D-I-TASSER Q8TEB9

D-I-TASSER results for Q8TEB9

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

Summary of the Protein

Uniprot ID: Q8TEB9
Protein Name: Rhomboid-related protein 4
Gene Name: RHBDD1

Input Sequence in FASTA format

>Q8TEB9 (315 residues)
MQRRSRGINTGLILLLSQIFHVGINNIPPVTLATLALNIWFFLNPQKPLYSSCLSVEKCY
QQKDWQRLLLSPLHHADDWHLYFNMASMLWKGINLERRLGSRWFAYVITAFSVLTGVVYL
LLQFAVAEFMDEPDFKRSCAVGFSGVLFALKVLNNHYCPGGFVNILGFPVPNRFACWVEL
VAIHLFSPGTSFAGHLAGILVGLMYTQGPLKKIMEACAGGFSSSVGYPGRQYYFNSSGSS
GYQDYYPHGRPDHYEEAPRNYDTYTAGLSEEEQLERALQASLWDRGNTRNSPPPYGFHLS
PEEMRRQRLHRFDSQ

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	Q8TEB9-D1	1-315	315		MQRRSRGINTGLILLLSQIFHVGINNIPPVTLATLALNIWFFLNPQKPLYSSCLSVEKCYQQKDWQRLLLSPLHHADDWHLYFNMASMLWKGINLERRLGSRWFAYVITAFSVLTGVVYLLLQFAVAEFMDEPDFKRSCAVGFSGVLFALKVLNNHYCPGGFVNILGFPVPNRFACWVELVAIHLFSPGTSFAGHLAGILVGLMYTQGPLKKIMEACAGGFSSSVGYPGRQYYFNSSGSSGYQDYYPHGRPDHYEEAPRNYDTYTAGLSEEEQLERALQASLWDRGNTRNSPPPYGFHLSPEEMRRQRLHRFDSQ

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6679

(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	2nr9A	0.50	2.85	0.189	0.565	model1_2nr9A.pdb.gz
2	7czbA	0.50	2.83	0.131	0.568	model1_7czbA.pdb.gz
3	2ic8A	0.49	2.31	0.208	0.533	model1_2ic8A.pdb.gz
4	5aexA	0.47	5.67	0.092	0.718	model1_5aexA.pdb.gz
5	5aezA	0.46	5.80	0.069	0.705	model1_5aezA.pdb.gz
6	7bvcA	0.45	5.57	0.037	0.676	model1_7bvcA.pdb.gz
7	7bvfA	0.45	5.63	0.045	0.679	model1_7bvfA.pdb.gz
8	2nuuD	0.45	5.62	0.084	0.682	model1_2nuuD.pdb.gz
9	2b2jA	0.45	5.59	0.097	0.679	model1_2b2jA.pdb.gz
10	7bveA	0.44	5.68	0.041	0.667	model1_7bveA.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:0003824	0.98	catalytic activity
GO:0004252	0.97	serine-type endopeptidase activity

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:0006508	1.00	proteolysis
GO:0009987	0.96	cellular process
GO:0044699	0.95	single-organism process
GO:0050794	0.94	regulation of cellular process
GO:0044260	0.94	cellular macromolecule metabolic process
GO:0080090	0.93	regulation of primary metabolic process
GO:0070887	0.93	cellular response to chemical stimulus
GO:0044767	0.93	single-organism developmental process
GO:0044710	0.93	single-organism metabolic process
GO:0043066	0.93	negative regulation of apoptotic process
GO:0034976	0.93	response to endoplasmic reticulum stress
GO:0032879	0.93	regulation of localization
GO:0031325	0.93	positive regulation of cellular metabolic process
GO:0030154	0.93	cell differentiation
GO:0010628	0.93	positive regulation of gene expression
GO:0006464	0.93	cellular protein modification process
GO:2000254	0.92	regulation of male germ cell proliferation
GO:0051047	0.92	positive regulation of secretion
GO:0048515	0.92	spermatid differentiation
GO:0045732	0.92	positive regulation of protein catabolic process
GO:0043687	0.92	post-translational protein modification
GO:0036503	0.92	ERAD pathway
GO:0034644	0.92	cellular response to UV
GO:0034620	0.92	cellular response to unfolded protein
GO:0031293	0.92	membrane protein intracellular domain proteolysis
GO:0010954	0.92	positive regulation of protein processing

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:0044464	1.00	cell part
GO:0016020	0.98	membrane
GO:0044424	0.97	intracellular part
GO:0044446	0.96	intracellular organelle part
GO:0044444	0.95	cytoplasmic part
GO:0016021	0.89	integral component of membrane
GO:0044322	0.88	endoplasmic reticulum quality control compartment
GO:0030176	0.88	integral component of endoplasmic reticulum membrane
GO:0005789	0.88	endoplasmic reticulum membrane
GO:0043226	0.64	organelle
GO:0043229	0.61	intracellular organelle
GO:0043227	0.58	membrane-bounded organelle
GO:0043231	0.55	intracellular membrane-bounded organelle

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	0.293	2nr9A	0.505	2.85	0.189	0.565	3.4.21.105	37,73,83,106,150
2	0.060	3en9A	0.392	6.48	0.063	0.667	3.4.24.57	150
3	0.060	1mo7A	0.252	5.88	0.044	0.394	3.6.3.9	97
4	0.060	1mhsA	0.402	5.66	0.053	0.603	3.6.3.6	NA
5	0.060	3b45A	0.485	2.23	0.211	0.527	3.4.21.105	42,83,89,191

	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	0.10	2xtvA	0.475	2.52	0.205	0.527	1.40	MC3	complex1.pdb.gz	114,118,197,201,204
2	0.04	3txtA	0.474	2.25	0.215	0.517	1.25	DFP	complex2.pdb.gz	80,84,141,142,143,144,148
3	0.04	2xowA	0.488	2.05	0.212	0.524	1.19	ISM	complex3.pdb.gz	80,84,140,141,142,143,144,186,188,190,191,194,195
4	0.04	2nr9A	0.505	2.85	0.189	0.565	1.04	PQE	complex4.pdb.gz	103,114,118,197,200,204,205
5	0.03	2xtvA	0.475	2.52	0.205	0.527	1.02	MC3	complex5.pdb.gz	83,86,87,89,90
6	0.01	3fyeA	0.363	5.98	0.069	0.587	0.80	DMU	complex6.pdb.gz	109,196,197,200,201,204
7	0.01	3dtuC	0.362	6.01	0.061	0.591	0.93	DXC	complex7.pdb.gz	145,148,149,152,200
8	0.01	3omiC	0.377	6.05	0.050	0.603	0.94	TRD	complex8.pdb.gz	192,195,199

	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.