D-I-TASSER Q9Y483

D-I-TASSER results for Q9Y483

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

Summary of the Protein

Uniprot ID: Q9Y483
Protein Name: Metal-response element-binding transcription factor 2
Gene Name: MTF2

Input Sequence in FASTA format

>Q9Y483 (593 residues)
MRDSTGAGNSLVHKRSPLRRNQKTPTSLTKLSLQDGHKAKKPACKFEEGQDVLARWSDGL
FYLGTIKKINILKQSCFIIFEDSSKSWVLWKDIQTGATGSGEMVCTICQEEYSEAPNEMV
ICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFATTTKRGGALKKGPNAKALQVMKQ
TLPYSVADLEWDAGHKTNVQQCYCYCGGPGDWYLKMLQCCKCKQWFHEACVQCLQKPMLF
GDRFYTFICSVCSSGPEYLKRLPLQWVDIAHLCLYNLSVIHKKKYFDSELELMTYINENW
DRLHPGELADTPKSERYEHVLEALNDYKTMFMSGKEIKKKKHLFGLRIRVPPVPPNVAFK
AEKEPEGTSHEFKIKGRKASKPISDSREVSNGIEKKGKKKSVGRPPGPYTRKMIQKTAEP
LLDKESISENPTLDLPCSIGRTEGTAHSSNTSDVDFTGASSAKETTSSSISRHYGLSDSR
KRTRTGRSWPAAIPHLRRRRGRLPRRALQTQNSEIVKDDEGKEDYQFDELNTEILNNLAD
QELQLNHLKNSITSYFGAAGRIACGEKYRVLARRVTLDGKVQYLVEWEGATAS

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	Q9Y483-D1	1-593	593		MRDSTGAGNSLVHKRSPLRRNQKTPTSLTKLSLQDGHKAKKPACKFEEGQDVLARWSDGLFYLGTIKKINILKQSCFIIFEDSSKSWVLWKDIQTGATGSGEMVCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFATTTKRGGALKKGPNAKALQVMKQTLPYSVADLEWDAGHKTNVQQCYCYCGGPGDWYLKMLQCCKCKQWFHEACVQCLQKPMLFGDRFYTFICSVCSSGPEYLKRLPLQWVDIAHLCLYNLSVIHKKKYFDSELELMTYINENWDRLHPGELADTPKSERYEHVLEALNDYKTMFMSGKEIKKKKHLFGLRIRVPPVPPNVAFKAEKEPEGTSHEFKIKGRKASKPISDSREVSNGIEKKGKKKSVGRPPGPYTRKMIQKTAEPLLDKESISENPTLDLPCSIGRTEGTAHSSNTSDVDFTGASSAKETTSSSISRHYGLSDSRKRTRTGRSWPAAIPHLRRRRGRLPRRALQTQNSEIVKDDEGKEDYQFDELNTEILNNLADQELQLNHLKNSITSYFGAAGRIACGEKYRVLARRVTLDGKVQYLVEWEGATAS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4338

