D-I-TASSER Q9H9V9

D-I-TASSER results for Q9H9V9

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

Summary of the Protein

Uniprot ID: Q9H9V9
Protein Name: 2-oxoglutarate and iron-dependent oxygenase JMJD4
Gene Name: JMJD4

Input Sequence in FASTA format

>Q9H9V9 (463 residues)
MRAGPEPQALAGQKRGALRLLVPRLVLTVSAPAEVRRRVLRPVLSWMDRETRALADSHFR
GLGVDVPGVGQAPGRVAFVSEPGAFSYADFVRGFLLPNLPCVFSSAFTQGWGSRRRWVTP
AGRPDFDHLLRTYGDVVVPVANCGVQEYNSNPKEHMTLRDYITYWKEYIQAGYSSPRGCL
YLKDWHLCRDFPVEDVFTLPVYFSSDWLNEFWDALDVDDYRFVYAGPAGSWSPFHADIFR
SFSWSVNVCGRKKWLLFPPGQEEALRDRHGNLPYDVTSPALCDTHLHPRNQLAGPPLEIT
QEAGEMVFVPSGWHHQVHNLDDTISINHNWVNGFNLANMWRFLQQELCAVQEEVSEWRDS
MPDWHHHCQVIMRSCSGINFEEFYHFLKVIAEKRLLVLREAAAEDGAGLGFEQAAFDVGR
ITEVLASLVAHPDFQRVDTSAFSPQPKELLQQLREAVDAAAAP

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	Q9H9V9-D1	1-330	330		MRAGPEPQALAGQKRGALRLLVPRLVLTVSAPAEVRRRVLRPVLSWMDRETRALADSHFRGLGVDVPGVGQAPGRVAFVSEPGAFSYADFVRGFLLPNLPCVFSSAFTQGWGSRRRWVTPAGRPDFDHLLRTYGDVVVPVANCGVQEYNSNPKEHMTLRDYITYWKEYIQAGYSSPRGCLYLKDWHLCRDFPVEDVFTLPVYFSSDWLNEFWDALDVDDYRFVYAGPAGSWSPFHADIFRSFSWSVNVCGRKKWLLFPPGQEEALRDRHGNLPYDVTSPALCDTHLHPRNQLAGPPLEITQEAGEMVFVPSGWHHQVHNLDDTISINHNW
2	Q9H9V9-D2	331-463	133		VNGFNLANMWRFLQQELCAVQEEVSEWRDSMPDWHHHCQVIMRSCSGINFEEFYHFLKVIAEKRLLVLREAAAEDGAGLGFEQAAFDVGRITEVLASLVAHPDFQRVDTSAFSPQPKELLQQLREAVDAAAAP

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.82

(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	5yknA	0.63	3.93	0.098	0.760	model1_5yknA.pdb.gz
2	6ip0A	0.61	4.05	0.090	0.743	model1_6ip0A.pdb.gz
3	5cehA	0.61	3.63	0.118	0.713	model1_5cehA.pdb.gz
4	5a1fA	0.60	3.87	0.120	0.719	model1_5a1fA.pdb.gz
5	3avrA	0.59	3.93	0.108	0.713	model1_3avrA.pdb.gz
6	3n9lA	0.59	5.10	0.109	0.762	model1_3n9lA.pdb.gz
7	2yu2A	0.59	4.42	0.122	0.724	model1_2yu2A.pdb.gz
8	3ptrB	0.58	4.64	0.100	0.721	model1_3ptrB.pdb.gz
9	2vd7A	0.51	3.86	0.113	0.598	model1_2vd7A.pdb.gz
10	3kv4A2	0.48	3.76	0.106	0.564	model1_3kv4A2.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	0.84	catalytic activity
GO:0016706	0.74	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors
GO:0043167	0.72	ion binding
GO:0046872	0.71	metal ion binding
GO:0032452	0.70	histone demethylase activity
GO:0003676	0.70	nucleic acid binding
GO:0070815	0.63	peptidyl-lysine 5-dioxygenase activity
GO:0046914	0.63	transition metal ion binding
GO:0042802	0.58	identical protein binding
GO:0033749	0.58	histone demethylase activity (H4-R3 specific)
GO:0033746	0.58	histone demethylase activity (H3-R2 specific)
GO:0005506	0.58	iron ion binding
GO:0003723	0.57	RNA binding
GO:0042803	0.55	protein homodimerization activity
GO:0003727	0.55	single-stranded 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:0009987	0.99	cellular process
GO:0008152	0.98	metabolic process
GO:0044260	0.96	cellular macromolecule metabolic process
GO:0044238	0.96	primary metabolic process
GO:0044699	0.95	single-organism process
GO:0043412	0.94	macromolecule modification
GO:0006464	0.89	cellular protein modification process
GO:0044710	0.85	single-organism metabolic process
GO:0071840	0.82	cellular component organization or biogenesis
GO:0065007	0.82	biological regulation
GO:0050789	0.82	regulation of biological process
GO:0016043	0.81	cellular component organization
GO:0006325	0.79	chromatin organization
GO:0050794	0.77	regulation of cellular process
GO:0080090	0.74	regulation of primary metabolic process
GO:0060255	0.74	regulation of macromolecule metabolic process
GO:0044763	0.74	single-organism cellular process
GO:0031323	0.74	regulation of cellular metabolic process
GO:0019219	0.71	regulation of nucleobase-containing compound metabolic process
GO:0010468	0.71	regulation of gene expression
GO:0051252	0.70	regulation of RNA metabolic process
GO:0016570	0.67	histone modification
GO:0044767	0.66	single-organism developmental process
GO:0055114	0.65	oxidation-reduction process
GO:0006482	0.64	protein demethylation
GO:0018193	0.63	peptidyl-amino acid modification
GO:0016577	0.62	histone demethylation
GO:0018126	0.58	protein hydroxylation
GO:0018395	0.56	peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine
GO:0016568	0.55	chromatin modification
GO:0070076	0.54	histone lysine demethylation
GO:0048518	0.54	positive regulation of biological process
GO:2000112	0.53	regulation of cellular macromolecule biosynthetic process
GO:0006355	0.52	regulation of transcription, DNA-templated
GO:0048646	0.51	anatomical structure formation involved in morphogenesis

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:0043227	0.97	membrane-bounded organelle
GO:0043231	0.96	intracellular membrane-bounded organelle
GO:0005634	0.95	nucleus
GO:0044422	0.84	organelle part
GO:0044446	0.83	intracellular organelle part
GO:0044428	0.81	nuclear part
GO:0005654	0.73	nucleoplasm
GO:0043232	0.57	intracellular non-membrane-bounded organelle
GO:0005730	0.54	nucleolus
GO:0005737	0.50	cytoplasm

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	0.074	2yu1A	0.587	4.57	0.126	0.730	1.14.11.27	NA
2	0.067	2ilmA	0.527	3.84	0.144	0.613	1.14.11.16	254,318
3	0.060	1jqnA	0.351	7.16	0.047	0.579	4.1.1.31	NA
4	0.060	3f2bA	0.336	7.57	0.038	0.581	2.7.7.7	106,109
5	0.060	3eifA	0.346	7.74	0.046	0.603	3.4.21.110	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	0.06	1yciA	0.520	3.73	0.150	0.603	0.74	UUU	complex1.pdb.gz	181,183,232,235,245,252,315,317,327
	2	0.02	2q8eB	0.509	3.92	0.115	0.603	0.70	III	complex2.pdb.gz	184,217,221,223,237,328,329,330,377

	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.