D-I-TASSER Q9BZJ7

D-I-TASSER results for Q9BZJ7

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

Summary of the Protein

Uniprot ID: Q9BZJ7
Protein Name: G-protein coupled receptor 62
Gene Name: GPR62

Input Sequence in FASTA format

>Q9BZJ7 (368 residues)
MANSTGLNASEVAGSLGLILAAVVEVGALLGNGALLVVVLRTPGLRDALYLAHLCVVDLL
AAASIMPLGLLAAPPPGLGRVRLGPAPCRAARFLSAALLPACTLGVAALGLARYRLIVHP
LRPGSRPPPVLVLTAVWAAAGLLGALSLLGTPPAPPPAPARCSVLAGGLGPFRPLWALLA
FALPALLLLGAYGGIFVVARRAALRPPRPARGSRLHSDSLDSRLSILPPLRPRLPGGKAA
LAPALAVGQFAACWLPYGCACLAPAARAAEAEAAVTWVAYSAFAAHPFLYGLLQRPVRLA
LGRLSRRALPGPVRACTPQAWHPRALLQCLQRPPEGPAVGPSEAPEQTPELAGGRSPAYQ
GPPESSLS

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	Q9BZJ7-D1	1-368	368		MANSTGLNASEVAGSLGLILAAVVEVGALLGNGALLVVVLRTPGLRDALYLAHLCVVDLLAAASIMPLGLLAAPPPGLGRVRLGPAPCRAARFLSAALLPACTLGVAALGLARYRLIVHPLRPGSRPPPVLVLTAVWAAAGLLGALSLLGTPPAPPPAPARCSVLAGGLGPFRPLWALLAFALPALLLLGAYGGIFVVARRAALRPPRPARGSRLHSDSLDSRLSILPPLRPRLPGGKAALAPALAVGQFAACWLPYGCACLAPAARAAEAEAAVTWVAYSAFAAHPFLYGLLQRPVRLALGRLSRRALPGPVRACTPQAWHPRALLQCLQRPPEGPAVGPSEAPEQTPELAGGRSPAYQGPPESSLS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.7583

