Job name:

3WPHA_dbase(3WPH chain A)

5737a12a-7b9d-4b0c-b5bd-0568e85f9bc8
Finished
Models Number of gaps:5 Gap lengths: 36, 7, 7, 7, 4
Model Entanglement Average DOPE-HR (by gap length) Smaller
DOPE-HR 1st gap2nd gap3rd gapgaps
Model 1 Non-trivial -61166

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 52+31 421-496 496-782 -- --
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
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


3W3G

A

Unknot

36.44%

263.89%

56.75%

1.36

..Target: TLPAFLPC-ELKPH--GLVDCNWLFLKSVPRFSAAASCSNITRLSLISNRIHHLHNSDFVHLSNLRQLNLKWNCPPTGLSPLHFSCHMTIEPRTFLAMRTLEELNLSYNGITTVPR-LPSSLVNLSLSHTNILVLDANSLAGLYSLRVLFMDGNCYYKNPCTGAVKVTPGALLGLSQLTHLSLKYNNLTKVPRQLPPSLEYLLVSYNLIVKLGPEDLAQLTSLRVLDVGGNCRRCDHAPNPCIEC-GQKSLHLHPETFHHLSHLEGLVLKDSSLHTLNSSWFQGLVQLSVLDLSENFLYESITHTNAFQNLTRLRKLNLSFNYRKKVSFARLHLASSFKNLVSLQELNMNGIFFRLLNKYTLRWLADLPKLHTLHLQMNFINQAQLSIFGTFRALRFVDLSDNRISGPSTLSEATPEEADDAEQEELLSA-DPHP--APLSTPASKNFMDRCKNFKFTMDLSRNNLVTIKPEMFVQLSRLQCLSLSHNSIAQAVNGSQFLPLTNLQVLDLSHNKLDLYHWKSFSELPQLQALDLSYNSQPFSMKGIGHQFSFVTHLSMLQSLSLAHNDIHTRVSSH-LNSNSVRFLDFSGNGMGRMW-DEGGLYLHFFQGLSGLLKLDLSQNNLHILRPQNLDNLPKSLKLLSLRDNYLSFFNWTSLSFLPNLEVLDLAGNQLKALTQGTLPNGTLLQKLDVSSNSIVSVVPAFFALAVELKEVNLSHNILKTVDRSWF-GPIVMQLTVLDVRSNPLHCAC----GAAFVDLLLEVQTKVPGLANGVKCGSPGQLQGRSIFAQDLRLC
Template: ---RSYPCDEKKQNDSVIAECSNRRLQEVPQ----TVGKYVTELDLSDNFITHITNESFQGLQNLTKINLNHN-PNV--------NGLNITDGAFLNLKNLRELLLEDNQLPQIPSGLPESLTELSLIQNNIYNITKEGISRLINLKNLYLAWNCYFNKVCE-KTNIEDGVFETLTNLELLSLSFNSLSHVPPKLPSSLRKLFLSNTQIKYISEEDFKGLINLTLLDLSGNCPRCFNAPFPCVPCDGGASINIDRFAFQNLTQLRYLNLSSTSLRKINAAWFKNMPHLKVLDLEFNYLVGEIASGAFLTMLPRLEILDLSFNYIKGSYPQHINISRNFSKLLSLRALHLRGYVFQELREDDFQPLMQLPNLSTINLGINFIKQIDFKLFQNFSNLEIIYLSENRIS-PLVK-------------------FDPHSNFYHFTRPLIK---PQCAAYGKALDLSLNSIFFIGPNQFENLPDIACLNLSANSNAQVLSGTEFSAIPHVKYLDLTNNRLDFDNASALTELSDLEVLDLSYNSHYFRIAGVTHHLEFIQNFTNLKVLNLSHNNIYTLTDKYNLESKSLVELVFSGNRLDILWNDDDNRYISIFKGLKNLTRLDLSLNRLKHIPNEAFLNLPASLTELHINDNMLKFFNWTLLQQFPRLELLDLRGNKLLFLTDSLSDFTSSLRTLLLSHNRISHLPSGFLSEVSSLKHLDLSSNLLKTINKSALETKTTTKLSMLELHGNPFECTCDIGDFRRWMDEHLNV--KIPRLVD-VICASPGDQRGKSI--VSLEL-


