D-I-TASSER P21583

D-I-TASSER results for P21583

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

Summary of the Protein

Uniprot ID: P21583
Protein Name: Kit ligand
Gene Name: KITLG

Input Sequence in FASTA format

>P21583 (273 residues)
MKKTQTWILTCIYLQLLLFNPLVKTEGICRNRVTNNVKDVTKLVANLPKDYMITLKYVPG
MDVLPSHCWISEMVVQLSDSLTDLLDKFSNISEGLSNYSIIDKLVNIVDDLVECVKENSS
KDLKKSFKSPEPRLFTPEEFFRIFNRSIDAFKDFVVASETSDCVVSSTLSPEKDSRVSVT
KPFMLPPVAASSLRNDSSSSNRKAKNPPGDSSLHWAAMALPALFSLIIGFAFGALYWKKR
QPSLTRAVENIQINEEDNEISMLQEKEREFQEV

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	P21583-D1	1-273	273		MKKTQTWILTCIYLQLLLFNPLVKTEGICRNRVTNNVKDVTKLVANLPKDYMITLKYVPGMDVLPSHCWISEMVVQLSDSLTDLLDKFSNISEGLSNYSIIDKLVNIVDDLVECVKENSSKDLKKSFKSPEPRLFTPEEFFRIFNRSIDAFKDFVVASETSDCVVSSTLSPEKDSRVSVTKPFMLPPVAASSLRNDSSSSNRKAKNPPGDSSLHWAAMALPALFSLIIGFAFGALYWKKRQPSLTRAVENIQINEEDNEISMLQEKEREFQEV

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5403

(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	4a01A	0.47	4.61	0.067	0.667	model1_4a01A.pdb.gz
2	6s4mA	0.46	5.22	0.072	0.678	model1_6s4mA.pdb.gz
3	4av3A	0.45	5.03	0.053	0.670	model1_4av3A.pdb.gz
4	6rtgA	0.44	6.13	0.061	0.773	model1_6rtgA.pdb.gz
5	6ei3A	0.44	5.83	0.037	0.711	model1_6ei3A.pdb.gz
6	5uv0A	0.43	5.82	0.094	0.700	model1_5uv0A.pdb.gz
7	1hxgA	0.43	5.81	0.036	0.700	model1_1hxgA.pdb.gz
8	2o26A	0.43	3.06	0.671	0.516	model1_2o26A.pdb.gz
9	4fjqA	0.43	5.75	0.050	0.700	model1_4fjqA.pdb.gz
10	4aipA	0.43	6.32	0.083	0.744	model1_4aipA.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:0005173	1.00	stem cell factor receptor binding
GO:0003824	0.61	catalytic activity
GO:0016740	0.58	transferase activity
GO:0016773	0.57	phosphotransferase activity, alcohol group as acceptor
GO:0016301	0.57	kinase activity
GO:0098772	0.56	molecular function regulator
GO:0046934	0.55	phosphatidylinositol-4,5-bisphosphate 3-kinase activity
GO:0005088	0.55	Ras guanyl-nucleotide exchange factor 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:0044699	1.00	single-organism process
GO:0050794	0.97	regulation of cellular process
GO:0048518	0.96	positive regulation of biological process
GO:0048856	0.95	anatomical structure development
GO:0048522	0.95	positive regulation of cellular process
GO:0044767	0.95	single-organism developmental process
GO:0044702	0.95	single organism reproductive process
GO:0003006	0.95	developmental process involved in reproduction
GO:0009987	0.81	cellular process
GO:0044763	0.75	single-organism cellular process
GO:0080090	0.70	regulation of primary metabolic process
GO:0060255	0.70	regulation of macromolecule metabolic process
GO:0031323	0.70	regulation of cellular metabolic process
GO:0048583	0.69	regulation of response to stimulus
GO:0031325	0.69	positive regulation of cellular metabolic process
GO:0051171	0.68	regulation of nitrogen compound metabolic process
GO:0010604	0.68	positive regulation of macromolecule metabolic process
GO:0007165	0.68	signal transduction
GO:2000112	0.67	regulation of cellular macromolecule biosynthetic process
GO:0045935	0.67	positive regulation of nucleobase-containing compound metabolic process
GO:0031328	0.67	positive regulation of cellular biosynthetic process
GO:0010557	0.67	positive regulation of macromolecule biosynthetic process
GO:0009966	0.67	regulation of signal transduction
GO:1902531	0.66	regulation of intracellular signal transduction
GO:0048534	0.66	hematopoietic or lymphoid organ development
GO:0048608	0.65	reproductive structure development
GO:0045740	0.65	positive regulation of DNA replication
GO:0035162	0.65	embryonic hemopoiesis
GO:0008284	0.60	positive regulation of cell proliferation

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:0030175	1.00	filopodium
GO:0030027	1.00	lamellipodium
GO:0005886	1.00	plasma membrane
GO:0005737	1.00	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	0.060	2oa6D	0.408	5.54	0.035	0.637	4.2.3.9	NA
2	0.060	1gz7A	0.402	6.23	0.035	0.689	3.1.1.3	NA
3	0.060	1ut9A	0.390	5.75	0.025	0.630	3.2.1.4	NA
4	0.060	1lpsA	0.389	6.48	0.058	0.678	3.1.1.3	NA
5	0.060	3igyB	0.398	6.13	0.041	0.674	5.4.2.1	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	0.09	2o270	0.389	2.81	0.704	0.458	1.05	III	complex1.pdb.gz	42,45,46,47,48,86,87,95,96,97

	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.