Model | Type | Knot core | Slipknot | Lasso | Piercing | Show | |||
---|---|---|---|---|---|---|---|---|---|
range | loop range | loop | position | in JSmol | |||||
Model 1 | Knot | K +31 | 306-564 | -- | -- | -- | |||
Lasso | SL 2++C | -- | -- | 113-422 | |||||
Model 2 | Knot | K +31 | 306-564 | -- | -- | -- | |||
Lasso | SL 2++C | -- | -- | 113-422 | |||||
Model 3 | Knot | K +31 | 306-565 | -- | -- | -- | |||
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 | ||||
---|---|---|---|---|---|---|---|---|---|---|---|
1II0 |
B |
Unknot |
100.00% |
150.21% |
150.21% |
0.66 |
..Target: MQFLQNIPPYLFFTGKGGVGKTSISCATAIRLAEQGKRVLLVSTDPASNVGQVFSQTIGNTIQAIASVPGLSALEIDPQAAAQQYRARIVDPIKGVLPDDVVSSINEQLSGACTTEIAAFDEFTGLLTDASLLTRFDHIIFDTAPTGHTIRLLQLPGAWSSFIDSNPEGASCLGPMAGLEKQREQYAYAVEALSDPKRTRLVLVARLQKSTLQEVARTHLELAAIGLKNQYLVINGVLPKTEAANDTLAAAIWEREQEALANLPADLAGLPTDTLFLQPVNMVGVSALSRLLSTQPVASPSSDEYLQQRPDIPSLSALVDDIARNEHGLIMLMGKGGVGKTTMAAAIAVRLADMGFDVHLTTSDPAAHLSMTLNGSLNNLQVSRIDPHEETERYRQHVLETKGKELDEAGKRLLEEDLRSPCTEEIAVFQAFSRVIREAGKRFVVMDTAPTGHTLLLLDATGAYHREIAKKMGEKGHFTTPMMLLQDPERTKVLLVTLPETTPVLEAANLQADLERAGIHPWGWIINNSLSIADTRSPLLRMRAQQELPQIESVKRQHASRVALVPVLASEPTGIDKLKQLAGHHHHHH |
||||
3IDQ |
A |
Unknot |
35.29% |
188.89% |
73.02% |
1.45 |
..Target: ---MQFLQNIPPYLFFTGKGGVGKTSISCATAIRLA--EQGKRVLLVSTDPASNVGQVFSQTIGNTIQAIASVPGLSALEIDPQAAAQQYRARIVDPIKGVLPDDVVSSINEQLSGACTTEIAAFDEFTGLLTDASLLTRFDHIIFDTAPTGHTIRLLQLPGAWSSFIDS-NPEGASCLGPMAGLEKQREQYAYAVEALSDPKRTRLVLVARLQKSTLQEVARTHLELAAIGLKNQYLVINGVLPKTEAANDTLAAAIWEREQEALANLPADLAGLPTDTLFLQPVNMVGVSALSRLLSTQPVASPSSDEYLQQRPDIPSLSALVDDIARNEHGLIMLMGKGGVGKTTMAAAIAVRLADMGFDVHLTTSDPAAHLSMTL--NGSLNNLQVSRIDPHEETERYRQHVLETKGKELDEAGKRLLEEDLRSPCTEEIAVFQAFSRVIREAGKRFVVMDTAPTGHTLLLLDATGAYHREIAKKMGEKGHFTTPMMLLQDPERTKVLLVTLPETTPVLEAANLQADLERAGIHPWGWIINNSLSIADTRSPLLRMRAQQELPQIESVKRQHASRVALVPVLASEPTGIDKLKQLAG-HHHHHH |
||||
4PWX |
A |
Unknot |
29.93% |
157.14% |
21.43% |
1.32 |
..Target: MQ------FLQNIPPYLFFTGKGGVGKTSISCATAIRLA--EQGKRVLLVSTDPASNVGQVFSQTIGNTIQAIASVPGLSALEIDPQAAAQQY-RARIVDPIKGVLPDDVVSSINEQLSGACTTEIAAFDEFTGLLTDASLLTRFDHIIFDTAPTGHTIRLLQLPGAWSSFIDSNPEGASCLGPM-AGLEKQREQYAYAVEALSDPKRTRLVLVARLQKSTLQEVARTHLELAAIGLKNQYLVINGVLPKTEAANDTLAAAIWEREQEALANLPADLAGLPTDTLFLQPVNMVGVSALSRLLSTQPVASPSSDEYLQQRPDIPSLSALVDDIARNEHGLIMLMGKGGVGKTTMAAAIAVRLADMGFDVHLTTSDPAAHLSMTLNGSLNNLQVSRIDPHEETERYRQHVLETKGKELDEAGKRLLEEDLRSPCTEEIAVFQAFSRVIREAGKRFVVMDTAPTGHTLLLLDATGAYHREIAKKMGEKGHFTTPMMLLQDPERTKVLLVTLPETTPVLEAANLQADLERAGIHPWGWIINNSLSIADTRSPLLRMRAQQELPQIESVKRQHASRVALVPVLASEPTGIDKL------------KQLAGH--HHHHH |
||||
3SJC |
F |
Unknot |
28.99% |
145.11% |
49.62% |
1.31 |
