D-I-TASSER Q9NTM9

D-I-TASSER results for Q9NTM9

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

Summary of the Protein

Uniprot ID: Q9NTM9
Protein Name: Copper homeostasis protein cutC homolog
Gene Name: CUTC

Input Sequence in FASTA format

>Q9NTM9 (273 residues)
MKRQGASSERKRARIPSGKAGAANGFLMEVCVDSVESAVNAERGGADRIELCSGLSEGGT
TPSMGVLQVVKQSVQIPVFVMIRPRGGDFLYSDREIEVMKADIRLAKLYGADGLVFGALT
EDGHIDKELCMSLMAICRPLPVTFHRAFDMVHDPMAALETLLTLGFERVLTSGCDSSALE
GLPLIKRLIEQAKGRIVVMPGGGITDRNLQRILEGSGATEFHCSARSTRDSGMKFRNSSV
AMGASLSCSEYSLKVTDVTKVRTLNAIAKNILV

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	Q9NTM9-D1	1-273	273		MKRQGASSERKRARIPSGKAGAANGFLMEVCVDSVESAVNAERGGADRIELCSGLSEGGTTPSMGVLQVVKQSVQIPVFVMIRPRGGDFLYSDREIEVMKADIRLAKLYGADGLVFGALTEDGHIDKELCMSLMAICRPLPVTFHRAFDMVHDPMAALETLLTLGFERVLTSGCDSSALEGLPLIKRLIEQAKGRIVVMPGGGITDRNLQRILEGSGATEFHCSARSTRDSGMKFRNSSVAMGASLSCSEYSLKVTDVTKVRTLNAIAKNILV

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.8466

(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	3iwpA	0.91	0.46	0.996	0.912	model1_3iwpA.pdb.gz
2	1x7iB	0.84	0.98	0.438	0.861	model1_1x7iB.pdb.gz
3	4r9xA	0.76	1.60	0.336	0.791	model1_4r9xA.pdb.gz
4	2fiqC	0.71	3.97	0.098	0.919	model1_2fiqC.pdb.gz
5	4rc1A	0.70	2.96	0.153	0.806	model1_4rc1A.pdb.gz
6	4n7qA	0.69	3.58	0.110	0.850	model1_4n7qA.pdb.gz
7	3epmA	0.68	3.71	0.127	0.846	model1_3epmA.pdb.gz
8	4ov4A	0.63	3.64	0.070	0.769	model1_4ov4A.pdb.gz
9	3b4uB	0.60	3.69	0.115	0.747	model1_3b4uB.pdb.gz
10	1y0eA	0.56	3.22	0.131	0.667	model1_1y0eA.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:0005507	1.00	copper ion 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:0009987	0.90	cellular process
GO:0065007	0.68	biological regulation
GO:0055070	0.63	copper ion homeostasis
GO:0044699	0.63	single-organism process
GO:0016043	0.60	cellular component organization
GO:0008152	0.59	metabolic process
GO:0022607	0.58	cellular component assembly
GO:0051262	0.57	protein tetramerization
GO:0071704	0.52	organic substance metabolic process

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:0044422	1.00	organelle part
GO:0005737	1.00	cytoplasm
GO:0005634	1.00	nucleus
GO:0044446	0.90	intracellular organelle part
GO:0044428	0.86	nuclear part
GO:0005730	0.85	nucleolus
GO:0044444	0.56	cytoplasmic part

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	0.287	1vlwB	0.607	2.98	0.128	0.703	4.1.3.16	50
2	0.287	2v81A	0.614	2.76	0.125	0.703	4.1.2.21	50
3	0.268	2yw3E	0.583	3.28	0.152	0.696	4.1.2.14	50
4	0.263	1v5xA	0.608	2.98	0.166	0.707	5.3.1.24	31
5	0.208	1tqxA	0.619	3.20	0.158	0.740	5.1.3.1	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	0.12	1it7A	0.676	4.06	0.100	0.865	0.62	GUN	complex1.pdb.gz	146,172,201,202,204,222
2	0.11	1ozqA	0.679	4.17	0.083	0.883	0.69	PRF	complex2.pdb.gz	145,170,172,201,202,203,222
3	0.10	1n2vA	0.681	4.20	0.086	0.886	0.60	BDI	complex3.pdb.gz	171,173,202,203,223,224
4	0.09	1q2rD	0.678	4.22	0.075	0.886	0.63	9DG	complex4.pdb.gz	52,59,81,116,117,144
5	0.09	1x7i0	0.838	1.07	0.443	0.861	1.54	III	complex5.pdb.gz	35,36,54,55,56,57,60,61,63,65,66,68,85,87,88,90,92,94,98,101,102,105,120,121,122,123,149,150,151,152,231,232,233,234,235,250,251,253

	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.