D-I-TASSER Q9NRG4

D-I-TASSER results for Q9NRG4

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Summary of the Protein

Uniprot ID: Q9NRG4
Protein Name: N-lysine methyltransferase SMYD2
Gene Name: SMYD2

Input Sequence in FASTA format

>Q9NRG4 (433 residues)
MRAEGLGGLERFCSPGKGRGLRALQPFQVGDLLFSCPAYAYVLTVNERGNHCEYCFTRKE
GLSKCGRCKQAFYCNVECQKEDWPMHKLECSPMVVFGENWNPSETVRLTARILAKQKIHP
ERTPSEKLLAVKEFESHLDKLDNEKKDLIQSDIAALHHFYSKHLGFPDNDSLVVLFAQVN
CNGFTIEDEELSHLGSAIFPDVALMNHSCCPNVIVTYKGTLAEVRAVQEIKPGEEVFTSY
IDLLYPTEDRNDRLRDSYFFTCECQECTTKDKDKAKVEIRKLSDPPKAEAIRDMVRYARN
VIEEFRRAKHYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGAL
QYGQKIIKPYSKHYPLYSLNVASMWLKLGRLYMGLEHKAAGEKALKKAIAIMEVAHGKDH
PYISEIKQEIESH

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	Q9NRG4-D1	1-238	238		MRAEGLGGLERFCSPGKGRGLRALQPFQVGDLLFSCPAYAYVLTVNERGNHCEYCFTRKEGLSKCGRCKQAFYCNVECQKEDWPMHKLECSPMVVFGENWNPSETVRLTARILAKQKIHPERTPSEKLLAVKEFESHLDKLDNEKKDLIQSDIAALHHFYSKHLGFPDNDSLVVLFAQVNCNGFTIEDEELSHLGSAIFPDVALMNHSCCPNVIVTYKGTLAEVRAVQEIKPGEEVFT
2	Q9NRG4-D2	239-433	195		SYIDLLYPTEDRNDRLRDSYFFTCECQECTTKDKDKAKVEIRKLSDPPKAEAIRDMVRYARNVIEEFRRAKHYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALQYGQKIIKPYSKHYPLYSLNVASMWLKLGRLYMGLEHKAAGEKALKKAIAIMEVAHGKDHPYISEIKQEIESH

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.975

(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	3qwvA	0.98	1.03	0.928	0.993	model1_3qwvA.pdb.gz
2	3n71A	0.82	3.69	0.290	0.979	model1_3n71A.pdb.gz
3	6yuhA	0.81	3.48	0.298	0.947	model1_6yuhA.pdb.gz
4	5cwwB	0.29	7.37	0.034	0.501	model1_5cwwB.pdb.gz
5	3bo5A	0.27	3.81	0.144	0.319	model1_3bo5A.pdb.gz
6	3rq4A	0.27	3.53	0.150	0.314	model1_3rq4A.pdb.gz
7	2r3aA	0.27	3.38	0.164	0.309	model1_2r3aA.pdb.gz
8	3s8pA	0.27	3.39	0.174	0.307	model1_3s8pA.pdb.gz
9	3opeA	0.27	3.37	0.173	0.300	model1_3opeA.pdb.gz
10	2bqzA	0.26	3.38	0.194	0.302	model1_2bqzA.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:0003824	0.82	catalytic activity
GO:0019899	0.79	enzyme binding
GO:0016740	0.79	transferase activity
GO:0008757	0.78	S-adenosylmethionine-dependent methyltransferase activity
GO:0016279	0.75	protein-lysine N-methyltransferase activity
GO:0018024	0.74	histone-lysine N-methyltransferase activity
GO:0044877	0.66	macromolecular complex binding
GO:0032403	0.65	protein complex binding
GO:0000993	0.64	RNA polymerase II core binding
GO:0046975	0.62	histone methyltransferase activity (H3-K36 specific)

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	0.95	cellular process
GO:0065007	0.84	biological regulation
GO:0050789	0.83	regulation of biological process
GO:0008152	0.79	metabolic process
GO:0060255	0.78	regulation of macromolecule metabolic process
GO:0044237	0.78	cellular metabolic process
GO:0010468	0.77	regulation of gene expression
GO:0044260	0.76	cellular macromolecule metabolic process
GO:0044238	0.76	primary metabolic process
GO:0048519	0.75	negative regulation of biological process
GO:0009892	0.74	negative regulation of metabolic process
GO:0010605	0.73	negative regulation of macromolecule metabolic process
GO:0050794	0.72	regulation of cellular process
GO:0010629	0.71	negative regulation of gene expression
GO:0043412	0.70	macromolecule modification
GO:0019538	0.70	protein metabolic process
GO:0006464	0.69	cellular protein modification process
GO:0043414	0.66	macromolecule methylation
GO:0018193	0.66	peptidyl-amino acid modification
GO:0080090	0.65	regulation of primary metabolic process
GO:0031323	0.65	regulation of cellular metabolic process
GO:0018022	0.65	peptidyl-lysine methylation
GO:0006355	0.64	regulation of transcription, DNA-templated
GO:0031324	0.61	negative regulation of cellular metabolic process
GO:0006357	0.60	regulation of transcription from RNA polymerase II promoter
GO:0045892	0.58	negative regulation of transcription, DNA-templated
GO:0048583	0.57	regulation of response to stimulus
GO:2001020	0.56	regulation of response to DNA damage stimulus
GO:1902531	0.56	regulation of intracellular signal transduction
GO:0044699	0.56	single-organism process
GO:0042127	0.56	regulation of cell proliferation
GO:0043516	0.55	regulation of DNA damage response, signal transduction by p53 class mediator
GO:0018027	0.55	peptidyl-lysine dimethylation
GO:0018026	0.55	peptidyl-lysine monomethylation
GO:0008285	0.55	negative regulation of cell proliferation
GO:0000122	0.55	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:0043226	0.93	organelle
GO:0043229	0.92	intracellular organelle
GO:0043231	0.90	intracellular membrane-bounded organelle
GO:0005634	0.87	nucleus
GO:0005737	0.84	cytoplasm
GO:0044444	0.80	cytoplasmic part
GO:0005829	0.73	cytosol

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	2epoA	0.393	7.09	0.041	0.647	3.2.1.52	NA
2	0.060	2ecfA	0.380	7.34	0.051	0.647	3.4.14.5	NA
3	0.060	1l2aE	0.371	6.53	0.038	0.577	3.2.1.4	NA
4	0.060	1orvA	0.389	7.41	0.058	0.658	3.4.14.5	NA
5	0.060	1jqoA	0.385	7.39	0.047	0.663	4.1.1.31	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	0.82	3tg4A	0.981	0.54	1.000	0.986	1.70	SAM	complex1.pdb.gz	16,17,19,137,181,182,203,204,206,207,240,258,260
2	0.54	3s7dA	0.990	0.25	0.998	0.991	1.94	III	complex2.pdb.gz	179,181,183,184,185,187,191,196,203,205,214,215,240,242,258,344,379,380
3	0.53	3s7bA	0.990	0.18	0.998	0.991	1.75	NH5	complex3.pdb.gz	105,141,145,149,177,180,181,182,183,184,185,203,238,239,240,257,258
4	0.03	2h23A	0.442	4.87	0.088	0.564	0.93	M3L	complex4.pdb.gz	181,182,183,184,185,205,240,258

	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.