D-I-TASSER P01135

D-I-TASSER results for P01135

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

Summary of the Protein

Uniprot ID: P01135
Protein Name: Protransforming growth factor alpha
Gene Name: TGFA

Input Sequence in FASTA format

>P01135 (160 residues)
MVPSAGQLALFALGIVLAACQALENSTSPLSADPPVAAAVVSHFNDCPDSHTQFCFHGTC
RFLVQEDKPACVCHSGYVGARCEHADLLAVVAASQKKQAITALVVVSIVALAVLIITCVL
IHCCQVRKHCEWCRALICRHEKPSALLKGRTACCHSETVV

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	P01135-D1	1-160	160		MVPSAGQLALFALGIVLAACQALENSTSPLSADPPVAAAVVSHFNDCPDSHTQFCFHGTCRFLVQEDKPACVCHSGYVGARCEHADLLAVVAASQKKQAITALVVVSIVALAVLIITCVLIHCCQVRKHCEWCRALICRHEKPSALLKGRTACCHSETVV

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5265

(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	6ewyA	0.61	3.23	0.080	0.769	model1_6ewyA.pdb.gz
2	3k29A	0.59	3.35	0.079	0.744	model1_3k29A.pdb.gz
3	6sihA2	0.58	3.34	0.052	0.775	model1_6sihA2.pdb.gz
4	1ciiA	0.58	4.01	0.097	0.819	model1_1ciiA.pdb.gz
5	6z9lA2	0.57	3.98	0.049	0.769	model1_6z9lA2.pdb.gz
6	6h7wB	0.57	3.56	0.052	0.750	model1_6h7wB.pdb.gz
7	5ijiA	0.56	3.61	0.080	0.762	model1_5ijiA.pdb.gz
8	3qweA	0.56	3.83	0.072	0.775	model1_3qweA.pdb.gz
9	6irdB	0.56	3.83	0.044	0.750	model1_6irdB.pdb.gz
10	4tqlA	0.56	3.58	0.062	0.725	model1_4tqlA.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:0005102	0.95	receptor binding
GO:0070851	0.93	growth factor receptor binding
GO:0005154	0.92	epidermal growth factor receptor binding
GO:0008083	0.91	growth 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:0065007	0.94	biological regulation
GO:0050789	0.94	regulation of biological process
GO:0050794	0.93	regulation of cellular process
GO:0048518	0.84	positive regulation of biological process
GO:0048522	0.83	positive regulation of cellular process
GO:0007165	0.80	signal transduction
GO:0008284	0.78	positive regulation of cell proliferation
GO:0007166	0.77	cell surface receptor signaling pathway
GO:0007173	0.72	epidermal growth factor receptor signaling pathway
GO:0019222	0.62	regulation of metabolic process
GO:0031323	0.61	regulation of cellular metabolic process
GO:0060255	0.60	regulation of macromolecule metabolic process
GO:0080090	0.58	regulation of primary metabolic process
GO:0031325	0.56	positive regulation of cellular metabolic process
GO:0019220	0.55	regulation of phosphate metabolic process
GO:0010604	0.55	positive regulation of macromolecule metabolic process
GO:0042325	0.54	regulation of phosphorylation
GO:0048583	0.53	regulation of response to stimulus
GO:0032268	0.53	regulation of cellular protein metabolic process
GO:0065009	0.52	regulation of molecular function
GO:0042327	0.52	positive regulation of phosphorylation
GO:0031399	0.52	regulation of protein modification process
GO:0009966	0.52	regulation of signal transduction
GO:0044093	0.51	positive regulation of molecular function
GO:0001934	0.51	positive regulation of protein phosphorylation
GO:0050790	0.50	regulation of catalytic activity
GO:0009967	0.50	positive regulation of signal transduction

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:0044421	0.93	extracellular region part
GO:0005615	0.92	extracellular space
GO:0044464	0.85	cell part
GO:0044425	0.62	membrane part
GO:0016021	0.60	integral component of membrane
GO:0044459	0.58	plasma membrane part
GO:0005887	0.57	integral component of plasma membrane
GO:0044424	0.51	intracellular 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	0.060	2iw5A	0.491	4.71	0.053	0.762	1.-.-.-	NA
2	0.060	2hkjA	0.331	4.25	0.029	0.469	5.99.1.3	80
3	0.060	1qhaA	0.436	4.95	0.071	0.731	2.7.1.1	NA
4	0.060	1zvuA	0.453	5.33	0.076	0.794	5.99.1.-	NA
5	0.060	1z0hB	0.235	5.36	0.027	0.419	3.4.24.69	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:

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	1mneA	0.365	4.06	0.077	0.519	0.47	POP	complex1.pdb.gz	57,58,59,79,84,85
2	0.01	3mylX	0.372	5.45	0.047	0.694	0.52	POP	complex2.pdb.gz	57,58,59,79,84,85
3	0.01	2w6dB	0.555	3.99	0.043	0.794	0.55	CPL	complex3.pdb.gz	57,58,59,83
4	0.01	3na7A	0.497	2.46	0.019	0.600	0.68	ZN	complex4.pdb.gz	55,58,73
5	0.01	2w6dA	0.544	4.20	0.043	0.806	0.49	GDP	complex5.pdb.gz	58,74,75,86

	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.