D-I-TASSER Q96EZ4

D-I-TASSER results for Q96EZ4

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

Summary of the Protein

Uniprot ID: Q96EZ4
Protein Name: Myeloma-overexpressed gene protein
Gene Name: MYEOV

Input Sequence in FASTA format

>Q96EZ4 (313 residues)
MALRICVTYTPALPIGLCTRCCLCLEQSPSWCHCLRGVSFLTFHLHQSVPLGDRDSLLMF
TRQAGHFVEGSKAGRSRGRLCLSQALRVAVRGAFVSLWFAAGAGDRERNKGDKGAQTGAG
LSQEAEDVDVSRARRVTDAPQGTLCGTGNRNSGSQSARVVGVAHLGEAFRVGVEQAISSC
PEEVHGRHGLSMEIMWARMDVALRSPGRGLLAGAGALCMTLAESSCPDYERGRRACLTLH
RHPTPHCSTWGLPLRVAGSWLTVVTVEALGGWRMGVRRTGQVGPTMHPPPVSGASPLLLH
HLLLLLLIIILTC

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	Q96EZ4-D1	1-80	80		MALRICVTYTPALPIGLCTRCCLCLEQSPSWCHCLRGVSFLTFHLHQSVPLGDRDSLLMFTRQAGHFVEGSKAGRSRGRL
2	Q96EZ4-D2	81-313	233		CLSQALRVAVRGAFVSLWFAAGAGDRERNKGDKGAQTGAGLSQEAEDVDVSRARRVTDAPQGTLCGTGNRNSGSQSARVVGVAHLGEAFRVGVEQAISSCPEEVHGRHGLSMEIMWARMDVALRSPGRGLLAGAGALCMTLAESSCPDYERGRRACLTLHRHPTPHCSTWGLPLRVAGSWLTVVTVEALGGWRMGVRRTGQVGPTMHPPPVSGASPLLLHHLLLLLLIIILTC