(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	4bgdA	0.42	7.69	0.040	0.669	model1_4bgdA.pdb.gz
2	4f91B	0.41	7.62	0.029	0.661	model1_4f91B.pdb.gz
3	5m59A	0.41	7.70	0.039	0.658	model1_5m59A.pdb.gz
4	5xfrA	0.40	3.88	0.795	0.455	model1_5xfrA.pdb.gz
5	5xfnA	0.39	3.65	0.441	0.440	model1_5xfnA.pdb.gz
6	6w2jA	0.39	7.18	0.040	0.590	model1_6w2jA.pdb.gz
7	5julA	0.38	7.87	0.036	0.627	model1_5julA.pdb.gz
8	5nrlP	0.38	8.08	0.037	0.631	model1_5nrlP.pdb.gz
9	6yejA	0.37	7.97	0.040	0.617	model1_6yejA.pdb.gz
10	5fvmA	0.37	7.81	0.046	0.604	model1_5fvmA.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:0042393	0.71	histone binding
GO:0035064	0.70	methylated histone 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:0009987	0.97	cellular process
GO:0065007	0.83	biological regulation
GO:0050794	0.82	regulation of cellular process
GO:0044699	0.78	single-organism process
GO:0080090	0.76	regulation of primary metabolic process
GO:0060255	0.76	regulation of macromolecule metabolic process
GO:0031323	0.76	regulation of cellular metabolic process
GO:0048519	0.74	negative regulation of biological process
GO:0044763	0.74	single-organism cellular process
GO:0048518	0.72	positive regulation of biological process
GO:0010468	0.72	regulation of gene expression
GO:0048522	0.71	positive regulation of cellular process
GO:0032502	0.71	developmental process
GO:0031325	0.70	positive regulation of cellular metabolic process
GO:0010605	0.70	negative regulation of macromolecule metabolic process
GO:0010604	0.70	positive regulation of macromolecule metabolic process
GO:0051128	0.68	regulation of cellular component organization
GO:0048523	0.68	negative regulation of cellular process
GO:0044767	0.68	single-organism developmental process
GO:0031062	0.67	positive regulation of histone methylation
GO:0061087	0.66	positive regulation of histone H3-K27 methylation
GO:0048869	0.66	cellular developmental process
GO:0010629	0.66	negative regulation of gene expression
GO:0031324	0.64	negative regulation of cellular metabolic process
GO:2000112	0.61	regulation of cellular macromolecule biosynthetic process
GO:0051171	0.61	regulation of nitrogen compound metabolic process
GO:0030154	0.61	cell differentiation
GO:0006355	0.60	regulation of transcription, DNA-templated
GO:0044707	0.57	single-multicellular organism process
GO:0006357	0.56	regulation of transcription from RNA polymerase II promoter
GO:0032269	0.55	negative regulation of cellular protein metabolic process
GO:2000113	0.54	negative regulation of cellular macromolecule biosynthetic process
GO:0051172	0.54	negative regulation of nitrogen compound metabolic process
GO:0031057	0.54	negative regulation of histone modification
GO:0061086	0.53	negative regulation of histone H3-K27 methylation
GO:0045892	0.53	negative regulation of transcription, DNA-templated
GO:0071704	0.52	organic substance metabolic process
GO:0044237	0.52	cellular metabolic process
GO:0044238	0.51	primary metabolic process
GO:0048863	0.50	stem cell differentiation
GO:0044260	0.50	cellular macromolecule metabolic process
GO:0019827	0.50	stem cell population maintenance
GO:0000122	0.50	negative regulation of transcription from RNA polymerase II promoter

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:0044422	0.92	organelle part
GO:0044446	0.91	intracellular organelle part
GO:0032991	0.91	macromolecular complex
GO:0044428	0.89	nuclear part
GO:0043234	0.87	protein complex
GO:1990234	0.81	transferase complex
GO:0044451	0.81	nucleoplasm part
GO:0043226	0.79	organelle
GO:0043229	0.78	intracellular organelle
GO:0043227	0.77	membrane-bounded organelle
GO:0034708	0.76	methyltransferase complex
GO:0005634	0.76	nucleus
GO:0035097	0.74	histone methyltransferase complex
GO:0031519	0.67	PcG protein complex
GO:0035098	0.66	ESC/E(Z) 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	3hmjA	0.323	8.29	0.064	0.555	2.3.1.86	NA
2	0.060	3ecqB	0.316	7.82	0.044	0.514	3.2.1.97	56
3	0.060	2np0A	0.357	8.02	0.039	0.585	3.4.24.69	NA
4	0.060	2vz9B	0.317	8.62	0.043	0.567	2.3.1.85	NA
5	0.060	1ob2A	0.191	6.76	0.051	0.278	3.6.1.48	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	3shfA	0.383	8.16	0.042	0.648	0.43	GBL	complex1.pdb.gz	104,105,128,130

	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.