D-I-TASSER Q03167

D-I-TASSER results for Q03167

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

Summary of the Protein

Uniprot ID: Q03167
Protein Name: Transforming growth factor beta receptor type 3
Gene Name: TGFBR3

Input Sequence in FASTA format

>Q03167 (851 residues)
MTSHYVIAIFALMSSCLATAGPEPGALCELSPVSASHPVQALMESFTVLSGCASRGTTGL
PQEVHVLNLRTAGQGPGQLQREVTLHLNPISSVHIHHKSVVFLLNSPHPLVWHLKTERLA
TGVSRLFLVSEGSVVQFSSANFSLTAETEERNFPHGNEHLLNWARKEYGAVTSFTELKIA
RNIYIKVGEDQVFPPKCNIGKNFLSLNYLAEYLQPKAAEGCVMSSQPQNEEVHIIELITP
NSNPYSAFQVDITIDIRPSQEDLEVVKNLILILKCKKSVNWVIKSFDVKGSLKIIAPNSI
GFGKESERSMTMTKSIRDDIPSTQGNLVKWALDNGYSPITSYTMAPVANRFHLRLENNAE
EMGDEEVHTIPPELRILLDPGALPALQNPPIRGGEGQNGGLPFPFPDISRRVWNEEGEDG
LPRPKDPVIPSIQLFPGLREPEEVQGSVDIALSVKCDNEKMIVAVEKDSFQASGYSGMDV
TLLDPTCKAKMNGTHFVLESPLNGCGTRPRWSALDGVVYYNSIVIQVPALGDSSGWPDGY
EDLESGDNGFPGDMDEGDASLFTRPEIVVFNCSLQQVRNPSSFQEQPHGNITFNMELYNT
DLFLVPSQGVFSVPENGHVYVEVSVTKAEQELGFAIQTCFISPYSNPDRMSHYTIIENIC
PKDESVKFYSPKRVHFPIPQADMDKKRFSFVFKPVFNTSLLFLQCELTLCTKMEKHPQKL
PKCVPPDEACTSLDASIIWAMMQNKKTFTKPLAVIHHEAESKEKGPSMKEPNPISPPIFH
GLDTLTVMGIAFAAFVIGALLTGALWYIYSHTGETAGRQQVPTSPPASENSSAAHSIGST
QSTPCSSSSTA

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	Q03167-D1	1-366,812-851	406		MTSHYVIAIFALMSSCLATAGPEPGALCELSPVSASHPVQALMESFTVLSGCASRGTTGLPQEVHVLNLRTAGQGPGQLQREVTLHLNPISSVHIHHKSVVFLLNSPHPLVWHLKTERLATGVSRLFLVSEGSVVQFSSANFSLTAETEERNFPHGNEHLLNWARKEYGAVTSFTELKIARNIYIKVGEDQVFPPKCNIGKNFLSLNYLAEYLQPKAAEGCVMSSQPQNEEVHIIELITPNSNPYSAFQVDITIDIRPSQEDLEVVKNLILILKCKKSVNWVIKSFDVKGSLKIIAPNSIGFGKESERSMTMTKSIRDDIPSTQGNLVKWALDNGYSPITSYTMAPVANRFHLRLENNAEEMGDEETGETAGRQQVPTSPPASENSSAAHSIGSTQSTPCSSSSTA
2	Q03167-D2	367-385,588-811	243		VHTIPPELRILLDPGALPAHGNITFNMELYNTDLFLVPSQGVFSVPENGHVYVEVSVTKAEQELGFAIQTCFISPYSNPDRMSHYTIIENICPKDESVKFYSPKRVHFPIPQADMDKKRFSFVFKPVFNTSLLFLQCELTLCTKMEKHPQKLPKCVPPDEACTSLDASIIWAMMQNKKTFTKPLAVIHHEAESKEKGPSMKEPNPISPPIFHGLDTLTVMGIAFAAFVIGALLTGALWYIYSH
3	Q03167-D3	386-587	202		LQNPPIRGGEGQNGGLPFPFPDISRRVWNEEGEDGLPRPKDPVIPSIQLFPGLREPEEVQGSVDIALSVKCDNEKMIVAVEKDSFQASGYSGMDVTLLDPTCKAKMNGTHFVLESPLNGCGTRPRWSALDGVVYYNSIVIQVPALGDSSGWPDGYEDLESGDNGFPGDMDEGDASLFTRPEIVVFNCSLQQVRNPSSFQEQP