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.47

(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	6pnsA	0.41	6.30	0.053	0.677	model1_6pnsA.pdb.gz
2	6ryrW	0.40	5.85	0.067	0.629	model1_6ryrW.pdb.gz
3	4v0qA	0.40	6.08	0.051	0.645	model1_4v0qA.pdb.gz
4	6ne3W	0.40	5.72	0.075	0.607	model1_6ne3W.pdb.gz
5	1ryxA	0.39	6.39	0.048	0.655	model1_1ryxA.pdb.gz
6	6uj6A	0.39	6.12	0.055	0.645	model1_6uj6A.pdb.gz
7	3mc2A	0.39	6.59	0.067	0.680	model1_3mc2A.pdb.gz
8	6bllA	0.39	5.68	0.049	0.610	model1_6bllA.pdb.gz
9	3hmjA	0.39	6.73	0.058	0.684	model1_3hmjA.pdb.gz
10	6ts8A	0.39	6.47	0.056	0.664	model1_6ts8A.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	0.63	heterocyclic compound binding
GO:0097159	0.63	organic cyclic compound binding
GO:0043169	0.62	cation binding
GO:0003676	0.61	nucleic acid binding
GO:0003824	0.60	catalytic activity
GO:0097367	0.59	carbohydrate derivative binding
GO:0042623	0.58	ATPase activity, coupled
GO:0035639	0.58	purine ribonucleoside triphosphate binding
GO:0032555	0.58	purine ribonucleotide binding
GO:0032550	0.58	purine ribonucleoside binding
GO:0032559	0.57	adenyl ribonucleotide binding
GO:0016740	0.57	transferase activity
GO:0070035	0.56	purine NTP-dependent helicase activity
GO:0034062	0.56	RNA polymerase activity
GO:0008236	0.56	serine-type peptidase activity
GO:0004175	0.56	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:0065007	0.73	biological regulation
GO:0050789	0.73	regulation of biological process
GO:0050794	0.72	regulation of cellular process
GO:0009987	0.72	cellular process
GO:0048518	0.65	positive regulation of biological process
GO:0008152	0.65	metabolic process
GO:0048522	0.64	positive regulation of cellular process
GO:0044260	0.64	cellular macromolecule metabolic process
GO:0044238	0.64	primary metabolic process
GO:0034641	0.64	cellular nitrogen compound metabolic process
GO:0080090	0.63	regulation of primary metabolic process
GO:0060255	0.63	regulation of macromolecule metabolic process
GO:0044271	0.63	cellular nitrogen compound biosynthetic process
GO:0034645	0.63	cellular macromolecule biosynthetic process
GO:0031323	0.63	regulation of cellular metabolic process
GO:0090304	0.61	nucleic acid metabolic process
GO:0050896	0.61	response to stimulus
GO:0006810	0.61	transport
GO:2001141	0.60	regulation of RNA biosynthetic process
GO:0051704	0.60	multi-organism process
GO:0048523	0.60	negative regulation of cellular process
GO:0010468	0.60	regulation of gene expression
GO:0006351	0.60	transcription, DNA-templated
GO:0048583	0.59	regulation of response to stimulus
GO:0023051	0.59	regulation of signaling
GO:0010646	0.59	regulation of cell communication
GO:2000112	0.58	regulation of cellular macromolecule biosynthetic process
GO:1903506	0.58	regulation of nucleic acid-templated transcription
GO:0065008	0.58	regulation of biological quality
GO:0051707	0.58	response to other organism
GO:0044419	0.58	interspecies interaction between organisms
GO:0016043	0.58	cellular component organization
GO:0009966	0.58	regulation of signal transduction
GO:0002682	0.58	regulation of immune system process
GO:0051817	0.57	modification of morphology or physiology of other organism involved in symbiotic interaction
GO:0050792	0.57	regulation of viral process
GO:0045088	0.57	regulation of innate immune response
GO:0023057	0.57	negative regulation of signaling
GO:0022610	0.57	biological adhesion
GO:0016032	0.57	viral process
GO:0010648	0.57	negative regulation of cell communication
GO:0075114	0.56	negative regulation by symbiont of host transmembrane receptor-mediated signal transduction
GO:0072583	0.56	clathrin-mediated endocytosis
GO:0060339	0.56	negative regulation of type I interferon-mediated signaling pathway
GO:0044800	0.56	multi-organism membrane fusion
GO:0044650	0.56	adhesion of symbiont to host cell
GO:0044033	0.56	multi-organism metabolic process
GO:0039703	0.56	RNA replication
GO:0039519	0.56	modulation by virus of host autophagy
GO:0039503	0.56	suppression by virus of host innate immune response
GO:0019065	0.56	receptor-mediated endocytosis of virus by host cell
GO:0010508	0.56	positive regulation of autophagy
GO:0031399	0.51	regulation of protein modification process
GO:0001932	0.50	regulation of protein phosphorylation

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:0005576	0.86	extracellular region
GO:0044464	0.78	cell part
GO:0016020	0.75	membrane
GO:0044424	0.66	intracellular part
GO:0016021	0.62	integral component of membrane
GO:0055036	0.61	virion membrane
GO:0033644	0.61	host cell membrane
GO:0019012	0.61	virion
GO:0042025	0.56	host cell nucleus
GO:0033655	0.56	host cell cytoplasm part
GO:0044167	0.50	host cell endoplasmic reticulum membrane
GO:0044165	0.50	host cell endoplasmic reticulum
GO:0019031	0.50	viral envelope
GO:0019028	0.50	viral capsid

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	2cunA	0.352	6.81	0.069	0.617	2.7.2.3	NA
2	0.060	1tqnA	0.360	5.86	0.053	0.559	1.14.13.67 1.14.13.32 1.14.13.97	NA
3	0.060	1s4fA	0.352	6.72	0.052	0.620	2.7.7.48	NA
4	0.060	1bxrA	0.357	6.59	0.040	0.617	6.3.5.5	NA
5	0.060	1kitA	0.390	6.77	0.061	0.700	3.2.1.18	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	1n04A	0.395	6.50	0.044	0.671	0.13	CO3	complex1.pdb.gz	1,25,51,52
	2	0.01	3s9nD	0.239	7.14	0.035	0.447	0.21	CO3	complex2.pdb.gz	2,51,52

	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.