D-I-TASSER P0C870

D-I-TASSER results for P0C870

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

Summary of the Protein

Uniprot ID: P0C870
Protein Name: Bifunctional peptidase and (3S)-lysyl hydroxylase JMJD7
Gene Name: JMJD7

Input Sequence in FASTA format

>P0C870 (316 residues)
MAEAALEAVRSELREFPAAARELCVPLAVPYLDKPPTPLHFYRDWVCPNRPCIIRNALQH
WPALQKWSLPYFRATVGSTEVSVAVTPDGYADAVRGDRFMMPAERRLPLSFVLDVLEGRA
QHPGVLYVQKQCSNLPSELPQLLPDLESHVPWASEALGKMPDAVNFWLGEAAAVTSLHKD
HYENLYCVVSGEKHFLFHPPSDRPFIPYELYTPATYQLTEEGTFKVVDEEAMEKVPWIPL
DPLAPDLARYPSYSQAQALRCTVRAGEMLYLPALWFHHVQQSQGCIAVNFWYDMEYDLKY
SYFQLLDSLTKASGLD

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	P0C870-D1	1-316	316		MAEAALEAVRSELREFPAAARELCVPLAVPYLDKPPTPLHFYRDWVCPNRPCIIRNALQHWPALQKWSLPYFRATVGSTEVSVAVTPDGYADAVRGDRFMMPAERRLPLSFVLDVLEGRAQHPGVLYVQKQCSNLPSELPQLLPDLESHVPWASEALGKMPDAVNFWLGEAAAVTSLHKDHYENLYCVVSGEKHFLFHPPSDRPFIPYELYTPATYQLTEEGTFKVVDEEAMEKVPWIPLDPLAPDLARYPSYSQAQALRCTVRAGEMLYLPALWFHHVQQSQGCIAVNFWYDMEYDLKYSYFQLLDSLTKASGLD

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.8946

(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	4qszA	0.99	0.67	0.895	0.997	model1_4qszA.pdb.gz
2	2w0xA	0.70	3.60	0.172	0.835	model1_2w0xA.pdb.gz
3	3al5A	0.68	3.19	0.206	0.775	model1_3al5A.pdb.gz
4	3uyjA	0.67	2.00	0.237	0.722	model1_3uyjA.pdb.gz
5	3ptrB	0.61	3.70	0.106	0.741	model1_3ptrB.pdb.gz
6	3kv4A	0.61	3.65	0.121	0.737	model1_3kv4A.pdb.gz
7	4diqA	0.52	4.03	0.121	0.655	model1_4diqA.pdb.gz
8	2xdvA1	0.45	3.82	0.113	0.557	model1_2xdvA1.pdb.gz
9	1fokA	0.31	6.34	0.034	0.516	model1_1fokA.pdb.gz
10	2b3bA	0.30	6.88	0.059	0.528	model1_2b3bA.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:0043167	0.71	ion binding
GO:0046872	0.70	metal ion binding
GO:0016491	0.67	oxidoreductase activity
GO:0016705	0.66	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
GO:0046914	0.64	transition metal ion binding
GO:0016706	0.64	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:0042802	0.63	identical protein binding
GO:0042803	0.61	protein homodimerization activity
GO:0005506	0.61	iron ion binding
GO:0044877	0.54	macromolecular complex binding
GO:0032452	0.50	histone demethylase activity
GO:0003676	0.50	nucleic acid 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	0.98	cellular process
GO:0008152	0.97	metabolic process
GO:0071704	0.95	organic substance metabolic process
GO:0044699	0.95	single-organism process
GO:0044238	0.95	primary metabolic process
GO:0044237	0.95	cellular metabolic process
GO:0044260	0.91	cellular macromolecule metabolic process
GO:0044710	0.90	single-organism metabolic process
GO:0043412	0.90	macromolecule modification
GO:0044763	0.85	single-organism cellular process
GO:0065007	0.80	biological regulation
GO:0050789	0.80	regulation of biological process
GO:0050794	0.74	regulation of cellular process
GO:0006464	0.74	cellular protein modification process
GO:0060255	0.71	regulation of macromolecule metabolic process
GO:0080090	0.70	regulation of primary metabolic process
GO:0031323	0.70	regulation of cellular metabolic process
GO:0016043	0.70	cellular component organization
GO:0010468	0.70	regulation of gene expression
GO:0051252	0.69	regulation of RNA metabolic process
GO:0006325	0.67	chromatin organization
GO:1901576	0.63	organic substance biosynthetic process
GO:0006355	0.62	regulation of transcription, DNA-templated
GO:0055114	0.60	oxidation-reduction process
GO:0006807	0.60	nitrogen compound metabolic process
GO:0044711	0.59	single-organism biosynthetic process
GO:0006139	0.59	nucleobase-containing compound metabolic process
GO:0016570	0.58	histone modification
GO:0016070	0.58	RNA metabolic process
GO:0016577	0.56	histone demethylation
GO:1901564	0.54	organonitrogen compound metabolic process
GO:1901135	0.54	carbohydrate derivative metabolic process
GO:0070076	0.54	histone lysine demethylation
GO:0048518	0.54	positive regulation of biological process
GO:0034470	0.53	ncRNA processing
GO:0032502	0.53	developmental process
GO:0018193	0.53	peptidyl-amino acid modification
GO:1901659	0.52	glycosyl compound biosynthetic process
GO:1901566	0.52	organonitrogen compound biosynthetic process
GO:0048522	0.52	positive regulation of cellular process
GO:0044767	0.52	single-organism developmental process
GO:0031590	0.52	wybutosine metabolic process
GO:0006400	0.52	tRNA modification
GO:1903047	0.51	mitotic cell cycle process
GO:0050896	0.51	response to stimulus
GO:0018126	0.51	protein hydroxylation
GO:0006810	0.50	transport

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	0.91	organelle
GO:0043229	0.90	intracellular organelle
GO:0043227	0.89	membrane-bounded organelle
GO:0043231	0.87	intracellular membrane-bounded organelle
GO:0005634	0.81	nucleus
GO:0044444	0.65	cytoplasmic part
GO:0044446	0.60	intracellular organelle part
GO:0044425	0.51	membrane part
GO:0032991	0.50	macromolecular 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	0.066	2yu1A	0.608	3.66	0.109	0.741	1.14.11.27	69
2	0.060	3hjbA	0.364	6.75	0.075	0.639	5.3.1.9	NA
3	0.060	1ywkA	0.361	4.61	0.066	0.481	5.3.1.17	NA
4	0.060	1up8A	0.359	6.16	0.053	0.585	1.11.1.18	NA
5	0.060	1w9yA	0.463	4.45	0.079	0.604	1.14.17.4	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	0.21	1yciA	0.701	3.57	0.179	0.832	0.77	UUU	complex1.pdb.gz	127,129,167,175,184,186,193,277,279,289,291
	2	0.06	2xxzB	0.619	4.00	0.080	0.772	0.49	8XQ	complex2.pdb.gz	169,171,175,178,187,195,277,279

	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.