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.43

(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	5hzwA	0.34	3.64	0.192	0.380	model1_5hzwA.pdb.gz
2	5xjcQ	0.32	9.00	0.047	0.523	model1_5xjcQ.pdb.gz
3	6mznA	0.31	3.60	0.356	0.350	model1_6mznA.pdb.gz
4	6drjA	0.31	8.23	0.038	0.475	model1_6drjA.pdb.gz
5	5amqA	0.31	9.18	0.051	0.511	model1_5amqA.pdb.gz
6	3qmzA	0.30	9.27	0.021	0.511	model1_3qmzA.pdb.gz
7	6eqoA	0.30	9.33	0.044	0.512	model1_6eqoA.pdb.gz
8	2vz8B	0.30	8.72	0.029	0.472	model1_2vz8B.pdb.gz
9	6mixA	0.30	8.66	0.031	0.470	model1_6mixA.pdb.gz
10	4xgtA	0.30	8.69	0.041	0.471	model1_4xgtA.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:0004871	0.94	signal transducer activity
GO:0038023	0.92	signaling receptor activity
GO:0004674	0.92	protein serine/threonine kinase activity
GO:0005024	0.91	transforming growth factor beta-activated receptor activity
GO:0005539	0.90	glycosaminoglycan binding
GO:0050431	0.88	transforming growth factor beta binding
GO:0070123	0.85	transforming growth factor beta receptor activity, type III
GO:0005102	0.61	receptor binding
GO:0005160	0.56	transforming growth factor beta receptor binding

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:0044699	0.99	single-organism process
GO:0050794	0.98	regulation of cellular process
GO:0009987	0.98	cellular process
GO:0044763	0.96	single-organism cellular process
GO:0032502	0.96	developmental process
GO:0044767	0.95	single-organism developmental process
GO:0048519	0.90	negative regulation of biological process
GO:0048523	0.88	negative regulation of cellular process
GO:0016043	0.87	cellular component organization
GO:0060255	0.86	regulation of macromolecule metabolic process
GO:0048856	0.86	anatomical structure development
GO:0010468	0.85	regulation of gene expression
GO:0048513	0.83	animal organ development
GO:0048869	0.80	cellular developmental process
GO:0048522	0.79	positive regulation of cellular process
GO:0009653	0.79	anatomical structure morphogenesis
GO:0051270	0.78	regulation of cellular component movement
GO:0001837	0.78	epithelial to mesenchymal transition
GO:0030154	0.72	cell differentiation
GO:0060317	0.69	cardiac epithelial to mesenchymal transition
GO:0001889	0.67	liver development
GO:0006928	0.62	movement of cell or subcellular component
GO:0016477	0.61	cell migration
GO:0010604	0.60	positive regulation of macromolecule metabolic process
GO:0040012	0.59	regulation of locomotion
GO:0009887	0.59	organ morphogenesis
GO:0030334	0.58	regulation of cell migration
GO:0003007	0.58	heart morphogenesis
GO:0010628	0.57	positive regulation of gene expression
GO:0050896	0.56	response to stimulus

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:0044425	0.98	membrane part
GO:0031224	0.92	intrinsic component of membrane
GO:0016021	0.91	integral component of membrane
GO:0044459	0.88	plasma membrane part
GO:0005887	0.76	integral component of plasma membrane
GO:0044424	0.65	intracellular part
GO:0016020	0.62	membrane
GO:0044421	0.61	extracellular region 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	1llwA	0.266	9.41	0.041	0.456	1.4.7.1	NA
2	0.060	1ea0A	0.254	9.26	0.023	0.430	1.4.1.13	NA
3	0.060	2vumA	0.258	9.43	0.034	0.440	2.7.7.6	NA
4	0.060	3hkzJ	0.259	9.08	0.039	0.423	2.7.7.6	NA
5	0.060	2j5wA	0.256	9.13	0.031	0.424	1.16.3.1	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:

No Binding sites was predicted

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

	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.