| Model | Type | Knot core | Slipknot | Lasso | Piercing | Show | |||
|---|---|---|---|---|---|---|---|---|---|
| range | loop range | loop | position | in JSmol | |||||
| Model 1 | Knot | K +31 | 307-565 | -- | -- | -- | |||
| Lasso | SL 2++C | -- | -- | 113-422 | |||||
| None | |||||||||
| 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 | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|
3SJC |
F |
Unknot |
28.99% |
149.15% |
47.44% |
1.31 |
..Target: MQ------FLQNIPPYLFFTGKGGVGKTSISCATAIRLA--EQGKRVLLVSTDPASNVGQVFSQTIGNTIQAIASVPGLSALEIDPQAAAQQYRARIVDPIKGVLPDDVVSSINEQLSGACTTEIAAFDEFTGLLTDASLLTRFDHIIFDTAPTGHTIRLLQLPGAWSSFIDSNPEGASCLGPMAGLEKQREQYAYAVEALSDPKRTRLVLVARLQKSTLQEVARTHLELAAIGLKNQYLVINGVLPKTEAANDTLAAAIWEREQEALANLPADLAGLPTDTLFLQPVNMVGVSALSRLLSTQPVASPSSDEYLQQRPDIPSLSALVDDIARNEHGLIMLMGKGGVGKTTMAAAIAVRLADMGFDVHLTTSDPAAHLSMTLNGSLNNLQVSRIDPHEETERYRQHVLETKGKELDEAGKRLLEEDLRSPCTEEIAVFQAFSRVIREAGKRFVVMDTAPTGHTLLLLDATGAYHREIAKKMGE-KGHFTTPMMLLQDPERTKVLLVTLPETTPVLEAANLQADLERAGIHPWGWIINNSL---SIADTRSPLLRMRAQQE-LPQIESVKRQHASRVALVPVLASEPTGIDKL------------KQLAGH--HHHHH |
||||
3IDQ |
A |
Unknot |
35.29% |
72.73% |
36.36% |
1.43 |
..Target: ---MQFLQNIPPYLFFTGKGGVGKTSISCATAIRLA--EQGKRVLLVSTDPASNVGQVFSQTIGNTIQAIASVPGLSALEIDPQAAAQQYRARIVDPIKGVLPDDVVSSINEQLSGACTTEIAAFDEFTGLLTDASLLTRFDHIIFDTAPTGHTIRLLQLPGAWSSFIDS-NPEGASCLGPMAGLEKQREQYAYAVEALSDPKRTRLVLVARLQKSTLQEVARTHLELAAIGLKNQYLVINGVLPKTEAANDTLAAAIWEREQEALANLPADLAGLPTDTLFLQPVNMVGVSALSRLLSTQPVASPSSDEYLQQRPDIPSLSALVDDIARNEHGLIMLMGKGGVGKTTMAAAIAVRLADMGFDVHLTTSDPAAHLSMTL--NGSLNNLQVSRIDPHEETERYRQHVLETKGKELDEAGKRLLEEDLRSPCTEEIAVFQAFSRVIREAGKRFVVMDTAPTGHTLLLLDATGAYHREIAKKMGEKGHFTTPMMLLQDPERTKVLLVTLPETTPVLEAANLQADLERAGIHPWGWIINNSLSIADTRSPLLRMRAQQELPQIESVKRQHASRVALVPVLASEPTGIDKLKQLAG-HHHHHH |
||||
3IO3 |
A |
Unknot |
30.87% |
92.31% |
7.69% |
1.22 |
..Target: --------MQFLQNIP-PYLFFTGKGGVGKTSISCATAIR--LAEQGKRVLLVSTDPASNVGQVFSQTIGNTIQAIASVPGLSALEIDPQAAAQQYRARIVDPIKGVLPDDVVSSINEQLSGACTTEIAAFDEFTGLLTDASLLTRFDHIIFDTAPTGHTIRLLQLPGAWSSFIDSNPEGASCLGPMAGLEKQREQYAYAVEALSDPKRTRLVLVARLQKSTLQEVARTHLELAAIGLKNQYLVINGVLPKTEAANDTLAAAIWEREQEALANLPADLAGLPTDTLFLQPVNMVGVSALSRLLSTQPVASPSSDEYLQQRPDIPSLSALVDDIARNEHGLIMLMGKGGVGKTTMAAAIAVRLADMGFDVHLTTSDPAAHLSMTLNGSLNNLQVSRIDPHEETERYRQHVLETKGKELDEAGKRLLEEDLRSPCTEEIAVFQAFSRVIREAGKRFVVMDTAPTGHTLLLLDATGAYHREIAKKMGEKGHFTTPMMLLQDPERTKVLLVTLPETTPVLEAANLQADLERAGIHPWGWIINNSLSIADTRSPLLRMRAQQELPQIESVKRQHASRVALVPVLASEPTGIDKLKQLAGHHHHHH |
||||
3ZS9 |
A |
Unknot |
31.40% |
66.67% |
22.22% |
1.06 |
..Target: MQ------FLQNIPPYLFFTGKGGVGKTSISCATAIRLA--EQGKRVLLVSTDPASNVGQVFSQTIGNTIQAIASVPGLSALEIDPQAAAQQYR--ARIVDPIKGVLPDDVVSSINEQLSGACTTEIAAFDEFTGLLTDASLLTRFDHIIFDTAPTGHTIRLLQLPGAWSSFIDSNPEGASCLGPMAGLEKQREQYAYAVEALSDPKRTRLVLVARLQKSTLQEVARTHLELAAIGLKNQYLVINGVLPKTEAANDTLAAAIWEREQEALANLPADLAGLPTDTLFLQPVNMVGVSALSRLLSTQPVASPSSDEYLQQRPDIPSLSALVDDIARNEHGLIMLMGKGGVGKTTMAAAIAVRLADMGFDVHLTTSDPAAHLSMTLNGSLNNLQVSRIDPHEETERYRQHVLETKGKELDEAGKRLLEEDLRSPCTEEIAVFQAFSRVIREAGKRFVVMDTAPTGHTLLLLDATGAYHREIAKKMGE-KGHFTTPMMLLQDPERTKVLLVTLPETTPVLEAANLQADLERAGIHPWGWIINNSLSIADT-RSPLLRMRAQQE-LPQIESVKRQHASRVALVPVLASEPTGIDKL------------KQLAGH--HHHHH |
