D-I-TASSER Q9Y3P4

D-I-TASSER results for Q9Y3P4

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

Summary of the Protein

Uniprot ID: Q9Y3P4
Protein Name: Rhomboid domain-containing protein 3
Gene Name: RHBDD3

Input Sequence in FASTA format

>Q9Y3P4 (386 residues)
MHARGPHGQLSPALPLASSVLMLLMSTLWLVGAGPGLVLAPELLLDPWQVHRLLTHALGH
TALPGLLLSLLLLPTVGWQQECHLGTLRFLHASALLALASGLLAVLLAGLGLSSAAGSCG
YMPVHLAMLAGEGHRPRRPRGALPPWLSPWLLLALTPLLSSEPPFLQLLCGLLAGLAYAA
GAFRWLEPSERRLQVLQEGVLCRTLAGCWPLRLLATPGSLAELPVTHPAGVRPPIPGPPY
VASPDLWSHWEDSALPPPSLRPVQPTWEGSSEAGLDWAGASFSPGTPMWAALDEQMLQEG
IQASLLDGPAQEPQSAPWLSKSSVSSLRLQQLERMGFPTEQAVVALAATGRVEGAVSLLV
GGQVGTETLVTHGKGGPAHSEGPGPP

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	Q9Y3P4-D1	1-386	386		MHARGPHGQLSPALPLASSVLMLLMSTLWLVGAGPGLVLAPELLLDPWQVHRLLTHALGHTALPGLLLSLLLLPTVGWQQECHLGTLRFLHASALLALASGLLAVLLAGLGLSSAAGSCGYMPVHLAMLAGEGHRPRRPRGALPPWLSPWLLLALTPLLSSEPPFLQLLCGLLAGLAYAAGAFRWLEPSERRLQVLQEGVLCRTLAGCWPLRLLATPGSLAELPVTHPAGVRPPIPGPPYVASPDLWSHWEDSALPPPSLRPVQPTWEGSSEAGLDWAGASFSPGTPMWAALDEQMLQEGIQASLLDGPAQEPQSAPWLSKSSVSSLRLQQLERMGFPTEQAVVALAATGRVEGAVSLLVGGQVGTETLVTHGKGGPAHSEGPGPP

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.651

(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	8dzzA	0.41	6.98	0.056	0.702	model1_8dzzA.pdb.gz
2	3qmzA	0.40	6.90	0.079	0.666	model1_3qmzA.pdb.gz
3	7czbA	0.39	3.02	0.167	0.451	model1_7czbA.pdb.gz
4	8bypX	0.39	6.99	0.045	0.661	model1_8bypX.pdb.gz
5	2nr9A	0.39	3.32	0.153	0.448	model1_2nr9A.pdb.gz
6	4zktB	0.39	6.81	0.035	0.655	model1_4zktB.pdb.gz
7	8fiaA	0.39	6.20	0.061	0.601	model1_8fiaA.pdb.gz
8	7vf2A	0.39	6.13	0.066	0.580	model1_7vf2A.pdb.gz
9	1vt4I	0.38	6.57	0.081	0.622	model1_1vt4I.pdb.gz
10	2ic8A	0.37	2.97	0.205	0.425	model1_2ic8A.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:0097159	0.45	organic cyclic compound binding
GO:1901363	0.44	heterocyclic compound binding
GO:0003824	0.40	catalytic activity
GO:0097367	0.39	carbohydrate derivative binding
GO:0036094	0.39	small molecule binding
GO:0035639	0.38	purine ribonucleoside triphosphate binding
GO:0032555	0.38	purine ribonucleotide binding
GO:0032550	0.38	purine ribonucleoside binding
GO:0032559	0.37	adenyl ribonucleotide binding
GO:0016787	0.34	hydrolase 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:0019538	0.99	protein metabolic process
GO:0009987	0.88	cellular process
GO:0050794	0.87	regulation of cellular process
GO:0044699	0.87	single-organism process
GO:0044237	0.83	cellular metabolic process
GO:0048583	0.82	regulation of response to stimulus
GO:0044763	0.82	single-organism cellular process
GO:0044260	0.82	cellular macromolecule metabolic process
GO:0051049	0.81	regulation of transport
GO:0050896	0.80	response to stimulus
GO:0050708	0.80	regulation of protein secretion
GO:0048518	0.80	positive regulation of biological process
GO:0044710	0.80	single-organism metabolic process
GO:0007165	0.80	signal transduction
GO:0080090	0.79	regulation of primary metabolic process
GO:0060255	0.79	regulation of macromolecule metabolic process
GO:0048523	0.79	negative regulation of cellular process
GO:0044267	0.79	cellular protein metabolic process
GO:0009894	0.79	regulation of catabolic process
GO:0080134	0.78	regulation of response to stress
GO:0048856	0.78	anatomical structure development
GO:0044767	0.78	single-organism developmental process
GO:0042176	0.78	regulation of protein catabolic process
GO:0035556	0.78	intracellular signal transduction
GO:0010604	0.78	positive regulation of macromolecule metabolic process
GO:0006464	0.78	cellular protein modification process
GO:0002682	0.78	regulation of immune system process
GO:0045732	0.77	positive regulation of protein catabolic process
GO:0032815	0.77	negative regulation of natural killer cell activation
GO:0009410	0.77	response to xenobiotic stimulus
GO:0002673	0.77	regulation of acute inflammatory response
GO:0001889	0.77	liver development
GO:0000165	0.77	MAPK cascade

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:0044424	1.00	intracellular part
GO:0044444	0.98	cytoplasmic part
GO:0044446	0.97	intracellular organelle part
GO:0016020	0.94	membrane
GO:0043226	0.81	organelle
GO:0043229	0.78	intracellular organelle
GO:0043227	0.77	membrane-bounded organelle
GO:0043231	0.74	intracellular membrane-bounded organelle
GO:0031090	0.73	organelle membrane
GO:0044425	0.68	membrane part
GO:0005634	0.57	nucleus
GO:0032991	0.56	macromolecular complex
GO:0043234	0.55	protein 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	0.060	1iduA	0.334	5.04	0.082	0.456	1.11.1.10	NA
2	0.060	2vdcA	0.369	7.23	0.059	0.642	1.4.1.13	NA
3	0.060	1h0hA	0.324	6.35	0.025	0.508	1.2.1.2	NA
4	0.060	2ztgA	0.334	6.75	0.025	0.547	6.1.1.7	73
5	0.060	2vuaA	0.267	6.79	0.037	0.438	3.4.24.69	121,166

	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	0.03	3txtA	0.362	3.07	0.205	0.414	1.19	DFP	complex1.pdb.gz	65,69,119,120,121,122,126
2	0.02	2xtvA	0.360	3.28	0.209	0.417	0.62	MC3	complex2.pdb.gz	68,71,72,74,75
3	0.02	2xtvA	0.360	3.28	0.209	0.417	0.55	MC3	complex3.pdb.gz	19,22,60,61,70
4	0.01	1lm1A	0.345	6.92	0.040	0.570	0.55	F3S	complex4.pdb.gz	59,60,61,62,63,67,69

	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.