D-I-TASSER Q8NEW7

D-I-TASSER results for Q8NEW7

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

Summary of the Protein

Uniprot ID: Q8NEW7
Protein Name: Transmembrane inner ear expressed protein
Gene Name: TMIE

Input Sequence in FASTA format

>Q8NEW7 (156 residues)
MAGWPGAGPLCVLGGAALGVCLAGVAGQLVEPSTAPPKPKPPPLTKETVVFWDMRLWHVV
GIFSLFVLSIIITLCCVFNCRVPRTRKEIEARYLQRKAAKMYTDKLETVPPLNELTEVPG
EDKKKKKKKKKDSVDTVAIKVEEDEKNEAKKKKGEK

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 DeepPotential. 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	Q8NEW7-D1	1-156	156		MAGWPGAGPLCVLGGAALGVCLAGVAGQLVEPSTAPPKPKPPPLTKETVVFWDMRLWHVVGIFSLFVLSIIITLCCVFNCRVPRTRKEIEARYLQRKAAKMYTDKLETVPPLNELTEVPGEDKKKKKKKKKDSVDTVAIKVEEDEKNEAKKKKGEK

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4846

(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 DeepPotential, 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	4a01A	0.54	4.45	0.026	0.827	model1_4a01A.pdb.gz
2	5w3sA	0.53	4.29	0.054	0.808	model1_5w3sA.pdb.gz
3	5eytA	0.53	4.20	0.071	0.788	model1_5eytA.pdb.gz
4	6hwhV	0.52	4.21	0.054	0.788	model1_6hwhV.pdb.gz
5	6pw4A	0.52	3.82	0.082	0.756	model1_6pw4A.pdb.gz
6	5ez3A	0.52	4.52	0.079	0.827	model1_5ez3A.pdb.gz
7	3ayxA	0.52	4.19	0.033	0.788	model1_3ayxA.pdb.gz
8	6sd8X	0.52	4.48	0.043	0.833	model1_6sd8X.pdb.gz
9	5z96A	0.52	4.27	0.071	0.795	model1_5z96A.pdb.gz
10	6ymxa	0.52	4.45	0.101	0.801	model1_6ymxa.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:1901363	0.55	heterocyclic compound binding
GO:0097159	0.55	organic cyclic compound binding
GO:0003824	0.55	catalytic activity
GO:0000166	0.51	nucleotide 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:0048598	1.00	embryonic morphogenesis
GO:0007605	1.00	sensory perception of sound
GO:0009987	0.79	cellular process
GO:0044763	0.75	single-organism cellular process
GO:0048856	0.66	anatomical structure development
GO:0048513	0.65	animal organ development
GO:0006928	0.65	movement of cell or subcellular component
GO:0048920	0.64	posterior lateral line neuromast primordium migration
GO:0048884	0.64	neuromast development
GO:0048839	0.64	inner ear development
GO:0048752	0.64	semicircular canal morphogenesis

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:0055120	1.00	striated muscle dense body
GO:0005737	1.00	cytoplasm
GO:0043226	0.89	organelle
GO:0043231	0.88	intracellular membrane-bounded organelle
GO:0044446	0.67	intracellular organelle part
GO:0005739	0.63	mitochondrion
GO:0005759	0.52	mitochondrial matrix

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	0.060	1bucA	0.469	4.23	0.031	0.724	1.3.99.2	24
2	0.060	2nyfA	0.482	4.65	0.054	0.788	4.3.1.5	NA
3	0.060	1b8fA	0.491	4.27	0.069	0.744	4.3.1.3	NA
4	0.060	1qleA	0.520	4.44	0.059	0.808	1.9.3.1	NA
5	0.060	1ivhA	0.475	4.29	0.025	0.750	1.3.99.10	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	0.01	1m56A	0.515	4.50	0.072	0.808	0.11	HEA	complex1.pdb.gz	53,56,57,60,61
2	0.01	3fyeA	0.518	4.56	0.057	0.814	0.11	HEA	complex2.pdb.gz	67,69,70,72,73,84,89,93,97
3	0.01	3hb3A	0.524	4.28	0.077	0.801	0.12	HEA	complex3.pdb.gz	136,139,143,144,148
4	0.01	3omaA	0.519	4.53	0.058	0.814	0.11	HEA	complex4.pdb.gz	59,60,95
5	0.01	3ayxA	0.519	4.19	0.033	0.788	0.37	UUU	complex5.pdb.gz	60,61,62,98,101
6	0.01	1qleA	0.520	4.44	0.059	0.808	0.14	HEA	complex6.pdb.gz	16,19,23,59,63,66,70,71,73,74

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.