4PUF

A

Unknot

26.54%

307.14%

87.30%

1.25

..Target: TL---------PAFLPC--ELKPHGLVDC----------NWLFLKSVPRFSAAASCSNITRLSLISNRIHHLHNSDFVHLSNLRQLNLKWNCPPTGLSPLHF-SCHMTIEPRTFLAMRTLEELNLSYNGITTVP-RLPSSLVNLSLSHTNILVLDANSLAGLYSLRVLFMDGNCYYKNPCTGAVKVTPGALLGLSQLTHLSLKYNNLTKVPRQLPPSLEYLLVSYNLIVKLGPEDLAQLTSLRVLDVGGNCRRCDHAPNPCIECGQKSLHLHPETFHHLSHLEGLVLKDSSLHTLNSSWFQGLVQLSVLDLSEN---FLYESITHTNAFQNLTRLRKLNLSFNYRKKVSFARLHLASSFKNLVSLQE----LNMNGIF-FRLLNKYTLRWLADLPKLHTLHLQMNFINQAQLSIFGTFRALRFVDLSDNRISGPSTLSEATPEEADDAEQEELLSADPHPAPLSTPASKNFMDRCKNFKFTMDLSRNNLVTIKPEMFVQLSRLQCLSLSHNSIAQAVNGSQFLPLTNLQVLDLSHNKLDLYHWKSFSELPQLQALDLSYNSQPFSMKGIGHQFSFVTHLSMLQSLSLAHNDI-HTRVSSHLNSNSVRFLDFSGNGMGRMWDEGGLYLHFFQGLSGLLKL-----DLSQNNLHILRPQNLDNLPKSLKLLSLRDNYLSFFNWTSLSFLPNLEVLDLAGNQLKALTQGTLPNGTLLQKLDVSSNSIVSVVPAFFALAVELKEVNLSHNILKTVDRSWFGPIVMQLTVLDVRSNPLHCACGAAFVDLLLEV-QTKVPGLANGVKCGSPGQLQGRSIFAQDLRLC
Template: ELIWSEWVKEAPAKEAANREEAVQRMRDCLKNNKTELRLKILGLTTIP----AYIPEQITTLILDNNELKSL-------PENL-QGNIK---------TLYANSNQLTSIPAT--LPDTIQEMELSINRITELPERLPSALQSLDLFHNKISCLPEN------------LPEELRYLSVYDNSIRTLP-AHLP-SEITHLNVQSNSLTALPETLPPGLKTLEAGENALTSL-PASLPP--ELQVLDV----------------------------------------------------------------SKNQITVLPETLPPTITTLDVSRNALTNLPEN----LPAALQIMQASRNNLVRLPESLPHFRGEGPQPTRIIVEYNPFSERTIQNMQRLMSSVDYQGPRVLFAMGDFSIVR--------VTRP--LHQAVQGWLTSLEEEDVNQWRAFEAEANAAAFSGFLD------YLGDTQNTRHPDFKEQVSAWLMR-----LAEDS---ALRETVFIIAMNATISCEDRVTL-AYHQMQEATL-----------------VHDAERGAFDSHLA---ELIMAGREIFRLEQIESLAREKVKRLFFI--------DEVEVFLGFQNQLRESLSLTTMTRDMRFYNVSGITESDLDEAEIRIKMAENRD----FHKWFAL-----------WGPWHKVL---------------------ERIAPE------EWREMMAKRDECIETD-EYQSRVNAELE--DLR---------AIGIKIMEEINQTLFTEIMENI-------LLKKEVSSLMSAYW