(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	2ks9A	0.82	2.60	0.198	0.894	model1_2ks9A.pdb.gz
2	2hpyA	0.78	2.17	0.149	0.840	model1_2hpyA.pdb.gz
3	2ziyA	0.77	2.91	0.147	0.851	model1_2ziyA.pdb.gz
4	4zwjA	0.75	2.99	0.145	0.832	model1_4zwjA.pdb.gz
5	6me6A	0.73	2.80	0.192	0.807	model1_6me6A.pdb.gz
6	6li0A	0.71	3.65	0.167	0.823	model1_6li0A.pdb.gz
7	6i9kA	0.71	2.23	0.143	0.755	model1_6i9kA.pdb.gz
8	4iaqA	0.71	2.93	0.215	0.785	model1_4iaqA.pdb.gz
9	6me2A	0.70	2.52	0.166	0.758	model1_6me2A.pdb.gz
10	5ztyA	0.70	3.24	0.149	0.799	model1_5ztyA.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:0004888	1.00	transmembrane signaling receptor activity
GO:0004930	0.93	G-protein coupled receptor activity
GO:0008227	0.59	G-protein coupled amine receptor activity
GO:0008528	0.58	G-protein coupled peptide receptor activity
GO:0097159	0.53	organic cyclic compound binding
GO:0008188	0.53	neuropeptide receptor activity
GO:0004935	0.52	adrenergic receptor activity
GO:1901338	0.50	catecholamine binding
GO:0044877	0.50	macromolecular complex 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:0050794	0.99	regulation of cellular process
GO:0007165	0.97	signal transduction
GO:0007186	0.94	G-protein coupled receptor signaling pathway
GO:0044699	0.67	single-organism process
GO:0032501	0.67	multicellular organismal process
GO:0009987	0.67	cellular process
GO:0003008	0.66	system process
GO:0044763	0.64	single-organism cellular process
GO:0050896	0.63	response to stimulus
GO:0080090	0.61	regulation of primary metabolic process
GO:0031323	0.61	regulation of cellular metabolic process
GO:0007187	0.61	G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger
GO:0051239	0.60	regulation of multicellular organismal process
GO:0050877	0.60	neurological system process
GO:0048519	0.59	negative regulation of biological process
GO:0048518	0.59	positive regulation of biological process
GO:0044057	0.59	regulation of system process
GO:0031326	0.59	regulation of cellular biosynthetic process
GO:0019219	0.59	regulation of nucleobase-containing compound metabolic process
GO:0007188	0.59	adenylate cyclase-modulating G-protein coupled receptor signaling pathway
GO:0048523	0.58	negative regulation of cellular process
GO:0019220	0.58	regulation of phosphate metabolic process
GO:0048522	0.57	positive regulation of cellular process
GO:0007154	0.57	cell communication
GO:0050790	0.56	regulation of catalytic activity
GO:0031325	0.56	positive regulation of cellular metabolic process
GO:0007267	0.56	cell-cell signaling
GO:0065008	0.55	regulation of biological quality
GO:0060255	0.55	regulation of macromolecule metabolic process
GO:0045935	0.55	positive regulation of nucleobase-containing compound metabolic process
GO:0007166	0.55	cell surface receptor signaling pathway
GO:0051930	0.54	regulation of sensory perception of pain
GO:0051606	0.54	detection of stimulus
GO:0048583	0.54	regulation of response to stimulus
GO:0045761	0.54	regulation of adenylate cyclase activity
GO:0031328	0.54	positive regulation of cellular biosynthetic process
GO:0023051	0.54	regulation of signaling
GO:0010646	0.54	regulation of cell communication
GO:0010604	0.54	positive regulation of macromolecule metabolic process
GO:0010468	0.53	regulation of gene expression
GO:0010033	0.53	response to organic substance
GO:0009966	0.53	regulation of signal transduction
GO:0007268	0.53	chemical synaptic transmission
GO:0007189	0.53	adenylate cyclase-activating G-protein coupled receptor signaling pathway
GO:1903522	0.52	regulation of blood circulation
GO:0051716	0.52	cellular response to stimulus
GO:0051254	0.52	positive regulation of RNA metabolic process
GO:0051240	0.52	positive regulation of multicellular organismal process
GO:0050906	0.52	detection of stimulus involved in sensory perception
GO:0050880	0.52	regulation of blood vessel size
GO:0045937	0.52	positive regulation of phosphate metabolic process
GO:0044707	0.52	single-multicellular organism process
GO:0044237	0.52	cellular metabolic process
GO:0044092	0.52	negative regulation of molecular function
GO:0042592	0.52	homeostatic process
GO:0032879	0.52	regulation of localization
GO:0010628	0.52	positive regulation of gene expression
GO:0010556	0.52	regulation of macromolecule biosynthetic process
GO:0006937	0.52	regulation of muscle contraction
GO:1903530	0.51	regulation of secretion by cell
GO:1903508	0.51	positive regulation of nucleic acid-templated transcription
GO:0071875	0.51	adrenergic receptor signaling pathway
GO:0071704	0.51	organic substance metabolic process
GO:0071702	0.51	organic substance transport
GO:0070887	0.51	cellular response to chemical stimulus
GO:0051241	0.51	negative regulation of multicellular organismal process
GO:0046903	0.51	secretion
GO:0045933	0.51	positive regulation of muscle contraction
GO:0044238	0.51	primary metabolic process
GO:0043408	0.51	regulation of MAPK cascade
GO:0043085	0.51	positive regulation of catalytic activity
GO:0019229	0.51	regulation of vasoconstriction
GO:0016043	0.51	cellular component organization
GO:0009967	0.51	positive regulation of signal transduction
GO:0009719	0.51	response to endogenous stimulus
GO:0009605	0.51	response to external stimulus
GO:0007610	0.51	behavior
GO:1903531	0.50	negative regulation of secretion by cell
GO:1902533	0.50	positive regulation of intracellular signal transduction
GO:1901700	0.50	response to oxygen-containing compound
GO:0051223	0.50	regulation of protein transport
GO:0051050	0.50	positive regulation of transport
GO:0032502	0.50	developmental process
GO:0030334	0.50	regulation of cell migration
GO:0010243	0.50	response to organonitrogen compound
GO:0009725	0.50	response to hormone
GO:0008217	0.50	regulation of blood pressure
GO:0007270	0.50	neuron-neuron synaptic transmission
GO:0006950	0.50	response to stress
GO:0006357	0.50	regulation of transcription from RNA polymerase II promoter
GO:0001934	0.50	positive regulation of protein phosphorylation

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	0.98	cell part
GO:0044425	0.88	membrane part
GO:0016021	0.87	integral component of membrane
GO:0044459	0.79	plasma membrane part
GO:0005887	0.78	integral component of plasma membrane
GO:0016020	0.74	membrane
GO:0005886	0.69	plasma membrane

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	2ohyB	0.405	6.42	0.088	0.666	5.4.3.6	NA
2	0.060	3e04D	0.394	6.54	0.041	0.647	4.2.1.2	NA
3	0.060	2nyfA	0.422	6.35	0.085	0.690	4.3.1.5	288
4	0.060	1yrqI	0.412	6.48	0.052	0.655	1.12.2.1	105
5	0.060	3d4sA	0.677	3.13	0.157	0.755	3.2.1.17	106,113,242

	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	0.08	2i37A	0.721	1.61	0.158	0.755	0.73	UUU	complex1.pdb.gz	105,110,133,134
2	0.05	3oaxB	0.784	2.12	0.149	0.840	0.71	4E6	complex2.pdb.gz	23,27,30,34
3	0.04	2rh1A	0.682	3.08	0.166	0.761	0.79	CLR	complex3.pdb.gz	26,30,33,34,63
4	0.04	3aymB	0.769	3.02	0.158	0.853	0.69	RET	complex4.pdb.gz	57,61,98,99,102,103,181,254,258,276,280
5	0.01	1c6gA	0.205	5.61	0.023	0.302	0.83	KR	complex5.pdb.gz	104,107,108,132
6	0.01	1li6A	0.203	5.36	0.041	0.291	0.60	5MP	complex6.pdb.gz	49,53,105,108,133

	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.