D-I-TASSER Q15011

D-I-TASSER results for Q15011

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Summary of the Protein

Uniprot ID: Q15011
Protein Name: Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein
Gene Name: HERPUD1

Input Sequence in FASTA format

>Q15011 (391 residues)
MESETEPEPVTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSG
KLLLDHQCLRDLLPKQEKRHVLHLVCNVKSPSKMPEINAKVAESTEEPAGSNRGQYPEDS
SSDGLRQREVLRNLSSPGWENISRPEAAQQAFQGLGPGFSGYTPYGWLQLSWFQQIYARQ
YYMQYLAATAASGAFVPPPSAQEIPVVSAPAPAPIHNQFPAENQPANQNAAPQVVVNPGA
NQNLRMNAQGGPIVEEDDEINRDWLDWTYSAATFSVFLSILYFYSSLSRFLMVMGATVVM
YLHHVGWFPFRPRPVQNFPNDGPPPDVVNQDPNNNLQEGTDPETEDPNHLPPDRDVLDGE
QTSPSFMSTAWLVFKTFFASLLPEGPPAIAN

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	Q15011-D1	1-391	391		MESETEPEPVTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLVCNVKSPSKMPEINAKVAESTEEPAGSNRGQYPEDSSSDGLRQREVLRNLSSPGWENISRPEAAQQAFQGLGPGFSGYTPYGWLQLSWFQQIYARQYYMQYLAATAASGAFVPPPSAQEIPVVSAPAPAPIHNQFPAENQPANQNAAPQVVVNPGANQNLRMNAQGGPIVEEDDEINRDWLDWTYSAATFSVFLSILYFYSSLSRFLMVMGATVVMYLHHVGWFPFRPRPVQNFPNDGPPPDVVNQDPNNNLQEGTDPETEDPNHLPPDRDVLDGEQTSPSFMSTAWLVFKTFFASLLPEGPPAIAN

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.574

(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	6sytA	0.37	6.32	0.035	0.568	model1_6sytA.pdb.gz
2	4bedA	0.35	7.51	0.037	0.644	model1_4bedA.pdb.gz
3	5ganA	0.35	7.13	0.038	0.599	model1_5ganA.pdb.gz
4	5x6oC	0.35	7.11	0.029	0.578	model1_5x6oC.pdb.gz
5	6l42A	0.34	6.60	0.045	0.552	model1_6l42A.pdb.gz
6	6vr4A	0.34	6.74	0.049	0.573	model1_6vr4A.pdb.gz
7	6b5bA	0.34	6.72	0.033	0.550	model1_6b5bA.pdb.gz
8	5f0oA	0.34	6.77	0.029	0.552	model1_5f0oA.pdb.gz
9	6bcuA	0.33	6.68	0.052	0.537	model1_6bcuA.pdb.gz
10	6uebA	0.33	7.03	0.016	0.563	model1_6uebA.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:0044325	1.00	ion channel 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:0065007	0.94	biological regulation
GO:0050794	0.93	regulation of cellular process
GO:0080090	0.88	regulation of primary metabolic process
GO:0060255	0.88	regulation of macromolecule metabolic process
GO:0048518	0.88	positive regulation of biological process
GO:0031323	0.88	regulation of cellular metabolic process
GO:0048584	0.87	positive regulation of response to stimulus
GO:0032268	0.87	regulation of cellular protein metabolic process
GO:0031325	0.87	positive regulation of cellular metabolic process
GO:0010604	0.87	positive regulation of macromolecule metabolic process
GO:1903071	0.86	positive regulation of ER-associated ubiquitin-dependent protein catabolic process
GO:0009987	0.81	cellular process
GO:0044699	0.80	single-organism process
GO:0050896	0.73	response to stimulus
GO:0007165	0.71	signal transduction
GO:0034976	0.70	response to endoplasmic reticulum stress
GO:0044763	0.68	single-organism cellular process
GO:0030968	0.68	endoplasmic reticulum unfolded protein response
GO:0048519	0.66	negative regulation of biological process
GO:0065008	0.65	regulation of biological quality
GO:0048523	0.65	negative regulation of cellular process
GO:1902531	0.64	regulation of intracellular signal transduction
GO:0042981	0.64	regulation of apoptotic process
GO:0009968	0.64	negative regulation of signal transduction
GO:0006874	0.64	cellular calcium ion homeostasis
GO:1902236	0.63	negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway
GO:0032469	0.63	endoplasmic reticulum calcium ion homeostasis

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:0044446	1.00	intracellular organelle part
GO:0043234	1.00	protein complex
GO:0044444	0.96	cytoplasmic part
GO:0043229	0.96	intracellular organelle
GO:0043227	0.96	membrane-bounded organelle
GO:0044425	0.95	membrane part
GO:0043231	0.95	intracellular membrane-bounded organelle
GO:0016020	0.95	membrane
GO:0034704	0.94	calcium channel complex
GO:0005789	0.94	endoplasmic reticulum membrane
GO:0005783	0.94	endoplasmic reticulum
GO:0097458	0.65	neuron part
GO:1990037	0.64	Lewy body core

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	2jfdA	0.147	6.78	0.014	0.243	2.3.1.85	NA
2	0.060	1jqoA	0.298	6.55	0.039	0.473	4.1.1.31	NA
3	0.060	3d8vA	0.265	6.86	0.027	0.430	2.7.7.23 2.3.1.157	NA
4	0.060	2vdcA	0.291	6.35	0.022	0.460	1.4.1.13	NA
5	0.060	3iayA	0.275	6.70	0.038	0.443	2.7.7.7	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:

Click to view	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	1ea0A	0.279	6.53	0.029	0.445	0.65	F3S	complex1.pdb.gz	12,27,28,29,30,33,69,70

	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.