1G9U

A

Unknot

37.11%

176.98%

30.56%

1.26

..Target: TLPAFLPCELKPHGLVDCNWLFLKSVPRFSAAASCSNITRLSLISNRIHHLHNSDFVHLSNLRQLNLKW--NCPPTGLSPLHFSCHMTIEPRTFLAMRTLEELNLSYNGITTVPRLPSSLVNLSLSHTNILVLDANSLAGLYSLRVLFMDGNCYYKNPCTGAVKVTPGALLGLSQLTHLSLKYNNLTKVPRQLPPSLEYLLVSYNLIVKLGPEDLAQLTSLRVLDVGGNCRRCDHAPNPCIECGQKSLHLHPETFHHLSHLEGLVLKDSSLHTLNSSWFQGLVQLSVLDLSENFLYESITHTNAFQNLTRLRKLNLSFNYRKKVSFARLHLASSFKNLVSLQELNMNGIFFRLLNKYTLRWLADLPKLHTLHLQMNFINQAQLSIFGTFRALRFVDLSDNRISGPSTLSEATPEEADDAEQEELLSADPHPAPLSTPASKNFMDRCKNFKFTMDLSRNNLVTIKPEMFVQLSRLQCLSLSHNSIAQAVNGSQFLP-LTNLQVLDLSHNKLDLYHWKSFSEL-PQLQALDLSYNSQPFSMKGIGHQFSFVTHLSMLQSLSLAHNDIHTRVSSHLNSNSVRFLDFSGNGMGRMWDEGGLYLHFFQGLSGLLKLDLSQNNLHILRPQNLDNLPKSLKLLSLRDNYLSFFNWTSLSFL-PNLEVLDLAGNQLKALTQGTLPNGTLLQKLDVSSNSIVSVVPAFFALAVELKEVNLSHNILKTVDRSWFGPIVMQ-LTVLDVRSNPLHCACGAAFVDLLLEVQTKVPGLANGVKCGSPGQLQGRSIFAQDLRL-C
Template: -----------------------KSKTEYYNAWS---------------------------------EWERNAPP-GNGEQR---EMAVSRLRDCLDRQAHELELNNLGLSSLPELP--------PHLESLVASCNSLT-----------------------------ELPELPQSLKSLLVDNNNLKALSDLPPLLEYLGVSNNQLEKL-PE------------------------------------------------------------LQNSSF-----LKIIDVDNN-------------SLKKLPDLPPSLEF----------IAAGNNQLEELPE------------------LQNLPFLTAIY------------------------------------------------------AD-----------------------------NNSLKKLPD----------LPLSLESIVAGNNILEELPELQNLPFLTTIYADNNLL--KTLPDLPPSLEAL----------------------------------------------------------------------------------------NVRDNYLTDLPELPQSLTFLDVSEN-----IFSGLSELPPNLYYLNASSNEIRSLCD--LP--PSLEELNVSNNKLIE-LP---ALPPRLERLIASFNHLAEV------PELPQNLKQLHVEYNP----------------LREFPDIPESV---------------EDLRMNS

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

PSTLSEATPEEADDAEQEELLSA-DPHP--APLSTPASKNFMDRC

3W3G A Unknot 13.89% 38.89%

PLVK-------------------FDPHSNFYHFTRPLIK---PQC

4PUF A Unknot 19.44% 100.00%

P--LHQAVQGWLTSLEEEDVNQWRAFEAEANAAAFSGFLD--

1G9U A Unknot 5.56% 5.56%

----------------------AD------------------

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

PTGLSPLHFSCHM

3W3G A Unknot 0.00% 0.00%

NV--------NGL

4PUF A Unknot 28.57% 71.43%

-----TLYANSNQL

1G9U A Unknot 0.00% 71.43%

P-GNGEQR---EM

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

FNYRKKVSFARLH

3W3G A Unknot 14.29% 100.00%

FNYIKGSYPQHIN

4PUF A Unknot 14.29% 57.14%

EN----LPAALQI

1G9U A Unknot 0.00% 0.00%

LEF----------

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

YNSQPFSMKGIGH

3W3G A Unknot 28.57% 100.00%

YNSHYFRIAGVTH

4PUF A Unknot 0.00% 28.57%

--------VHDAE

1G9U A Unknot 0.00% 0.00%

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

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

PRFSAAASCS

3W3G A Unknot 0.00% 25.00%

PQ----TVGK

4PUF A Unknot 25.00% 50.00%

P----AYIPE

1G9U A Unknot 25.00% 100.00%

TEYYNAWS--


Models
Similarity profile
Modelling alignment
Raw knot fingerprint matrices:
Model_1