..Target: MQ------FLQNIPPYLFFTGKGGVGKTSISCATAIRLA--EQGKRVLLVSTDPASNVGQVFSQTIGNTIQAIASVPGLSALEIDPQAAAQQYRARIVDPIKGVLPDDVVSSINEQLSGACTTEIAAFDEFTGLLTDASLLTRFDHIIFDTAPTGHTIRLLQLPGAWSSFIDSNPEGASCLGPMAGLEKQREQYAYAVEALSDPKRTRLVLVARLQKSTLQEVARTHLELAAIGLKNQYLVINGVLPKTEAANDTLAAAIWEREQEALANLPADLAGLPTDTLFLQPVNMVGVSALSRLLSTQPVASPSSDEYLQQRPDIPSLSALVDDIARNEHGLIMLMGKGGVGKTTMAAAIAVRLADMGFDVHLTTSDPAAHLSMTLNGSLNNLQVSRIDPHEETERYRQHVLETKGKELDEAGKRLLEEDLRSPCTEEIAVFQAFSRVIREAGKRFVVMDTAPTGHTLLLLDATGAYHREIAKKMGE-KGHFTTPMMLLQDPERTKVLLVTLPETTPVLEAANLQADLERAGIHPWGWIINNSL---SIADTRSPLLRMRAQQE-LPQIESVKRQHASRVALVPVLASEPTGIDKL------------KQLAGH--HHHHH |
||||
3ZS9 |
A |
Unknot |
31.40% |
68.42% |
26.32% |
1.04 |
..Target: MQ------FLQNIPPYLFFTGKGGVGKTSISCATAIRLA--EQGKRVLLVSTDPASNVGQVFSQTIGNTIQAIASVPGLSALEIDPQAAAQQYR--ARIVDPIKGVLPDDVVSSINEQLSGACTTEIAAFDEFTGLLTDASLLTRFDHIIFDTAPTGHTIRLLQLPGAWSSFIDSNPEGASCLGPMAGLEKQREQYAYAVEALSDPKRTRLVLVARLQKSTLQEVARTHLELAAIGLKNQYLVINGVLPKTEAANDTLAAAIWEREQEALANLPADLAGLPTDTLFLQPVNMVGVSALSRLLSTQPVASPSSDEYLQQRPDIPSLSALVDDIARNEHGLIMLMGKGGVGKTTMAAAIAVRLADMGFDVHLTTSDPAAHLSMTLNGSLNNLQVSRIDPHEETERYRQHVLETKGKELDEAGKRLLEEDLRSPCTEEIAVFQAFSRVIREAGKRFVVMDTAPTGHTLLLLDATGAYHREIAKKMGE-KGHFTTPMMLLQDPERTKVLLVTLPETTPVLEAANLQADLERAGIHPWGWIINNSLSIADT-RSPLLRMRAQQE-LPQIESVKRQHASRVALVPVLASEPTGIDKL------------KQLAGH--HHHHH |
PDB code |
Chain | Knot type |
Gap coverage |
Gap identity |
>Target_Sequence: gap | DATGAYHREIAKKMGEKGHFTTPMM |
|||
---|---|---|---|---|---|---|---|---|---|
1II0 | B | Unknot | 10.53% | 10.53% | DAT-----------------TTPMM |
||||
3IDQ | A | Unknot | 0.00% | 0.00% | ------------------------- |
||||
4PWX | A | Unknot | 0.00% | 0.00% | ------------------------- |
||||
3SJC | F | Unknot | 21.05% | 73.68% | QLPNT-----SGKLNELKANVETIRQ |
||||
3ZS9 | A | Unknot | 26.32% | 68.42% | ---------ISGKLNELKANVETIRQ |
PDB code |
Chain | Knot type |
Gap coverage |
Gap identity |
>Target_Sequence: gap | STQPVASPSSDEYLQQRPDI |
|||
---|---|---|---|---|---|---|---|---|---|
1II0 | B | Unknot | 28.57% | 28.57% | STQP----------QQRPDI |
||||
3IDQ | A | Unknot | 0.00% | 0.00% | -------------------- |
||||
4PWX | A | Unknot | 7.14% | 85.71% | FAE--CKRCQARWKMQKKYL |
||||
3SJC | F | Unknot | 28.57% | 71.43% | ----GSIPGIDEAL------ |
||||
3ZS9 | A | Unknot | 0.00% | 0.00% | -------------------- |
PDB code |
Chain | Knot type |
Gap coverage |
Gap identity |
>Target_Sequence: gap | AAHLSMTLNGSLNNL |
|||
---|---|---|---|---|---|---|---|---|---|
1II0 | B | Unknot | 11.11% | 11.11% | AA---------LNNL |
||||
3IDQ | A | Unknot | 44.44% | 88.89% | ---VKMPLEIRG-LNNL |
||||
4PWX | A | Unknot | 0.00% | 0.00% | --------------- |
||||
3SJC | F | Unknot | 0.00% | 0.00% | --------------- |
