D-I-TASSER P0C264

D-I-TASSER results for P0C264

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

Summary of the Protein

Uniprot ID: P0C264
Protein Name: Uncharacterized serine/threonine-protein kinase SBK3
Gene Name: SBK3

Input Sequence in FASTA format

>P0C264 (359 residues)
MERRASETPEDGDPEEDTATALQRLVELTTSRVTPVRSLRDQYHLIRKLGSGSYGRVLLA
QPHQGGPAVALKLLRRDLVLRSTFLREFCVGRCVSAHPGLLQTLAGPLQTPRYFAFAQEY
APCGDLSGMLQERGLPELLVKRVVAQLAGALDFLHSRGLVHADVKPDNVLVFDPVCSRVA
LGDLGLTRPEGSPTPAPPVPLPTAPPELCLLLPPDTLPLRPAVDSWGLGVLLFCAATACF
PWDVALAPNPEFEAFAGWVTTKPQPPQPPPPWDQFAPPALALLQGLLDLDPETRSPPLAV
LDFLGDDWGLQGNREGPGVLGSAVSYEDREEGGSSLEEWTDEGDDSKSGGRTGTDGGAP

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	P0C264-D1	1-120	120		MERRASETPEDGDPEEDTATALQRLVELTTSRVTPVRSLRDQYHLIRKLGSGSYGRVLLAQPHQGGPAVALKLLRRDLVLRSTFLREFCVGRCVSAHPGLLQTLAGPLQTPRYFAFAQEY
2	P0C264-D2	121-200,296-359	144		APCGDLSGMLQERGLPELLVKRVVAQLAGALDFLHSRGLVHADVKPDNVLVFDPVCSRVALGDLGLTRPEGSPTPAPPVPPPLAVLDFLGDDWGLQGNREGPGVLGSAVSYEDREEGGSSLEEWTDEGDDSKSGGRTGTDGGAP
3	P0C264-D3	201-295	95		LPTAPPELCLLLPPDTLPLRPAVDSWGLGVLLFCAATACFPWDVALAPNPEFEAFAGWVTTKPQPPQPPPPWDQFAPPALALLQGLLDLDPETRS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.73

(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	2f2uA	0.67	3.66	0.193	0.797	model1_2f2uA.pdb.gz
2	3tkuA	0.67	3.77	0.180	0.799	model1_3tkuA.pdb.gz
3	2vd5A	0.67	3.78	0.197	0.791	model1_2vd5A.pdb.gz
4	2y7jA	0.66	2.77	0.210	0.738	model1_2y7jA.pdb.gz
5	6o6qA	0.66	2.94	0.177	0.747	model1_6o6qA.pdb.gz
6	6l1zA	0.66	3.07	0.196	0.752	model1_6l1zA.pdb.gz
7	4fi1A	0.66	3.10	0.170	0.755	model1_4fi1A.pdb.gz
8	1ql6A	0.66	2.46	0.195	0.719	model1_1ql6A.pdb.gz
9	5ig1A	0.65	2.95	0.192	0.741	model1_5ig1A.pdb.gz
10	1f0qA	0.65	3.09	0.183	0.752	model1_1f0qA.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:0004672	0.97	protein kinase activity
GO:0004674	0.88	protein serine/threonine kinase 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:0009987	0.93	cellular process
GO:0044260	0.89	cellular macromolecule metabolic process
GO:0044238	0.89	primary metabolic process
GO:0006468	0.88	protein phosphorylation
GO:0065007	0.85	biological regulation
GO:0050789	0.85	regulation of biological process
GO:0050794	0.84	regulation of cellular process
GO:0007165	0.74	signal transduction
GO:0050896	0.64	response to stimulus
GO:0046777	0.64	protein autophosphorylation
GO:0035556	0.64	intracellular signal transduction
GO:0051716	0.58	cellular response to stimulus
GO:0009628	0.56	response to abiotic stimulus
GO:0009605	0.56	response to external stimulus
GO:0071496	0.55	cellular response to external stimulus
GO:0071214	0.55	cellular response to abiotic stimulus
GO:0018193	0.55	peptidyl-amino acid modification
GO:0071260	0.54	cellular response to mechanical stimulus
GO:0044699	0.54	single-organism process
GO:0044763	0.51	single-organism cellular process

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:0044464	1.00	cell part
GO:0044424	0.95	intracellular part
GO:0005737	0.83	cytoplasm
GO:0043226	0.81	organelle
GO:0043229	0.77	intracellular organelle
GO:0043227	0.77	membrane-bounded organelle
GO:0043231	0.72	intracellular membrane-bounded organelle
GO:0005634	0.64	nucleus
GO:0044444	0.58	cytoplasmic part
GO:0016020	0.57	membrane

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	0.260	3lm0A	0.640	2.64	0.189	0.710	2.7.11.1	163,165,170
2	0.124	1ql6A	0.656	2.46	0.195	0.719	2.7.11.19 2.7.1.38	NA
3	0.113	3eqrB	0.619	3.18	0.216	0.708	2.7.10.2	NA
4	0.112	2zv2A	0.607	3.10	0.190	0.688	2.7.11.17	NA
5	0.108	2z2wA	0.613	2.75	0.217	0.685	2.7.10.2	53

	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	0.61	3owjA	0.660	3.01	0.199	0.752	1.37	1EL	complex1.pdb.gz	50,57,70,121,167,170,182
2	0.61	3r0tA	0.661	3.06	0.197	0.755	1.48	FU9	complex2.pdb.gz	49,50,51,57,70,72,118,119,120,121,123,170,182,183
3	0.60	1pjkA	0.658	3.06	0.201	0.752	1.42	ANP	complex3.pdb.gz	52,53,54,55,57,70,72,101,119,121,170,182,183
4	0.34	3h30B	0.655	3.02	0.203	0.749	1.36	RFZ	complex4.pdb.gz	50,51,52,57,70,101,121,122,182
5	0.33	1m2pA	0.656	3.06	0.188	0.752	1.42	HNA	complex5.pdb.gz	49,50,51,57,72,101,118,182,183
6	0.31	2oxyA	0.655	3.09	0.184	0.752	1.25	K17	complex6.pdb.gz	49,57,70,101,118,119,121,170,182
7	0.27	2esmB	0.673	3.68	0.187	0.799	0.82	M77	complex7.pdb.gz	49,56,71,117,118,119,120,125,167,169,182,183
8	0.04	2phkA	0.647	2.40	0.198	0.708	0.87	III	complex8.pdb.gz	53,125,127,165,186,197,199,200,202

	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.