D-I-TASSER H3BV60

D-I-TASSER results for H3BV60

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Summary of the Protein

Uniprot ID: H3BV60
Protein Name: Transforming growth factor-beta receptor type 3-like protein
Gene Name: TGFBR3L

Input Sequence in FASTA format

>H3BV60 (316 residues)
MGESAAATASLFQRRRRGRGGRVTFPGGLKGSARFLSFGPPFPAPPAPPFPAAPGPWLRR
PLFSLKLSDTEDVFPRRAGPLEVPADSRVFVQAALARPSPRWGLALHRCSVTPSSRPAPG
PALALLREGCPADTSVAFPPPPPPSPGAARPARFSFRLRPVFNASVQFLHCQLSRCRRLR
GVRRAPAPLTPPPPPPPSRCLPQDEACADTGSGSAEGLAADGPHLHTLTQPIVVTVPRPP
PRPPKSVPGRAVRPEPPAPAPAALEPAPVVALVLAAFVLGAALAAGLGLVCAHSAPHAPG
PPARASPSGPQPRRSQ

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	H3BV60-D1	1-316	316		MGESAAATASLFQRRRRGRGGRVTFPGGLKGSARFLSFGPPFPAPPAPPFPAAPGPWLRRPLFSLKLSDTEDVFPRRAGPLEVPADSRVFVQAALARPSPRWGLALHRCSVTPSSRPAPGPALALLREGCPADTSVAFPPPPPPSPGAARPARFSFRLRPVFNASVQFLHCQLSRCRRLRGVRRAPAPLTPPPPPPPSRCLPQDEACADTGSGSAEGLAADGPHLHTLTQPIVVTVPRPPPRPPKSVPGRAVRPEPPAPAPAALEPAPVVALVLAAFVLGAALAAGLGLVCAHSAPHAPGPPARASPSGPQPRRSQ

Top 1 final models from D-I-TASSER

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Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5504

(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

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Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	3qw9A	0.51	1.19	0.265	0.525	model1_3qw9A.pdb.gz
2	4wrnA	0.46	3.31	0.114	0.535	model1_4wrnA.pdb.gz
3	1y1uA	0.44	4.68	0.043	0.595	model1_1y1uA.pdb.gz
4	1bg1A	0.43	5.38	0.100	0.620	model1_1bg1A.pdb.gz
5	1yvlB	0.43	5.13	0.072	0.604	model1_1yvlB.pdb.gz
6	6rutB	0.43	6.67	0.055	0.731	model1_6rutB.pdb.gz
7	6ux2A	0.43	5.22	0.081	0.604	model1_6ux2A.pdb.gz
8	6rc9A	0.42	6.64	0.053	0.734	model1_6rc9A.pdb.gz
9	3f8uD	0.42	4.76	0.096	0.563	model1_3f8uD.pdb.gz
10	5yu5A	0.41	5.27	0.056	0.582	model1_5yu5A.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	0.78	signal transducer activity
GO:0005539	0.76	glycosaminoglycan binding
GO:0038023	0.70	signaling receptor activity
GO:0004675	0.69	transmembrane receptor protein serine/threonine kinase activity
GO:0019955	0.68	cytokine binding
GO:0019838	0.68	growth factor binding
GO:0032403	0.57	protein complex binding
GO:0005160	0.55	transforming growth factor beta receptor binding
GO:0022891	0.50	substrate-specific transmembrane transporter 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	0.98	single-organism process
GO:0044763	0.95	single-organism cellular process
GO:0065007	0.92	biological regulation
GO:0050789	0.91	regulation of biological process
GO:0032502	0.85	developmental process
GO:0048518	0.80	positive regulation of biological process
GO:0044767	0.80	single-organism developmental process
GO:0048856	0.79	anatomical structure development
GO:0050794	0.76	regulation of cellular process
GO:0048519	0.76	negative regulation of biological process
GO:0016043	0.74	cellular component organization
GO:0048523	0.73	negative regulation of cellular process
GO:0060255	0.72	regulation of macromolecule metabolic process
GO:0010468	0.71	regulation of gene expression
GO:0050896	0.70	response to stimulus
GO:0048869	0.70	cellular developmental process
GO:0048522	0.70	positive regulation of cellular process
GO:0051270	0.69	regulation of cellular component movement
GO:0009653	0.69	anatomical structure morphogenesis
GO:0000904	0.63	cell morphogenesis involved in differentiation
GO:0010033	0.60	response to organic substance
GO:0009719	0.60	response to endogenous stimulus
GO:0003007	0.58	heart morphogenesis
GO:0048583	0.57	regulation of response to stimulus
GO:0006810	0.56	transport
GO:0080090	0.55	regulation of primary metabolic process
GO:0031323	0.55	regulation of cellular metabolic process
GO:0010556	0.55	regulation of macromolecule biosynthetic process
GO:0009966	0.55	regulation of signal transduction
GO:0048584	0.54	positive regulation of response to stimulus
GO:0002376	0.54	immune system process
GO:0065009	0.53	regulation of molecular function
GO:0009967	0.53	positive regulation of signal transduction
GO:0006355	0.53	regulation of transcription, DNA-templated
GO:0070848	0.52	response to growth factor
GO:0009725	0.51	response to hormone

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	0.93	membrane part
GO:0044459	0.85	plasma membrane part
GO:0044421	0.81	extracellular region part
GO:0044424	0.79	intracellular part
GO:0016020	0.76	membrane
GO:0043234	0.71	protein complex
GO:0042597	0.66	periplasmic space
GO:0031224	0.66	intrinsic component of membrane
GO:0098797	0.64	plasma membrane protein complex
GO:1902494	0.61	catalytic complex
GO:0043226	0.61	organelle
GO:0031012	0.61	extracellular matrix
GO:0044444	0.60	cytoplasmic part
GO:0016021	0.58	integral component of membrane
GO:0043227	0.57	membrane-bounded organelle
GO:1990060	0.54	maltose transport complex
GO:0055052	0.54	ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing
GO:0030288	0.54	outer membrane-bounded periplasmic space
GO:0043229	0.53	intracellular organelle
GO:0005576	0.53	extracellular region
GO:0044446	0.52	intracellular organelle 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

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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	3gidB	0.374	6.68	0.068	0.661	6.4.1.2 6.3.4.14	NA
2	0.060	3b9jI	0.191	5.68	0.017	0.301	1.17.1.4 1.17.3.2	NA
3	0.060	3fn9C	0.365	5.32	0.053	0.528	3.2.1.23	NA
4	0.060	2wghB	0.394	6.70	0.043	0.699	1.17.4.1	NA
5	0.060	1kv9A	0.391	6.49	0.063	0.668	1.1.99.-	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

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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	3o8oA	0.387	6.82	0.052	0.683	0.26	F6P	complex1.pdb.gz	104,105,106,190
2	0.01	3hnfB	0.390	6.72	0.051	0.690	0.26	TTP	complex2.pdb.gz	125,126,130
3	0.01	3o8oC	0.382	6.69	0.037	0.668	0.27	F6P	complex3.pdb.gz	104,105,106
4	0.01	2wghB	0.394	6.70	0.043	0.699	0.39	DTP	complex4.pdb.gz	125,126,127,133,154

	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.