D-I-TASSER Q8NE35

D-I-TASSER results for Q8NE35

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

Summary of the Protein

Uniprot ID: Q8NE35
Protein Name: Cytoplasmic polyadenylation element-binding protein 3
Gene Name: CPEB3

Input Sequence in FASTA format

>Q8NE35 (698 residues)
MQDDLLMDKSKTQPQPQQQQRQQQQPQPESSVSEAPSTPLSSETPKPEENSAVPALSPAA
APPAPNGPDKMQMESPLLPGLSFHQPPQQPPPPQEPAAPGASLSPSFGSTWSTGTTNAVE
DSFFQGITPVNGTMLFQNFPHHVNPVFGGTFSPQIGLAQTQHHQQPPPPAPAPQPAQPAQ
PPQAQPPQQRRSPASPSQAPYAQRSAAAAYGHQPIMTSKPSSSSAVAAAAAAAAASSASS
SWNTHQSVNAAWSAPSNPWGGLQAGRDPRRAVGVGVGVGVGVPSPLNPISPLKKPFSSNV
IAPPKFPRAAPLTSKSWMEDNAFRTDNGNNLLPFQDRSRPYDTFNLHSLENSLMDMIRTD
HEPLKGKHYPPSGPPMSFADIMWRNHFAGRMGINFHHPGTDNIMALNNAFLDDSHGDQAL
SSGLSSPTRCQNGERVERYSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSY
FPPKGYAFLLFQEESSVQALIDACLEEDGKLYLCVSSPTIKDKPVQIRPWNLSDSDFVMD
GSQPLDPRKTIFVGGVPRPLRAVELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFSN
QQSYIAAISARFVQLQHNDIDKRVEVKPYVLDDQMCDECQGTRCGGKFAPFFCANVTCLQ
YYCEYCWASIHSRAGREFHKPLVKEGGDRPRHVPFRWS

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	Q8NE35-D1	1-698	698		MQDDLLMDKSKTQPQPQQQQRQQQQPQPESSVSEAPSTPLSSETPKPEENSAVPALSPAAAPPAPNGPDKMQMESPLLPGLSFHQPPQQPPPPQEPAAPGASLSPSFGSTWSTGTTNAVEDSFFQGITPVNGTMLFQNFPHHVNPVFGGTFSPQIGLAQTQHHQQPPPPAPAPQPAQPAQPPQAQPPQQRRSPASPSQAPYAQRSAAAAYGHQPIMTSKPSSSSAVAAAAAAAAASSASSSWNTHQSVNAAWSAPSNPWGGLQAGRDPRRAVGVGVGVGVGVPSPLNPISPLKKPFSSNVIAPPKFPRAAPLTSKSWMEDNAFRTDNGNNLLPFQDRSRPYDTFNLHSLENSLMDMIRTDHEPLKGKHYPPSGPPMSFADIMWRNHFAGRMGINFHHPGTDNIMALNNAFLDDSHGDQALSSGLSSPTRCQNGERVERYSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEEDGKLYLCVSSPTIKDKPVQIRPWNLSDSDFVMDGSQPLDPRKTIFVGGVPRPLRAVELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFSNQQSYIAAISARFVQLQHNDIDKRVEVKPYVLDDQMCDECQGTRCGGKFAPFFCANVTCLQYYCEYCWASIHSRAGREFHKPLVKEGGDRPRHVPFRWS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4301

(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	2zjaA	0.71	4.38	0.052	0.831	model1_2zjaA.pdb.gz
2	2va8B	0.69	4.65	0.062	0.830	model1_2va8B.pdb.gz
3	5agaA	0.69	5.25	0.076	0.867	model1_5agaA.pdb.gz
4	2p6rA	0.65	5.15	0.059	0.814	model1_2p6rA.pdb.gz
5	4bgdA2	0.63	5.68	0.074	0.815	model1_4bgdA2.pdb.gz
6	5gm6B	0.63	5.75	0.069	0.817	model1_5gm6B.pdb.gz
7	5m59A	0.62	5.81	0.060	0.808	model1_5m59A.pdb.gz
8	7abis	0.62	5.79	0.058	0.801	model1_7abis.pdb.gz
9	4a4zA2	0.58	5.47	0.061	0.739	model1_4a4zA2.pdb.gz
10	5mc6h	0.58	5.47	0.061	0.739	model1_5mc6h.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:0003723	1.00	RNA binding
GO:0003729	0.99	mRNA binding
GO:0000900	0.96	translation repressor activity, nucleic acid binding
GO:0003730	0.95	mRNA 3'-UTR binding
GO:0043022	0.94	ribosome binding
GO:0008135	0.94	translation factor activity, RNA 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	1.00	biological regulation
GO:0050789	1.00	regulation of biological process
GO:0006417	0.99	regulation of translation
GO:0048519	0.97	negative regulation of biological process
GO:0017148	0.96	negative regulation of translation
GO:2000766	0.95	negative regulation of cytoplasmic translation
GO:0009987	0.59	cellular process

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:0043229	0.98	intracellular organelle
GO:0030529	0.97	intracellular ribonucleoprotein complex
GO:0005737	0.97	cytoplasm
GO:0005634	0.97	nucleus
GO:0097458	0.94	neuron part
GO:1990124	0.93	messenger ribonucleoprotein complex
GO:0043005	0.93	neuron projection
GO:0045202	0.92	synapse

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	3e90D	0.118	5.84	0.029	0.158	3.4.21.91	NA
2	0.060	1n1hA	0.350	8.32	0.041	0.576	2.7.7.48	NA
3	0.060	3gm8A	0.307	8.38	0.049	0.501	3.2.1.-	NA
4	0.060	3ffzA	0.337	8.54	0.035	0.554	3.4.24.69	NA
5	0.060	2ipyA	0.295	8.26	0.030	0.477	4.2.1.3	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	0.02	1n38A	0.353	8.33	0.043	0.579	0.39	CH1	complex1.pdb.gz	469,486,487,488
2	0.01	2p6rA	0.653	5.15	0.059	0.814	0.20	QNA	complex2.pdb.gz	145,146,220,415,536
3	0.01	1dy9A	0.115	6.00	0.068	0.156	0.15	III	complex3.pdb.gz	416,417,423,424,429
4	0.01	1ns3B	0.118	6.39	0.061	0.168	0.13	III	complex4.pdb.gz	417,419,446
5	0.01	2fm2A	0.116	6.20	0.050	0.161	0.13	3BC	complex5.pdb.gz	441,552,553,554,555
6	0.01	3lrrB	0.083	4.55	0.012	0.100	0.20	RQA	complex6.pdb.gz	441,442,457
7	0.01	1jxpA	0.112	6.18	0.045	0.153	0.15	III	complex7.pdb.gz	433,434,464,465,466,467
8	0.01	2oc7A	0.107	5.68	0.050	0.140	0.19	III	complex8.pdb.gz	416,417,421,422,427,466,467,468,469
9	0.01	2gvfC	0.104	5.59	0.040	0.138	0.26	III	complex9.pdb.gz	348,349,421,423,469,470
10	0.01	1n1lA	0.116	5.99	0.065	0.158	0.12	III	complex10.pdb.gz	429,434,464,465,466

	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.