D-I-TASSER P61812

D-I-TASSER results for P61812

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

Summary of the Protein

Uniprot ID: P61812
Protein Name: Transforming growth factor beta-2 proprotein
Gene Name: TGFB2

Input Sequence in FASTA format

>P61812 (414 residues)
MHYCVLSAFLILHLVTVALSLSTCSTLDMDQFMRKRIEAIRGQILSKLKLTSPPEDYPEP
EEVPPEVISIYNSTRDLLQEKASRRAAACERERSDEEYYAKEVYKIDMPPFFPSENAIPP
TFYRPYFRIVRFDVSAMEKNASNLVKAEFRVFRLQNPKARVPEQRIELYQILKSKDLTSP
TQRYIDSKVVKTRAEGEWLSFDVTDAVHEWLHHKDRNLGFKISLHCPCCTFVPSNNYIIP
NKSEELEARFAGIDGTSTYTSGDQKTIKSTRKKNSGKTPHLLLMLLPSYRLESQQTNRRK
KRALDAAYCFRNVQDNCCLRPLYIDFKRDLGWKWIHEPKGYNANFCAGACPYLWSSDTQH
SRVLSLYNTINPEASASPCCVSQDLEPLTILYYIGKTPKIEQLSNMIVKSCKCS

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 DeepPotential. 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	P61812-D1	1-51	51		MHYCVLSAFLILHLVTVALSLSTCSTLDMDQFMRKRIEAIRGQILSKLKLT
2	P61812-D2	52-101,290-414	175		SPPEDYPEPEEVPPEVISIYNSTRDLLQEKASRRAAACERERSDEEYYAKRLESQQTNRRKKRALDAAYCFRNVQDNCCLRPLYIDFKRDLGWKWIHEPKGYNANFCAGACPYLWSSDTQHSRVLSLYNTINPEASASPCCVSQDLEPLTILYYIGKTPKIEQLSNMIVKSCKCS
3	P61812-D3	102-289	188		EVYKIDMPPFFPSENAIPPTFYRPYFRIVRFDVSAMEKNASNLVKAEFRVFRLQNPKARVPEQRIELYQILKSKDLTSPTQRYIDSKVVKTRAEGEWLSFDVTDAVHEWLHHKDRNLGFKISLHCPCCTFVPSNNYIIPNKSEELEARFAGIDGTSTYTSGDQKTIKSTRKKNSGKTPHLLLMLLPSY