||||
3ZS9 | A | Unknot | 0.00% | 0.00% | --------------- |
Models Similarity profile Modelling alignment Raw knot fingerprint matrices: Model_1 Model_2 Model_3 |
Sun Jul 23 14:55:41 2017 JOB CREATED : e79038bb-6add-4273-b421-a4d109c7836b Sun Jul 23 16:40:02 2017 STATUS CHANGED : N -> R Sun Jul 23 16:40:02 2017 INFO : JOB STARTED AT: 2017-07-23 16:40:02.587931 Sun Jul 23 16:40:02 2017 INFO : METHOD: 1 Sun Jul 23 16:40:02 2017 INFO : Precalculated profile found... Sun Jul 23 16:40:02 2017 INFO : Homologue pool found... Sun Jul 23 16:40:02 2017 INFO : Verifying structure sequences of homologues... Sun Jul 23 16:45:10 2017 INFO : Starting homologue filtering... Sun Jul 23 16:46:11 2017 INFO : Getting structures from PDB... Sun Jul 23 16:46:33 2017 INFO : Creating modelling alignment... Sun Jul 23 16:46:33 2017 INFO : Modelling... Sun Jul 23 17:28:04 2017 INFO : Model 1 built Sun Jul 23 17:28:04 2017 INFO : 2 gaps will be remodelled Sun Jul 23 17:44:49 2017 INFO : Validating Calpha distances... Sun Jul 23 17:44:49 2017 INFO : Model 1 distances correct: False Sun Jul 23 17:44:49 2017 INFO : Modelling... Sun Jul 23 18:28:00 2017 INFO : Model 2 built Sun Jul 23 18:28:00 2017 INFO : 3 gaps will be remodelled Sun Jul 23 18:56:38 2017 INFO : Validating Calpha distances... Sun Jul 23 18:56:38 2017 INFO : Model 2 distances correct: False Sun Jul 23 18:56:38 2017 INFO : Modelling... Sun Jul 23 19:42:55 2017 INFO : Model 3 built Sun Jul 23 19:42:55 2017 INFO : 3 gaps will be remodelled Sun Jul 23 20:13:37 2017 INFO : Validating Calpha distances... Sun Jul 23 20:13:37 2017 INFO : Model 3 distances correct: False Sun Jul 23 20:13:37 2017 INFO : Modelling... Sun Jul 23 20:56:37 2017 INFO : Model 4 built Sun Jul 23 20:56:37 2017 INFO : 3 gaps will be remodelled Sun Jul 23 21:25:42 2017 INFO : Validating Calpha distances... Sun Jul 23 21:25:42 2017 INFO : Model 4 distances correct: False Sun Jul 23 21:25:42 2017 INFO : Modelling... Sun Jul 23 22:06:11 2017 INFO : Model 5 built Sun Jul 23 22:06:11 2017 INFO : 2 gaps will be remodelled Sun Jul 23 22:29:03 2017 INFO : Validating Calpha distances... Sun Jul 23 22:29:03 2017 INFO : Model 5 distances correct: False Sun Jul 23 22:29:03 2017 INFO : None of the models passed the CA-distance validation Sun Jul 23 22:29:03 2017 ERROR : Modelling already was de novo, finishing with error Sun Jul 23 22:29:03 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 16:54:02.016220 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 16:57:06 2017 INFO : Starting homologue filtering... Mon Jul 24 16:57:46 2017 INFO : Getting structures from PDB... Mon Jul 