||||
| PDB code |
Chain | Knot type |
Gap coverage |
Gap identity |
>Target_Sequence: gap | DATGAYHREIAKKMGE-KGHFTTPM |
|||
|---|---|---|---|---|---|---|---|---|---|
| 3SJC | F | Unknot | 16.67% | 72.22% | QLPNT-----SGKLNELKANVETIR |
||||
| 3IDQ | A | Unknot | 0.00% | 0.00% | ------------------------ |
||||
| 3IO3 | A | Unknot | 0.00% | 0.00% | D----------------------- |
||||
| 3ZS9 | A | Unknot | 22.22% | 66.67% | ---------ISGKLNELKANVETIR |
||||
|
Models Similarity profile Modelling alignment Raw knot fingerprint matrices: Model_1 |
Sun Jul 23 14:55:38 2017 JOB CREATED : 7976ca7f-1010-47d0-9454-429db9e2e017 Sun Jul 23 16:27:02 2017 STATUS CHANGED : N -> R Sun Jul 23 16:27:02 2017 INFO : JOB STARTED AT: 2017-07-23 16:27:02.562756 Sun Jul 23 16:27:02 2017 INFO : METHOD: 1 Sun Jul 23 16:27:02 2017 INFO : Precalculated profile found... Sun Jul 23 16:27:02 2017 INFO : Homologue pool found... Sun Jul 23 16:27:02 2017 INFO : Verifying structure sequences of homologues... Sun Jul 23 16:32:15 2017 INFO : Starting homologue filtering... Sun Jul 23 16:33:10 2017 INFO : Getting structures from PDB... Sun Jul 23 16:33:21 2017 INFO : Creating modelling alignment... Sun Jul 23 16:33:21 2017 INFO : Modelling... Sun Jul 23 17:06:23 2017 INFO : Model 1 built Sun Jul 23 17:06:23 2017 INFO : 3 gaps will be remodelled Sun Jul 23 17:33:15 2017 INFO : Validating Calpha distances... Sun Jul 23 17:33:15 2017 INFO : Model 1 distances correct: False Sun Jul 23 17:33:15 2017 INFO : Modelling... Sun Jul 23 18:08:21 2017 INFO : Model 2 built Sun Jul 23 18:08:21 2017 INFO : 3 gaps will be remodelled Sun Jul 23 18:37:13 2017 INFO : Validating Calpha distances... Sun Jul 23 18:37:13 2017 INFO : Model 2 distances correct: False Sun Jul 23 18:37:13 2017 INFO : Modelling... Sun Jul 23 19:15:50 2017 INFO : Model 3 built Sun Jul 23 19:15:50 2017 INFO : 3 gaps will be remodelled Sun Jul 23 19:44:29 2017 INFO : Validating Calpha distances... Sun Jul 23 19:44:29 2017 INFO : Model 3 distances correct: False Sun Jul 23 19:44:29 2017 INFO : Modelling... Sun Jul 23 20:22:14 2017 INFO : Model 4 built Sun Jul 23 20:22:14 2017 INFO : 3 gaps will be remodelled Sun Jul 23 20:53:47 2017 INFO : Validating Calpha distances... Sun Jul 23 20:53:47 2017 INFO : Model 4 distances correct: False Sun Jul 23 20:53:47 2017 INFO : Modelling... Sun Jul 23 21:29:33 2017 INFO : Model 5 built Sun Jul 23 21:29:33 2017 INFO : 3 gaps will be remodelled Sun Jul 23 21:58:47 2017 INFO : Validating Calpha distances... Sun Jul 23 21:58:47 2017 INFO : Model 5 distances correct: False Sun Jul 23 21:58:47 2017 INFO : None of the models passed the CA-distance validation Sun Jul 23 21:58:47 2017 ERROR : Modelling already was de novo, finishing with error Sun Jul 23 21:58:47 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 16:54:02.089066 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 16:57:05 2017 INFO : Starting homologue filtering... Mon Jul 24 16:57:45 2017 INFO : Getting structures from PDB... Mon Jul 24 16:57:53 2017 INFO : Creating modelling alignment... Mon Jul 24 16:57:53 2017 INFO : Modelling... Mon Jul 24 17:23:39 2017 INFO : Model 1 built Mon Jul 24 17:23:39 2017 INFO : 3 gaps will be remodelled Mon Jul 24 18:47:36 2017 INFO : Validating Calpha distances... Mon Jul 24 18:47:36 2017 INFO : Model 1 distances correct: False Mon Jul 24 18:47:36 2017 INFO : Modelling... Mon Jul 24 19:13:56 2017 INFO : Model 2 built Mon Jul 24 19:13:56 2017 INFO : 3 gaps will be remodelled Mon Jul 24 20:23:09 2017 INFO : Validating Calpha distances... Mon Jul 24 20:23:09 2017 INFO : Model 2 distances correct: False Mon Jul 24 20:23:09 2017 INFO : Modelling... Mon Jul 24 20:50:03 2017 INFO : Model 3 built Mon Jul 24 20:50:03 2017 INFO : 3 gaps will be remodelled Mon Jul 24 22:30:26 2017 INFO : Validating Calpha distances... Mon Jul 24 22:30:26 2017 INFO : Model 3 distances correct: False Mon Jul 24 22:30:26 2017 INFO : Modelling... Mon Jul 24 22:56:27 2017 INFO : Model 4 built Mon Jul 24 22:56:27 2017 INFO : 2 gaps will be remodelled Mon Jul 24 23:58:21 2017 INFO : Validating Calpha distances... Mon Jul 24 23:58:21 2017 INFO : Model 4 distances correct: False Mon Jul 24 23:58:21 2017 INFO : Modelling... Tue Jul 25 00:24:02 2017 INFO : Model 5 built Tue Jul 25 00:24:02 2017 INFO : 3 gaps will be remodelled Tue Jul 25 02:02:33 2017 INFO : Validating Calpha distances... Tue Jul 25 02:02:33 2017 INFO : Model 5 distances correct: False Tue Jul 25 02:02:33 2017 INFO : None of the models passed the CA-distance validation Tue Jul 25 02:02:33 2017 ERROR : Modelling already was de novo, finishing with error Tue Jul 25 02:02:33 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 10:07:01.975753 Tue Jul 25 10:07:01 2017 INFO : METHOD: 1 Tue Jul 25 10:07:02 2017 INFO : Precalculated profile found... Tue Jul 25 10:07:02 2017 INFO : Homologue pool found... Tue Jul 25 10:07:02 2017 INFO : Verifying structure sequences of homologues... Tue Jul 25 10:10:14 2017 INFO : Starting homologue filtering... Tue Jul 25 10:10:54 2017 INFO : Getting structures from PDB... Tue Jul 25 10:11:01 2017 INFO : Creating modelling alignment... Tue Jul 25 10:11:01 2017 INFO : Modelling... Tue Jul 25 10:36:07 2017 INFO : Model 1 built Tue Jul 25 10:36:07 2017 INFO : 3/3 gaps will be remodelled Tue Jul 25 11:20:14 2017 INFO : Validating Calpha distances... Tue Jul 25 11:20:14 2017 INFO : Model 1 distances correct: False Tue Jul 25 11:20:14 2017 INFO : Modelling... Tue Jul 25 11:45:55 2017 INFO : Model 2 built Tue Jul 25 11:45:55 2017 INFO : 3/3 gaps will be remodelled Tue Jul 25 12:24:25 2017 INFO : Validating Calpha distances... Tue Jul 25 12:24:25 2017 INFO : Model 2 distances correct: False Tue Jul 25 12:24:25 2017 INFO : Modelling... Tue Jul 25 12:49:16 2017 INFO : Model 3 built Tue Jul 25 12:49:16 2017 INFO : 3/3 gaps will be remodelled Tue Jul 25 13:34:32 2017 INFO : Validating Calpha distances... Tue