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6

(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 DeepPotential, 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	7auwA	0.42	5.87	0.051	0.606	model1_7auwA.pdb.gz
2	1uc2A	0.38	6.53	0.076	0.597	model1_1uc2A.pdb.gz
3	3aibA	0.37	6.77	0.036	0.599	model1_3aibA.pdb.gz
4	5lfcA	0.37	7.09	0.029	0.616	model1_5lfcA.pdb.gz
5	3ecqB	0.37	6.29	0.032	0.558	model1_3ecqB.pdb.gz
6	3hz3A3	0.36	6.95	0.039	0.604	model1_3hz3A3.pdb.gz
7	3rjrA	0.36	4.80	0.159	0.459	model1_3rjrA.pdb.gz
8	2epgB	0.36	6.26	0.049	0.548	model1_2epgB.pdb.gz
9	1wzaA	0.32	7.34	0.050	0.541	model1_1wzaA.pdb.gz
10	1g5aA	0.31	7.06	0.031	0.514	model1_1g5aA.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	0.99	receptor binding
GO:0005160	0.97	transforming growth factor beta receptor binding
GO:0005114	0.61	type II transforming growth factor beta receptor binding
GO:0034714	0.56	type III transforming growth factor beta receptor binding
GO:0005125	0.54	cytokine 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	0.99	biological regulation
GO:0050789	0.99	regulation of biological process
GO:0050794	0.98	regulation of cellular process
GO:0044699	0.96	single-organism process
GO:0009987	0.92	cellular process
GO:0048518	0.91	positive regulation of biological process
GO:0080090	0.90	regulation of primary metabolic process
GO:0060255	0.90	regulation of macromolecule metabolic process
GO:0048522	0.90	positive regulation of cellular process
GO:0044767	0.90	single-organism developmental process
GO:0044763	0.90	single-organism cellular process
GO:0031323	0.90	regulation of cellular metabolic process
GO:0048583	0.89	regulation of response to stimulus
GO:0031325	0.88	positive regulation of cellular metabolic process
GO:0010604	0.88	positive regulation of macromolecule metabolic process
GO:0007165	0.88	signal transduction
GO:0023051	0.79	regulation of signaling
GO:0010646	0.79	regulation of cell communication
GO:0048869	0.78	cellular developmental process
GO:0009967	0.78	positive regulation of signal transduction
GO:0001932	0.78	regulation of protein phosphorylation
GO:0007178	0.77	transmembrane receptor protein serine/threonine kinase signaling pathway
GO:0001934	0.77	positive regulation of protein phosphorylation
GO:0043408	0.76	regulation of MAPK cascade
GO:0010556	0.75	regulation of macromolecule biosynthetic process
GO:0048856	0.72	anatomical structure development
GO:0048519	0.71	negative regulation of biological process
GO:0051239	0.70	regulation of multicellular organismal process
GO:0048523	0.70	negative regulation of cellular process
GO:0050793	0.68	regulation of developmental process
GO:0042981	0.68	regulation of apoptotic process
GO:2000026	0.67	regulation of multicellular organismal development
GO:0045595	0.65	regulation of cell differentiation
GO:0051241	0.64	negative regulation of multicellular organismal process
GO:0042127	0.59	regulation of cell proliferation
GO:0051240	0.57	positive regulation of multicellular organismal process
GO:0050896	0.57	response to stimulus
GO:0010862	0.57	positive regulation of pathway-restricted SMAD protein phosphorylation
GO:0009653	0.57	anatomical structure morphogenesis
GO:0031324	0.56	negative regulation of cellular metabolic process
GO:0010557	0.56	positive regulation of macromolecule biosynthetic process
GO:0051094	0.55	positive regulation of developmental process
GO:0042221	0.55	response to chemical
GO:0016043	0.55	cellular component organization
GO:0045597	0.54	positive regulation of cell differentiation
GO:0032501	0.54	multicellular organismal process
GO:0010033	0.54	response to organic substance
GO:0007179	0.54	transforming growth factor beta receptor signaling pathway
GO:0051128	0.53	regulation of cellular component organization
GO:0048585	0.53	negative regulation of response to stimulus
GO:0044707	0.53	single-multicellular organism process
GO:2000112	0.52	regulation of cellular macromolecule biosynthetic process
GO:0030278	0.52	regulation of ossification
GO:0022603	0.52	regulation of anatomical structure morphogenesis
GO:0019219	0.52	regulation of nucleobase-containing compound metabolic process
GO:0010468	0.52	regulation of gene expression
GO:0009719	0.52	response to endogenous stimulus
GO:0002682	0.52	regulation of immune system process
GO:1901700	0.51	response to oxygen-containing compound
GO:0060284	0.51	regulation of cell development
GO:0045778	0.51	positive regulation of ossification
GO:0009887	0.51	organ morphogenesis
GO:0006950	0.51	response to stress
GO:0006355	0.51	regulation of transcription, DNA-templated
GO:0001817	0.51	regulation of cytokine production
GO:0051130	0.50	positive regulation of cellular component organization
GO:0050776	0.50	regulation of immune response
GO:0033993	0.50	response to lipid
GO:0014070	0.50	response to organic cyclic compound
GO:0010720	0.50	positive regulation of cell development
GO:0009725	0.50	response to hormone
GO:0008285	0.50	negative regulation of cell proliferation
GO:0002683	0.50	negative regulation of immune system 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:0044421	0.98	extracellular region part
GO:0005615	0.87	extracellular space
GO:0044464	0.62	cell part
GO:0044424	0.52	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	2uxwA	0.331	7.42	0.034	0.577	1.3.99.-	NA
2	0.060	2x7jA	0.339	7.18	0.026	0.573	2.2.1.9	NA
3	0.060	1v03A	0.330	6.83	0.050	0.527	3.2.1.21	NA
4	0.060	2b3xA	0.327	6.94	0.036	0.548	4.2.1.3	NA
5	0.060	1qbaA	0.334	7.22	0.057	0.568	3.2.1.52	83

	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	2e7zA	0.344	7.00	0.034	0.580	0.32	SF4	complex1.pdb.gz	316,317,378,379
2	0.01	1mczA	0.340	7.23	0.035	0.580	0.14	TDP	complex2.pdb.gz	40,329,330
3	0.01	1bfdA	0.339	7.33	0.038	0.582	0.12	TPP	complex3.pdb.gz	23,24,348,349

	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.