Sun Jul 23 14:59:48 2017	JOB CREATED : 5737a12a-7b9d-4b0c-b5bd-0568e85f9bc8
Mon Jul 24 02:20:02 2017	STATUS CHANGED : N -> R
Mon Jul 24 02:20:02 2017	INFO : JOB STARTED AT: 2017-07-24 02:20:02.170489
Mon Jul 24 02:20:02 2017	INFO : METHOD: 1
Mon Jul 24 02:20:02 2017	INFO : Precalculated profile found...
Mon Jul 24 02:20:02 2017	INFO : Homologue pool found...
Mon Jul 24 02:20:02 2017	INFO : Verifying structure sequences of homologues...
Mon Jul 24 02:35:53 2017	INFO : Starting homologue filtering...
Mon Jul 24 02:37:06 2017	INFO : Getting structures from PDB...
Mon Jul 24 02:37:31 2017	INFO : Creating modelling alignment...
Mon Jul 24 02:37:31 2017	INFO : Modelling...
Mon Jul 24 03:55:00 2017	INFO : Model 1 built
Mon Jul 24 03:55:00 2017	INFO : 1 gaps will be remodelled
Mon Jul 24 04:21:10 2017	INFO : Validating Calpha distances...
Mon Jul 24 04:21:10 2017	INFO : Model 1 distances correct: False
Mon Jul 24 04:21:10 2017	INFO : Modelling...
Mon Jul 24 05:40:20 2017	INFO : Model 2 built
Mon Jul 24 05:40:20 2017	INFO : 1 gaps will be remodelled
Mon Jul 24 06:05:10 2017	INFO : Validating Calpha distances...
Mon Jul 24 06:05:10 2017	INFO : Model 2 distances correct: False
Mon Jul 24 06:05:10 2017	INFO : Modelling...
Mon Jul 24 07:13:55 2017	INFO : Model 3 built
Mon Jul 24 07:13:55 2017	INFO : 1 gaps will be remodelled
Mon Jul 24 07:35:12 2017	INFO : Validating Calpha distances...
Mon Jul 24 07:35:12 2017	INFO : Model 3 distances correct: False
Mon Jul 24 07:35:12 2017	INFO : Modelling...
Mon Jul 24 08:38:05 2017	INFO : Model 4 built
Mon Jul 24 08:38:05 2017	INFO : 1 gaps will be remodelled
Mon Jul 24 08:58:54 2017	INFO : Validating Calpha distances...
Mon Jul 24 08:58:54 2017	INFO : Model 4 distances correct: False
Mon Jul 24 08:58:54 2017	INFO : Modelling...
Mon Jul 24 09:56:43 2017	INFO : Model 5 built
Mon Jul 24 09:56:43 2017	INFO : 1 gaps will be remodelled
Mon Jul 24 10:14:13 2017	INFO : Validating Calpha distances...
Mon Jul 24 10:14:13 2017	INFO : Model 5 distances correct: False
Mon Jul 24 10:14:13 2017	INFO : None of the models passed the CA-distance validation
Mon Jul 24 10:14:13 2017	ERROR : Modelling already was de novo, finishing with error
Mon Jul 24 10:14:13 2017	STATUS CHANGED : R -> E
Mon Jul 24 16:54:02 2017	STATUS CHANGED : N -> R
Mon Jul 24 16:54:02 2017	INFO : JOB STARTED AT: 2017-07-24 16:54:02.032559
Mon Jul 24 16:54:02 2017	INFO : METHOD: 1
Mon Jul 24 16:54:02 2017	INFO : Precalculated profile found...
Mon Jul 24 16:54:02 2017	INFO : Homologue pool found...
Mon Jul 24 16:54:02 2017	INFO : Verifying structure sequences of homologues...
Mon Jul 24 17:04:11 2017	INFO : Starting homologue filtering...
Mon Jul 24 17:05:05 2017	INFO : Getting structures from PDB...
Mon Jul 24 17:05:25 2017	INFO : Creating modelling alignment...
Mon Jul 24 17:05:25 2017	INFO : Modelling...
Mon Jul 24 18:03:40 2017	INFO : Model 1 built
Mon Jul 24 18:03:40 2017	INFO : 1 gaps will be remodelled
Mon Jul 24 19:31:24 2017	INFO : Validating Calpha distances...
Mon Jul 24 19:31:24 2017	INFO : Model 1 distances correct: False
Mon Jul 24 19:31:24 2017	INFO : Modelling...
Mon Jul 24 20:30:16 2017	INFO : Model 2 built
Mon Jul 24 20:30:16 2017	INFO : 1 gaps will be remodelled
Mon Jul 24 21:57:43 2017	INFO : Validating Calpha distances...
Mon Jul 24 21:57:43 2017	INFO : Model 2 distances correct: False
Mon Jul 24 21:57:43 2017	INFO : Modelling...
Mon Jul 24 22:54:58 2017	INFO : Model 3 built
