D-I-TASSER Q969P6

D-I-TASSER results for Q969P6

[Click result.zip to download all results on this page]

Summary of the Protein

Uniprot ID: Q969P6
Protein Name: DNA topoisomerase I, mitochondrial
Gene Name: TOP1MT

Input Sequence in FASTA format

>Q969P6 (601 residues)
MRVVRLLRLRAALTLLGEVPRRPASRGVPGSRRTQKGSGARWEKEKHEDGVKWRQLEHKG
PYFAPPYEPLPDGVRFFYEGRPVRLSVAAEEVATFYGRMLDHEYTTKEVFRKNFFNDWRK
EMAVEEREVIKSLDKCDFTEIHRYFVDKAAARKVLSREEKQKLKEEAEKLQQEFGYCILD
GHQEKIGNFKIEPPGLFRGRGDHPKMGMLKRRITPEDVVINCSRDSKIPEPPAGHQWKEV
RSDNTVTWLAAWTESVQNSIKYIMLNPCSKLKGETAWQKFETARRLRGFVDEIRSQYRAD
WKSREMKTRQRAVALYFIDKLALRAGNEKEDGEAADTVGCCSLRVEHVQLHPEADGCQHV
VEFDFLGKDCIRYYNRVPVEKPVYKNLQLFMENKDPRDDLFDRLTTTSLNKHLQELMDGL
TAKVFRTYNASITLQEQLRALTRAEDSIAAKILSYNRANRVVAILCNHQRATPSTFEKSM
QNLQTKIQAKKEQVAEARAELRRARAEHKAQGDGKSRSVLEKKRRLLEKLQEQLAQLSVQ
ATDKEENKQVALGTSKLNYLDPRISIAWCKRFRVPVEKIYSKTQRERFAWALAMAGEDFE
F

Predicted Contact and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (right figure) derived based on confidence scores of AttentionPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	Q969P6-D1	1-42,266-288,419-601	248		MRVVRLLRLRAALTLLGEVPRRPASRGVPGSRRTQKGSGARWNPCSKLKGETAWQKFETARRLRGGLTAKVFRTYNASITLQEQLRALTRAEDSIAAKILSYNRANRVVAILCNHQRATPSTFEKSMQNLQTKIQAKKEQVAEARAELRRARAEHKAQGDGKSRSVLEKKRRLLEKLQEQLAQLSVQATDKEENKQVALGTSKLNYLDPRISIAWCKRFRVPVEKIYSKTQRERFAWALAMAGEDFEF
2	Q969P6-D2	43-265	223		EKEKHEDGVKWRQLEHKGPYFAPPYEPLPDGVRFFYEGRPVRLSVAAEEVATFYGRMLDHEYTTKEVFRKNFFNDWRKEMAVEEREVIKSLDKCDFTEIHRYFVDKAAARKVLSREEKQKLKEEAEKLQQEFGYCILDGHQEKIGNFKIEPPGLFRGRGDHPKMGMLKRRITPEDVVINCSRDSKIPEPPAGHQWKEVRSDNTVTWLAAWTESVQNSIKYIML
3	Q969P6-D3	289-418	130		FVDEIRSQYRADWKSREMKTRQRAVALYFIDKLALRAGNEKEDGEAADTVGCCSLRVEHVQLHPEADGCQHVVEFDFLGKDCIRYYNRVPVEKPVYKNLQLFMENKDPRDDLFDRLTTTSLNKHLQELMD

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.68

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of AttentionPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	1sc7A	0.51	4.00	0.473	0.587	model1_1sc7A.pdb.gz
2	2b9sA	0.42	4.41	0.264	0.484	model1_2b9sA.pdb.gz
3	5nrlA	0.37	7.74	0.042	0.592	model1_5nrlA.pdb.gz
4	2z64A	0.25	7.91	0.034	0.399	model1_2z64A.pdb.gz
5	4fxqA	0.21	7.16	0.034	0.320	model1_4fxqA.pdb.gz
6	1oisA1	0.21	1.07	0.535	0.211	model1_1oisA1.pdb.gz
7	4r7oA	0.19	6.23	0.050	0.276	model1_4r7oA.pdb.gz
8	2h7fX2	0.19	2.41	0.205	0.203	model1_2h7fX2.pdb.gz
9	2nvuB3	0.17	5.67	0.043	0.223	model1_2nvuB3.pdb.gz
10	1v9dB2	0.15	5.56	0.030	0.206	model1_1v9dB2.pdb.gz

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0003917	0.99	DNA topoisomerase type I activity
GO:1901363	0.53	heterocyclic compound binding
GO:0097159	0.53	organic cyclic compound binding

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0044699	1.00	single-organism process
GO:0009987	1.00	cellular process
GO:0090304	0.99	nucleic acid metabolic process
GO:0044260	0.99	cellular macromolecule metabolic process
GO:0016043	0.99	cellular component organization
GO:0006265	0.98	DNA topological change
GO:0006338	0.97	chromatin remodeling
GO:0044763	0.96	single-organism cellular process
GO:0044249	0.96	cellular biosynthetic process
GO:0009059	0.96	macromolecule biosynthetic process
GO:0006260	0.95	DNA replication
GO:0007059	0.93	chromosome segregation

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0043229	1.00	intracellular organelle
GO:0044446	0.97	intracellular organelle part
GO:0044428	0.96	nuclear part
GO:0043232	0.95	intracellular non-membrane-bounded organelle
GO:0043234	0.94	protein complex
GO:0005730	0.94	nucleolus
GO:0044427	0.93	chromosomal part
GO:0031298	0.92	replication fork protection complex

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.244	1a31A	0.423	4.25	0.417	0.482	5.99.1.2	324,426
2	0.060	2fhcA	0.319	7.88	0.028	0.521	3.2.1.41	NA
3	0.060	3c46B	0.328	7.55	0.038	0.514	2.7.7.6	429
4	0.060	2a4zA	0.302	8.35	0.038	0.514	2.7.1.153	NA
5	0.060	3cskA	0.300	8.02	0.041	0.496	3.4.14.4	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.18	1lpqA	0.482	4.44	0.465	0.576	0.72	QNA	complex1.pdb.gz	192,193,197,199,200,203,254,261,368
2	0.18	1a36A	0.481	4.48	0.461	0.576	0.74	QNA	complex2.pdb.gz	52,102,198,200,246,247,248,260,262,264,368
3	0.07	1rrjA	0.517	3.87	0.474	0.591	0.80	UUU	complex3.pdb.gz	368,369,554
4	0.06	1t8iA	0.517	3.82	0.474	0.589	0.72	QNA	complex4.pdb.gz	192,197,198,199,200,203,210,257,368
5	0.05	1rr8C	0.442	4.40	0.358	0.507	0.82	QNA	complex5.pdb.gz	324,325,327,329,337,368,369,410,421

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.