D-I-TASSER Q9H4X1

D-I-TASSER results for Q9H4X1

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

Summary of the Protein

Uniprot ID: Q9H4X1
Protein Name: Regulator of cell cycle RGCC
Gene Name: RGCC

Input Sequence in FASTA format

>Q9H4X1 (137 residues)
MKPPAAQGSPAAAAAAAPALDSAAAEDLSDALCEFDAVLADFASPFHERHFHYEEHLERM
KRRSSASVSDSSGFSDSESADSLYRNSFSFSDEKLNSPTDSTPALLSATVTPQKAKLGDT
KELEAFIADLDKTLASM

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	Q9H4X1-D1	1-137	137		MKPPAAQGSPAAAAAAAPALDSAAAEDLSDALCEFDAVLADFASPFHERHFHYEEHLERMKRRSSASVSDSSGFSDSESADSLYRNSFSFSDEKLNSPTDSTPALLSATVTPQKAKLGDTKELEAFIADLDKTLASM

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5329

(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	5zizA	0.65	3.98	0.100	0.934	model1_5zizA.pdb.gz
2	5ytiA	0.61	4.15	0.067	0.942	model1_5ytiA.pdb.gz
3	6x80A	0.61	3.64	0.076	0.876	model1_6x80A.pdb.gz
4	2zbiB	0.60	3.17	0.094	0.803	model1_2zbiB.pdb.gz
5	4ecgA	0.59	3.65	0.083	0.781	model1_4ecgA.pdb.gz
6	2d4xA	0.59	4.11	0.096	0.920	model1_2d4xA.pdb.gz
7	5xbjA	0.59	4.27	0.044	0.934	model1_5xbjA.pdb.gz
8	6sihA2	0.59	3.99	0.105	0.883	model1_6sihA2.pdb.gz
9	3mk4A	0.59	3.74	0.063	0.912	model1_3mk4A.pdb.gz
10	4a01A	0.59	4.16	0.015	0.890	model1_4a01A.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:0019901	1.00	protein kinase binding
GO:0098772	0.70	molecular function regulator
GO:0019887	0.69	protein kinase regulator activity
GO:0070412	0.68	R-SMAD binding
GO:0030295	0.68	protein kinase activator activity

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:2000112	1.00	regulation of cellular macromolecule biosynthetic process
GO:0072537	1.00	fibroblast activation
GO:0045935	1.00	positive regulation of nucleobase-containing compound metabolic process
GO:0031328	1.00	positive regulation of cellular biosynthetic process
GO:0010557	1.00	positive regulation of macromolecule biosynthetic process
GO:0000079	1.00	regulation of cyclin-dependent protein serine/threonine kinase activity
GO:0071704	0.72	organic substance metabolic process
GO:0048519	0.72	negative regulation of biological process
GO:0044238	0.72	primary metabolic process
GO:0048523	0.71	negative regulation of cellular process
GO:0043170	0.71	macromolecule metabolic process
GO:0006355	0.71	regulation of transcription, DNA-templated
GO:0050896	0.70	response to stimulus
GO:0045893	0.70	positive regulation of transcription, DNA-templated
GO:0022402	0.70	cell cycle process
GO:2000573	0.69	positive regulation of DNA biosynthetic process
GO:2000026	0.69	regulation of multicellular organismal development
GO:1903047	0.69	mitotic cell cycle process
GO:0051716	0.69	cellular response to stimulus
GO:0051240	0.69	positive regulation of multicellular organismal process
GO:0051128	0.69	regulation of cellular component organization
GO:0048583	0.69	regulation of response to stimulus
GO:0045786	0.69	negative regulation of cell cycle
GO:0043085	0.69	positive regulation of catalytic activity
GO:0042221	0.69	response to chemical
GO:0019538	0.69	protein metabolic process
GO:0010564	0.69	regulation of cell cycle process
GO:0007346	0.69	regulation of mitotic cell cycle
GO:0001934	0.69	positive regulation of protein phosphorylation
GO:2000353	0.68	positive regulation of endothelial cell apoptotic process
GO:2000048	0.68	negative regulation of cell-cell adhesion mediated by cadherin
GO:1901203	0.68	positive regulation of extracellular matrix assembly
GO:0090272	0.68	negative regulation of fibroblast growth factor production
GO:0071850	0.68	mitotic cell cycle arrest
GO:0071456	0.68	cellular response to hypoxia
GO:0071158	0.68	positive regulation of cell cycle arrest
GO:0051496	0.68	positive regulation of stress fiber assembly
GO:0051091	0.68	positive regulation of sequence-specific DNA binding transcription factor activity
GO:0050715	0.68	positive regulation of cytokine secretion
GO:0050710	0.68	negative regulation of cytokine secretion
GO:0045944	0.68	positive regulation of transcription from RNA polymerase II promoter
GO:0045840	0.68	positive regulation of mitotic nuclear division
GO:0043537	0.68	negative regulation of blood vessel endothelial cell migration
GO:0032967	0.68	positive regulation of collagen biosynthetic process
GO:0031659	0.68	positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle
GO:0016525	0.68	negative regulation of angiogenesis
GO:0010718	0.68	positive regulation of epithelial to mesenchymal transition
GO:0006956	0.68	complement activation
GO:0003331	0.68	positive regulation of extracellular matrix constituent secretion
GO:0001937	0.68	negative regulation of endothelial cell proliferation
GO:0001100	0.68	negative regulation of exit from mitosis

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:0005737	1.00	cytoplasm
GO:0044446	0.76	intracellular organelle part
GO:0043226	0.76	organelle
GO:0043229	0.75	intracellular organelle
GO:0043231	0.73	intracellular membrane-bounded organelle
GO:0005634	0.72	nucleus
GO:0043232	0.70	intracellular non-membrane-bounded organelle
GO:0005815	0.69	microtubule organizing center
GO:0005813	0.68	centrosome
GO:0044444	0.55	cytoplasmic part

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	1tqgA	0.494	3.32	0.078	0.657	2.7.13.3	NA
2	0.060	3cxhN	0.478	4.34	0.015	0.752	1.10.2.2	NA
3	0.060	2uz5A	0.340	4.39	0.078	0.547	5.2.1.8	NA
4	0.060	3g61A	0.528	4.50	0.071	0.825	3.6.3.44	NA
5	0.060	2e9fB	0.503	3.52	0.071	0.686	4.3.2.1	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	3hb3A	0.393	4.55	0.058	0.657	0.16	HEA	complex1.pdb.gz	112,118,123,126,129,130
	2	0.01	1m56A	0.547	4.33	0.030	0.883	0.18	HEA	complex2.pdb.gz	39,40,60,63,64,67,68,121,129,133

	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.