SVSQGLINAREGKLKSQ

4BX8 B Unknot 23.08% 84.62%

-TGSQNSIFPVFDN-----


Models
Similarity profile
Modelling alignment
Raw knot fingerprint matrices:
Model_1
Model_3

Sun Jul 23 14:58:52 2017	JOB CREATED : dbf8fc6c-5c0d-49f7-b878-96576bc462d5
Sun Jul 23 21:59:01 2017	STATUS CHANGED : N -> R
Sun Jul 23 21:59:01 2017	INFO : JOB STARTED AT: 2017-07-23 21:59:01.898500
Sun Jul 23 21:59:01 2017	INFO : METHOD: 1
Sun Jul 23 21:59:01 2017	INFO : Precalculated profile found...
Sun Jul 23 21:59:01 2017	INFO : Homologue pool found...
Sun Jul 23 21:59:01 2017	INFO : Verifying structure sequences of homologues...
Sun Jul 23 21:59:42 2017	INFO : Starting homologue filtering...
Sun Jul 23 22:00:53 2017	INFO : Getting structures from PDB...
Sun Jul 23 22:01:12 2017	INFO : Creating modelling alignment...
Sun Jul 23 22:01:12 2017	INFO : Modelling...
Sun Jul 23 23:26:29 2017	INFO : Model 1 built
Sun Jul 23 23:26:29 2017	INFO : 2 gaps will be remodelled
Sun Jul 23 23:50:41 2017	INFO : Validating Calpha distances...
Sun Jul 23 23:50:41 2017	INFO : Model 1 distances correct: True
Sun Jul 23 23:50:41 2017	INFO : Modelling...
Mon Jul 24 00:47:18 2017	INFO : Model 2 built
Mon Jul 24 00:47:18 2017	INFO : Validating Calpha distances...
Mon Jul 24 00:47:18 2017	INFO : Model 2 distances correct: True
Mon Jul 24 00:47:18 2017	INFO : Modelling...
Mon Jul 24 01:58:41 2017	INFO : Model 3 built
Mon Jul 24 01:58:41 2017	INFO : 1 gaps will be remodelled
Mon Jul 24 02:07:58 2017	INFO : Validating Calpha distances...
Mon Jul 24 02:07:58 2017	INFO : Model 3 distances correct: True
Mon Jul 24 02:07:58 2017	INFO : Modelling...
Mon Jul 24 03:51:10 2017	INFO : Model 4 built
Mon Jul 24 03:51:10 2017	INFO : 1 gaps will be remodelled
Mon Jul 24 04:06:36 2017	INFO : Validating Calpha distances...
Mon Jul 24 04:06:36 2017	INFO : Model 4 distances correct: True
Mon Jul 24 04:06:36 2017	INFO : Modelling...
Mon Jul 24 05:48:13 2017	INFO : Model 5 built
Mon Jul 24 05:48:13 2017	INFO : 1 gaps will be remodelled
Mon Jul 24 05:59:53 2017	INFO : Validating Calpha distances...
Mon Jul 24 05:59:53 2017	INFO : Model 5 distances correct: False
Mon Jul 24 06:00:38 2017	INFO : Finished modelling
Mon Jul 24 06:00:38 2017	STATUS CHANGED : R -> P
Mon Jul 24 06:00:38 2017	INFO : Checking topology...
Mon Jul 24 06:56:41 2017	INFO : Knot matrices done...
Mon Jul 24 06:59:54 2017	INFO : Some knots found!
Mon Jul 24 06:59:54 2017	INFO : No lassos found...
Mon Jul 24 06:59:54 2017	INFO : Finishing...
Mon Jul 24 06:59:55 2017	INFO : Job done
Mon Jul 24 06:59:55 2017	STATUS CHANGED : P -> F
Mon Jul 24 06:59:55 2017	STATUS CHANGED : F -> F

GapRepairer | Interdisciplinary Laboratory of Biological Systems Modelling