Mon Jul 24 22:54:58 2017	INFO : 1 gaps will be remodelled
Tue Jul 25 00:24:21 2017	INFO : Validating Calpha distances...
Tue Jul 25 00:24:21 2017	INFO : Model 3 distances correct: False
Tue Jul 25 00:24:21 2017	INFO : Modelling...
Tue Jul 25 01:23:14 2017	INFO : Model 4 built
Tue Jul 25 01:23:14 2017	INFO : 1 gaps will be remodelled
Tue Jul 25 02:50:34 2017	INFO : Validating Calpha distances...
Tue Jul 25 02:50:34 2017	INFO : Model 4 distances correct: False
Tue Jul 25 02:50:34 2017	INFO : Modelling...
Tue Jul 25 03:46:35 2017	INFO : Model 5 built
Tue Jul 25 03:46:35 2017	INFO : 1 gaps will be remodelled
Tue Jul 25 05:11:40 2017	INFO : Validating Calpha distances...
Tue Jul 25 05:11:40 2017	INFO : Model 5 distances correct: False
Tue Jul 25 05:11:40 2017	INFO : None of the models passed the CA-distance validation
Tue Jul 25 05:11:40 2017	ERROR : Modelling already was de novo, finishing with error
Tue Jul 25 05:11:40 2017	STATUS CHANGED : R -> E
Tue Jul 25 10:07:01 2017	STATUS CHANGED : N -> R
Tue Jul 25 10:07:01 2017	INFO : JOB STARTED AT: 2017-07-25 10:07:01.939181
Tue Jul 25 10:07:01 2017	INFO : METHOD: 1
Tue Jul 25 10:07:01 2017	INFO : Precalculated profile found...
Tue Jul 25 10:07:01 2017	INFO : Homologue pool found...
Tue Jul 25 10:07:01 2017	INFO : Verifying structure sequences of homologues...
Tue Jul 25 10:16:54 2017	INFO : Starting homologue filtering...
Tue Jul 25 10:17:46 2017	INFO : Getting structures from PDB...
Tue Jul 25 10:18:05 2017	INFO : Creating modelling alignment...
Tue Jul 25 10:18:05 2017	INFO : Modelling...
Tue Jul 25 11:13:12 2017	INFO : Model 1 built
Tue Jul 25 11:13:12 2017	INFO : 1/5 gaps will be remodelled
Tue Jul 25 11:52:21 2017	INFO : Validating Calpha distances...
Tue Jul 25 11:52:21 2017	INFO : Model 1 distances correct: True
Tue Jul 25 11:52:21 2017	INFO : Modelling...
Tue Jul 25 12:48:22 2017	INFO : Model 2 built
Tue Jul 25 12:48:22 2017	INFO : 1/5 gaps will be remodelled
Tue Jul 25 13:31:13 2017	INFO : Validating Calpha distances...
Tue Jul 25 13:31:13 2017	INFO : Model 2 distances correct: False
Tue Jul 25 13:31:13 2017	INFO : Modelling...
Tue Jul 25 14:29:49 2017	INFO : Model 3 built
Tue Jul 25 14:29:49 2017	INFO : 1/5 gaps will be remodelled
Tue Jul 25 15:14:01 2017	INFO : Validating Calpha distances...
Tue Jul 25 15:14:01 2017	INFO : Model 3 distances correct: False
Tue Jul 25 15:14:01 2017	INFO : Modelling...
Tue Jul 25 16:12:17 2017	INFO : Model 4 built
Tue Jul 25 16:12:17 2017	INFO : 1/5 gaps will be remodelled
Tue Jul 25 16:52:10 2017	INFO : Validating Calpha distances...
Tue Jul 25 16:52:10 2017	INFO : Model 4 distances correct: False
Tue Jul 25 16:52:10 2017	INFO : Modelling...
Tue Jul 25 17:48:12 2017	INFO : Model 5 built
Tue Jul 25 17:48:12 2017	INFO : 1/5 gaps will be remodelled
Tue Jul 25 18:27:43 2017	INFO : Validating Calpha distances...
Tue Jul 25 18:27:43 2017	INFO : Model 5 distances correct: False
Tue Jul 25 18:27:54 2017	INFO : Finished modelling
Tue Jul 25 18:27:54 2017	STATUS CHANGED : R -> P
Tue Jul 25 18:27:54 2017	INFO : Checking topology...
Wed Jul 26 09:33:03 2017	INFO : Knot matrices done...
Wed Jul 26 09:33:51 2017	INFO : Some knots found!
Wed Jul 26 09:33:51 2017	INFO : No lassos found...
Wed Jul 26 09:33:51 2017	INFO : Finishing...
Wed Jul 26 09:33:52 2017	INFO : Job done
Wed Jul 26 09:33:52 2017	STATUS CHANGED : P -> F
Wed Jul 26 09:33:52 2017	STATUS CHANGED : F -> F

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