D-I-TASSER Q9NPF4

D-I-TASSER results for Q9NPF4

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

Summary of the Protein

Uniprot ID: Q9NPF4
Protein Name: Probable tRNA N6-adenosine threonylcarbamoyltransferase
Gene Name: OSGEP

Input Sequence in FASTA format

>Q9NPF4 (335 residues)
MPAVLGFEGSANKIGVGVVRDGKVLANPRRTYVTPPGTGFLPGDTARHHRAVILDLLQEA
LTESGLTSQDIDCIAYTKGPGMGAPLVSVAVVARTVAQLWNKPLVGVNHCIGHIEMGRLI
TGATSPTVLYVSGGNTQVIAYSEHRYRIFGETIDIAVGNCLDRFARVLKISNDPSPGYNI
EQMAKRGKKLVELPYTVKGMDVSFSGILSFIEDVAHRMLATGECTPEDLCFSLQETVFAM
LVEITERAMAHCGSQEALIVGGVGCNVRLQEMMATMCQERGARLFATDERFCIDNGAMIA
QAGWEMFRAGHRTPLSDSGVTQRYRTDEVEVTWRD

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	Q9NPF4-D1	1-107	107		MPAVLGFEGSANKIGVGVVRDGKVLANPRRTYVTPPGTGFLPGDTARHHRAVILDLLQEALTESGLTSQDIDCIAYTKGPGMGAPLVSVAVVARTVAQLWNKPLVGV
2	Q9NPF4-D2	108-335	228		NHCIGHIEMGRLITGATSPTVLYVSGGNTQVIAYSEHRYRIFGETIDIAVGNCLDRFARVLKISNDPSPGYNIEQMAKRGKKLVELPYTVKGMDVSFSGILSFIEDVAHRMLATGECTPEDLCFSLQETVFAMLVEITERAMAHCGSQEALIVGGVGCNVRLQEMMATMCQERGARLFATDERFCIDNGAMIAQAGWEMFRAGHRTPLSDSGVTQRYRTDEVEVTWRD

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.976

(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	6gwjK	0.99	0.55	1.000	0.997	model1_6gwjK.pdb.gz
2	6z81A	0.93	1.87	0.330	0.985	model1_6z81A.pdb.gz
3	3enoA	0.92	1.60	0.448	0.973	model1_3enoA.pdb.gz
4	3en9A	0.92	1.69	0.492	0.964	model1_3en9A.pdb.gz
5	2ivoA	0.92	1.59	0.474	0.970	model1_2ivoA.pdb.gz
6	6nbjA	0.83	3.21	0.265	0.970	model1_6nbjA.pdb.gz
7	8ideA	0.83	2.61	0.272	0.922	model1_8ideA.pdb.gz
8	3venA	0.72	3.52	0.142	0.857	model1_3venA.pdb.gz
9	3vthA	0.70	3.32	0.113	0.839	model1_3vthA.pdb.gz
10	1okjB	0.50	3.82	0.196	0.615	model1_1okjB.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:0003824	0.88	catalytic activity
GO:0016787	0.80	hydrolase activity
GO:0070011	0.79	peptidase activity, acting on L-amino acid peptides
GO:0004175	0.78	endopeptidase activity
GO:1901363	0.77	heterocyclic compound binding
GO:0097159	0.77	organic cyclic compound binding
GO:0004222	0.75	metalloendopeptidase activity
GO:0016740	0.72	transferase activity
GO:0016747	0.71	transferase activity, transferring acyl groups other than amino-acyl groups
GO:0061711	0.70	N(6)-L-threonylcarbamoyladenine synthase
GO:0043167	0.63	ion binding
GO:0046872	0.62	metal ion binding
GO:0046914	0.61	transition metal ion binding
GO:0097367	0.59	carbohydrate derivative binding
GO:0005506	0.58	iron ion binding
GO:0003676	0.57	nucleic acid binding
GO:0036094	0.56	small molecule binding
GO:0000166	0.55	nucleotide binding
GO:0035639	0.54	purine ribonucleoside triphosphate binding
GO:0032555	0.54	purine ribonucleotide binding
GO:0032550	0.54	purine ribonucleoside binding
GO:0005524	0.53	ATP 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:0044238	1.00	primary metabolic process
GO:0043170	1.00	macromolecule metabolic process
GO:0044237	0.99	cellular metabolic process
GO:0002949	0.98	tRNA threonylcarbamoyladenosine modification

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:0000408	0.99	EKC/KEOPS complex

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	0.559	2ivpA	0.934	1.35	0.474	0.970	3.4.24.57	11,34,80,132,134,137,152,155,159,174,177,263,294
2	0.505	3en9A	0.923	1.69	0.492	0.964	3.4.24.57	11,132,134,137,151,155,159,161,177,205,208,263,294
3	0.095	2h3gX	0.560	3.26	0.112	0.669	2.7.1.33	9,12,152
4	0.075	3djcG	0.554	3.53	0.118	0.681	2.7.1.33	261
5	0.073	3bf3A	0.548	3.41	0.121	0.669	2.7.1.33	9,262

	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	0.63	2vwbB	0.906	1.22	0.498	0.934	1.49	ANP	complex1.pdb.gz	11,13,109,113,130,132,133,134,158,161,162,176,181,262,263,265,266,293,294
2	0.49	3en9A	0.923	1.69	0.492	0.964	0.94	MG	complex2.pdb.gz	109,113,294
3	0.41	3enhA	0.869	1.40	0.505	0.904	1.35	TBR	complex3.pdb.gz	12,133,159,162,166

	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.