D-I-TASSER Q9UBU3

D-I-TASSER results for Q9UBU3

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

Summary of the Protein

Uniprot ID: Q9UBU3
Protein Name: Appetite-regulating hormone
Gene Name: GHRL

Input Sequence in FASTA format

>Q9UBU3 (117 residues)
MPSPGTVCSLLLLGMLWLDLAMAGSSFLSPEHQRVQQRKESKKPPAKLQPRALAGWLRPE
DGGQAEGAEDELEVRFNAPFDVGIKLSGVQYQQHSQALGKFLQDILWEEAKEAPADK

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	Q9UBU3-D1	1-117	117		MPSPGTVCSLLLLGMLWLDLAMAGSSFLSPEHQRVQQRKESKKPPAKLQPRALAGWLRPEDGGQAEGAEDELEVRFNAPFDVGIKLSGVQYQQHSQALGKFLQDILWEEAKEAPADK

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4668

(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	7jh5A	0.55	3.61	0.088	0.829	model1_7jh5A.pdb.gz
2	6bs9A	0.53	4.07	0.092	0.838	model1_6bs9A.pdb.gz
3	3mk7A	0.53	4.52	0.060	0.872	model1_3mk7A.pdb.gz
4	1r5zA	0.53	3.97	0.113	0.786	model1_1r5zA.pdb.gz
5	6hraA	0.53	4.25	0.078	0.838	model1_6hraA.pdb.gz
6	6xkwn	0.52	4.41	0.104	0.863	model1_6xkwn.pdb.gz
7	5ys3A	0.52	3.79	0.093	0.786	model1_5ys3A.pdb.gz
8	6idfB	0.52	4.12	0.057	0.821	model1_6idfB.pdb.gz
9	1xmeA	0.52	4.00	0.054	0.786	model1_1xmeA.pdb.gz
10	3dy5A	0.52	4.13	0.070	0.821	model1_3dy5A.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:0001664	1.00	G-protein coupled receptor binding
GO:0016608	0.96	growth hormone-releasing hormone activity
GO:0031768	0.95	ghrelin receptor binding
GO:0098772	0.58	molecular function regulator
GO:0030234	0.57	enzyme regulator activity
GO:0030296	0.56	protein tyrosine kinase activator 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	0.97	biological regulation
GO:0050789	0.97	regulation of biological process
GO:0050794	0.95	regulation of cellular process
GO:0065008	0.93	regulation of biological quality
GO:0048518	0.92	positive regulation of biological process
GO:0048522	0.91	positive regulation of cellular process
GO:0010817	0.90	regulation of hormone levels
GO:0032102	0.89	negative regulation of response to external stimulus
GO:0032095	0.89	regulation of response to food
GO:0010604	0.88	positive regulation of macromolecule metabolic process
GO:0044699	0.87	single-organism process
GO:0046887	0.86	positive regulation of hormone secretion
GO:0031325	0.85	positive regulation of cellular metabolic process
GO:0065009	0.84	regulation of molecular function
GO:0080134	0.83	regulation of response to stress
GO:0043085	0.83	positive regulation of catalytic activity
GO:0090277	0.82	positive regulation of peptide hormone secretion
GO:0080090	0.82	regulation of primary metabolic process
GO:0001934	0.80	positive regulation of protein phosphorylation
GO:0050728	0.79	negative regulation of inflammatory response
GO:0045860	0.79	positive regulation of protein kinase activity
GO:0009987	0.74	cellular process
GO:0044765	0.73	single-organism transport
GO:0046903	0.72	secretion
GO:0007165	0.72	signal transduction
GO:0060124	0.71	positive regulation of growth hormone secretion
GO:0032501	0.69	multicellular organismal process
GO:0003008	0.68	system process
GO:0050896	0.67	response to stimulus
GO:0044707	0.65	single-multicellular organism process
GO:0044763	0.64	single-organism cellular process
GO:0009755	0.63	hormone-mediated signaling pathway
GO:0001696	0.63	gastric acid secretion
GO:0051239	0.62	regulation of multicellular organismal process
GO:0048584	0.60	positive regulation of response to stimulus
GO:0051480	0.59	regulation of cytosolic calcium ion concentration
GO:0042221	0.58	response to chemical
GO:0050731	0.57	positive regulation of peptidyl-tyrosine phosphorylation
GO:0010033	0.57	response to organic substance
GO:0061098	0.56	positive regulation of protein tyrosine kinase activity
GO:0051240	0.56	positive regulation of multicellular organismal process
GO:0048856	0.56	anatomical structure development
GO:0048523	0.56	negative regulation of cellular process
GO:0009725	0.56	response to hormone
GO:0050796	0.55	regulation of insulin secretion
GO:0016043	0.55	cellular component organization
GO:0007204	0.55	positive regulation of cytosolic calcium ion concentration
GO:0032097	0.54	positive regulation of response to food
GO:0032024	0.54	positive regulation of insulin secretion
GO:0031326	0.52	regulation of cellular biosynthetic process
GO:0044767	0.51	single-organism developmental process
GO:0010556	0.51	regulation of macromolecule biosynthetic process
GO:1902533	0.50	positive regulation of intracellular signal transduction
GO:0050793	0.50	regulation of developmental process
GO:0001817	0.50	regulation of cytokine production

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:0005615	1.00	extracellular space
GO:0044464	0.79	cell part
GO:0005576	0.71	extracellular region
GO:0097458	0.57	neuron part
GO:0030424	0.56	axon

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	1ad1A	0.495	4.29	0.052	0.821	2.5.1.15	NA
2	0.060	2wl2B	0.484	3.71	0.056	0.735	5.99.1.3	NA
3	0.060	3bcfA	0.492	4.57	0.073	0.872	3.2.1.98	81
4	0.060	2p2wA	0.482	4.21	0.045	0.795	2.3.3.-	NA
5	0.060	2rgrA	0.492	3.30	0.081	0.701	5.99.1.3	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	1ofrD	0.468	4.60	0.038	0.846	0.46	PHE	complex1.pdb.gz	94,98,99
2	0.01	1q2rB	0.508	4.28	0.063	0.838	0.43	9DG	complex2.pdb.gz	23,84,88
3	0.01	1og0G	0.462	4.16	0.031	0.786	0.41	PHE	complex3.pdb.gz	98,101,102
4	0.01	1ofrC	0.488	4.05	0.040	0.812	0.54	PHE	complex4.pdb.gz	88,91,92,95
5	0.01	1efzA	0.507	4.29	0.063	0.838	0.40	PRF	complex5.pdb.gz	11,81,83

	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.