24 16:58:02 2017 INFO : Creating modelling alignment... Mon Jul 24 16:58:02 2017 INFO : Modelling... Mon Jul 24 17:30:30 2017 INFO : Model 1 built Mon Jul 24 17:30:30 2017 INFO : 2 gaps will be remodelled Mon Jul 24 18:33:00 2017 INFO : Validating Calpha distances... Mon Jul 24 18:33:00 2017 INFO : Model 1 distances correct: False Mon Jul 24 18:33:00 2017 INFO : Modelling... Mon Jul 24 19:05:05 2017 INFO : Model 2 built Mon Jul 24 19:05:05 2017 INFO : 3 gaps will be remodelled Mon Jul 24 20:31:55 2017 INFO : Validating Calpha distances... Mon Jul 24 20:31:55 2017 INFO : Model 2 distances correct: False Mon Jul 24 20:31:55 2017 INFO : Modelling... Mon Jul 24 21:04:08 2017 INFO : Model 3 built Mon Jul 24 21:04:08 2017 INFO : 3 gaps will be remodelled Mon Jul 24 22:29:11 2017 INFO : Validating Calpha distances... Mon Jul 24 22:29:11 2017 INFO : Model 3 distances correct: False Mon Jul 24 22:29:11 2017 INFO : Modelling... Mon Jul 24 23:01:40 2017 INFO : Model 4 built Mon Jul 24 23:01:40 2017 INFO : 2 gaps will be remodelled Tue Jul 25 00:18:30 2017 INFO : Validating Calpha distances... Tue Jul 25 00:18:30 2017 INFO : Model 4 distances correct: False Tue Jul 25 00:18:30 2017 INFO : Modelling... Tue Jul 25 00:51:39 2017 INFO : Model 5 built Tue Jul 25 00:51:39 2017 INFO : 2 gaps will be remodelled Tue Jul 25 01:54:56 2017 INFO : Validating Calpha distances... Tue Jul 25 01:54:56 2017 INFO : Model 5 distances correct: False Tue Jul 25 01:54:56 2017 INFO : None of the models passed the CA-distance validation Tue Jul 25 01:54:56 2017 ERROR : Modelling already was de novo, finishing with error Tue Jul 25 01:54:56 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 10:07:01.987143 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 10:10:06 2017 INFO : Starting homologue filtering... Tue Jul 25 10:10:45 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 10:42:25 2017 INFO : Model 1 built Tue Jul 25 10:42:25 2017 INFO : 2/4 gaps will be remodelled Tue Jul 25 11:10:24 2017 INFO : Validating Calpha distances... Tue Jul 25 11:10:24 2017 INFO : Model 1 distances correct: False Tue Jul 25 11:10:24 2017 INFO : Modelling... Tue Jul 25 11:41:13 2017 INFO : Model 2 built Tue Jul 25 11:41:13 2017 INFO : 3/4 gaps will be remodelled Tue Jul 25 12:30:25 2017 INFO : Validating Calpha distances... Tue Jul 25 12:30:25 2017 INFO : Model 2 distances correct: False Tue Jul 25 12:30:25 2017 INFO : Modelling... Tue Jul 25 13:03:10 2017 INFO : Model 3 built Tue Jul 25 13:03:10 2017 INFO : 3/4 gaps will be remodelled Tue Jul 25 13:50:05 2017 INFO : Validating Calpha distances... Tue Jul 25 13:50:05 2017 INFO : Model 3 distances correct: False Tue Jul 25 13:50:05 2017 INFO : Modelling... Tue Jul 25 14:19:27 2017 INFO : Model 4 built Tue Jul 25 14:19:27 2017 INFO : 3/4 gaps will be remodelled Tue Jul 25 15:08:41 2017 INFO : Validating Calpha distances... Tue Jul 25 15:08:41 2017 INFO : Model 4 distances correct: False Tue Jul 25 15:08:41 2017 INFO : Modelling... Tue Jul 25 15:37:25 2017 INFO : Model 5 built Tue Jul 25 15:37:25 2017 INFO : 2/4 gaps will be remodelled Tue Jul 25 16:06:21 2017 INFO : Validating Calpha distances... Tue Jul 25 16:06:21 2017 INFO : Model 5 distances correct: False Tue Jul 25 16:06:21 2017 INFO : None of the models passed the CA-distance validation Tue Jul 25 16:06:21 2017 STATUS CHANGED : R -> E Tue Jul 25 16:06:21 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 16:37:01.626451 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 16:40:04 2017 INFO : Starting homologue filtering... Tue Jul 25 16:40:46 2017 INFO : Getting structures from PDB... Tue Jul 25 16:41:02 2017 INFO : Creating modelling alignment... Tue Jul 25 16:41:02 2017 INFO : Modelling... Tue Jul 25 17:13:41 2017 INFO : Model 1 built Tue Jul 25 17:13:41 2017 INFO : Validating Calpha distances... Tue Jul 25 17:13:42 2017 INFO : Model 1 distances correct: True Tue Jul 25 17:13:42 2017 INFO : Modelling... Tue Jul 25 17:45:20 2017 INFO : Model 2 built Tue Jul 25 17:45:20 2017 INFO : Validating Calpha distances... Tue Jul 25 17:45:20 2017 INFO : Model 2 distances correct: True Tue Jul 25 17:45:20 2017 INFO : Modelling... Tue Jul 25 18:17:28 2017 INFO : Model 3 built Tue Jul 25 18:17:28 2017 INFO : Validating Calpha distances... Tue Jul 25 18:17:28 2017 INFO : Model 3 distances correct: False Tue Jul 25 18:17:28 2017 INFO : Modelling... Tue Jul 25 18:48:34 2017 INFO : Model 4 built Tue Jul 25 18:48:34 2017 INFO : Validating Calpha distances... Tue Jul 25 18:48:34 2017 INFO : Model 4 distances correct: True Tue Jul 25 18:48:34 2017 INFO : Modelling... Tue Jul 25 19:19:43 2017 INFO : Model 5 built Tue Jul 25 19:19:43 2017 INFO : Validating Calpha distances... Tue Jul 25 19:19:43 2017 INFO : Model 5 distances correct: False Tue Jul 25 19:20:08 2017 INFO : Finished modelling Tue Jul 25 19:20:08 2017 STATUS CHANGED : R -> P Tue Jul 25 19:20:08 2017 INFO : Checking topology... Tue Jul 25 19:50:40 2017 INFO : Knot matrices done... Tue Jul 25 19:52:52 2017 INFO : Some knots found! Tue Jul 25 19:53:40 2017 INFO : Some lassos found! Tue Jul 25 19:53:40 2017 INFO : Finishing... Tue Jul 25 19:53:41 2017 INFO : Job done Tue Jul 25 19:53:41 2017 STATUS CHANGED : P -> F Tue Jul 25 19:53:41 2017 STATUS CHANGED : F -> F |