Jul 25 13:34:32 2017 INFO : Model 3 distances correct: False Tue Jul 25 13:34:32 2017 INFO : Modelling... Tue Jul 25 14:00:08 2017 INFO : Model 4 built Tue Jul 25 14:00:08 2017 INFO : 3/3 gaps will be remodelled Tue Jul 25 14:45:02 2017 INFO : Validating Calpha distances... Tue Jul 25 14:45:02 2017 INFO : Model 4 distances correct: False Tue Jul 25 14:45:02 2017 INFO : Modelling... Tue Jul 25 15:09:56 2017 INFO : Model 5 built Tue Jul 25 15:09:56 2017 INFO : 3/3 gaps will be remodelled Tue Jul 25 15:57:36 2017 INFO : Validating Calpha distances... Tue Jul 25 15:57:36 2017 INFO : Model 5 distances correct: False Tue Jul 25 15:57:36 2017 INFO : None of the models passed the CA-distance validation Tue Jul 25 15:57:36 2017 STATUS CHANGED : R -> E Tue Jul 25 15:57:36 2017 ERROR : Error while modelling Tue Jul 25 16:37:01 2017 STATUS CHANGED : N -> R Tue Jul 25 16:37:01 2017 INFO : JOB STARTED AT: 2017-07-25 16:37:01.719681 Tue Jul 25 16:37:01 2017 INFO : METHOD: 1 Tue Jul 25 16:37:01 2017 INFO : Precalculated profile found... Tue Jul 25 16:37:01 2017 INFO : Homologue pool found... Tue Jul 25 16:37:01 2017 INFO : Verifying structure sequences of homologues... Tue Jul 25 16:40:21 2017 INFO : Starting homologue filtering... Tue Jul 25 16:41:04 2017 INFO : Getting structures from PDB... Tue Jul 25 16:41:12 2017 INFO : Creating modelling alignment... Tue Jul 25 16:41:12 2017 INFO : Modelling... Tue Jul 25 17:07:22 2017 INFO : Model 1 built Tue Jul 25 17:07:22 2017 INFO : Validating Calpha distances... Tue Jul 25 17:07:22 2017 INFO : Model 1 distances correct: False Tue Jul 25 17:07:22 2017 INFO : Modelling... Tue Jul 25 17:32:09 2017 INFO : Model 2 built Tue Jul 25 17:32:09 2017 INFO : Validating Calpha distances... Tue Jul 25 17:32:09 2017 INFO : Model 2 distances correct: False Tue Jul 25 17:32:09 2017 INFO : Modelling... Tue Jul 25 17:57:34 2017 INFO : Model 3 built Tue Jul 25 17:57:34 2017 INFO : Validating Calpha distances... Tue Jul 25 17:57:34 2017 INFO : Model 3 distances correct: False Tue Jul 25 17:57:34 2017 INFO : Modelling... Tue Jul 25 18:23:10 2017 INFO : Model 4 built Tue Jul 25 18:23:10 2017 INFO : Validating Calpha distances... Tue Jul 25 18:23:10 2017 INFO : Model 4 distances correct: True Tue Jul 25 18:23:10 2017 INFO : Modelling... Tue Jul 25 18:48:25 2017 INFO : Model 5 built Tue Jul 25 18:48:25 2017 INFO : Validating Calpha distances... Tue Jul 25 18:48:25 2017 INFO : Model 5 distances correct: False Tue Jul 25 18:48:33 2017 INFO : Finished modelling Tue Jul 25 18:48:33 2017 STATUS CHANGED : R -> P Tue Jul 25 18:48:33 2017 INFO : Checking topology... Tue Jul 25 19:20:18 2017 INFO : Knot matrices done... Tue Jul 25 19:21:03 2017 INFO : Some knots found! Tue Jul 25 19:21:10 2017 INFO : Some lassos found! Tue Jul 25 19:21:10 2017 INFO : Finishing... Tue Jul 25 19:21:10 2017 INFO : Job done Tue Jul 25 19:21:10 2017 STATUS CHANGED : P -> F Tue Jul 25 19:21:10 2017 STATUS CHANGED : F -> F |
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