D-I-TASSER Q9NRG1

D-I-TASSER results for Q9NRG1

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

Summary of the Protein

Uniprot ID: Q9NRG1
Protein Name: Phosphoribosyltransferase domain-containing protein 1
Gene Name: PRTFDC1

Input Sequence in FASTA format

>Q9NRG1 (225 residues)
MAGSSEEAPDYGRGVVIMDDWPGYDLNLFTYPQHYYGDLEYVLIPHGIIVDRIERLAKDI
MKDIGYSDIMVLCVLKGGYKFCADLVEHLKNISRNSDRFVSMKVDFIRLKSYRNDQSMGE
MQIIGGDDLSTLAGKNVLIVEDVVGTGRTMKALLSNIEKYKPNMIKVASLLVKRTSRSDG
FRPDYAGFEIPNLFVVGYALDYNEYFRDLNHICVINEHGKEKYRV

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	Q9NRG1-D1	1-225	225		MAGSSEEAPDYGRGVVIMDDWPGYDLNLFTYPQHYYGDLEYVLIPHGIIVDRIERLAKDIMKDIGYSDIMVLCVLKGGYKFCADLVEHLKNISRNSDRFVSMKVDFIRLKSYRNDQSMGEMQIIGGDDLSTLAGKNVLIVEDVVGTGRTMKALLSNIEKYKPNMIKVASLLVKRTSRSDGFRPDYAGFEIPNLFVVGYALDYNEYFRDLNHICVINEHGKEKYRV

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.9553

(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	2jbhB	0.90	1.62	1.000	0.942	model1_2jbhB.pdb.gz
2	1fsgA	0.88	1.83	0.312	0.933	model1_1fsgA.pdb.gz
3	1cjbC	0.87	2.07	0.413	0.933	model1_1cjbC.pdb.gz
4	1d6nA	0.87	1.84	0.637	0.929	model1_1d6nA.pdb.gz
5	5ipfA	0.85	1.24	0.485	0.880	model1_5ipfA.pdb.gz
6	8fwyA	0.76	2.09	0.283	0.836	model1_8fwyA.pdb.gz
7	1p17B	0.75	1.93	0.331	0.804	model1_1p17B.pdb.gz
8	6aqoA	0.73	1.88	0.302	0.796	model1_6aqoA.pdb.gz
9	3kb8A	0.73	1.96	0.293	0.791	model1_3kb8A.pdb.gz
10	2gebA	0.73	1.90	0.304	0.787	model1_2gebA.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:0004422	0.99	hypoxanthine phosphoribosyltransferase activity
GO:0000287	0.97	magnesium ion 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:0009987	1.00	cellular process
GO:0008152	1.00	metabolic process
GO:0044763	0.99	single-organism cellular process
GO:0044281	0.99	small molecule metabolic process
GO:0043101	0.99	purine-containing compound salvage
GO:0046129	0.98	purine ribonucleoside biosynthetic process
GO:0009117	0.98	nucleotide metabolic process
GO:0006166	0.97	purine ribonucleoside salvage
GO:0006164	0.97	purine nucleotide biosynthetic process
GO:0046100	0.96	hypoxanthine metabolic process
GO:0009259	0.95	ribonucleotide metabolic process
GO:0046040	0.94	IMP metabolic process
GO:0046037	0.94	GMP metabolic process
GO:0006178	0.93	guanine salvage
GO:0009260	0.89	ribonucleotide biosynthetic process
GO:0006188	0.88	IMP biosynthetic process
GO:0006177	0.88	GMP biosynthetic process
GO:0006168	0.88	adenine salvage
GO:0032264	0.87	IMP salvage
GO:0032263	0.87	GMP salvage

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:0044424	1.00	intracellular part
GO:0044444	0.96	cytoplasmic part
GO:0005829	0.94	cytosol

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	0.476	1fsgA	0.878	1.83	0.312	0.933	2.4.2.8	110
2	0.474	1bzyA	0.887	1.85	0.659	0.933	2.4.2.8	141,142,173,177
3	0.450	1p17B	0.746	1.93	0.331	0.804	2.4.2.8	141,142,173,177
4	0.426	1hgxA	0.687	1.43	0.331	0.724	2.4.2.8	141,142,173
5	0.414	2gebA	0.726	1.90	0.304	0.787	2.4.2.8	141,142,173

	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	0.92	2jbhA	0.897	1.19	0.995	0.924	1.77	5GP	complex1.pdb.gz	141,142,143,145,146,147,148,149,173,194,195,200,201
2	0.79	1bzyA	0.887	1.85	0.659	0.933	1.21	POP	complex2.pdb.gz	76,77,201,207
3	0.77	1d6nA	0.868	1.84	0.637	0.929	1.61	PPO	complex3.pdb.gz	143,145,173,193,194,195,201
4	0.48	3ozfA	0.869	1.89	0.405	0.929	1.09	PO4	complex4.pdb.gz	145,146,147,149
5	0.48	1p18A	0.736	1.75	0.326	0.791	1.52	PRP	complex5.pdb.gz	76,77,141,142,143,145,146,147,201,207
6	0.46	1fsgA	0.878	1.83	0.312	0.933	1.00	9DG	complex6.pdb.gz	173,194,195,200,201
7	0.08	1cjb0	0.869	2.07	0.413	0.933	1.50	III	complex7.pdb.gz	15,24,28,29,30,45,46,47,48,51,52,54,55,58
8	0.08	1cjb1	0.872	2.03	0.413	0.933	1.34	III	complex8.pdb.gz	30,32,33,34,35,37,76,79,83,86,90,94,95,97,99,104,106,124,125,127,207,208
9	0.06	1pzm0	0.691	1.45	0.311	0.729	1.10	III	complex9.pdb.gz	75,76,79,80,82,83,84,86,87,88,102,103,104,105,106,198,204,205,208,210

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.