D-I-TASSER P56597

D-I-TASSER results for P56597

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

Summary of the Protein

Uniprot ID: P56597
Protein Name: Nucleoside diphosphate kinase homolog 5
Gene Name: NME5

Input Sequence in FASTA format

>P56597 (212 residues)
MEISMPPPQIYVEKTLAIIKPDIVDKEEEIQDIILRSGFTIVQRRKLRLSPEQCSNFYVE
KYGKMFFPNLTAYMSSGPLVAMILARHKAISYWLELLGPNNSLVAKETHPDSLRAIYGTD
DLRNALHGSNDFAAAEREIRFMFPEVIVEPIPIGQAAKDYLNLHIMPTLLEGLTELCKQK
PADPLIWLADWLLKNNPNKPKLCHHPIVEEPY

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	P56597-D1	1-212	212		MEISMPPPQIYVEKTLAIIKPDIVDKEEEIQDIILRSGFTIVQRRKLRLSPEQCSNFYVEKYGKMFFPNLTAYMSSGPLVAMILARHKAISYWLELLGPNNSLVAKETHPDSLRAIYGTDDLRNALHGSNDFAAAEREIRFMFPEVIVEPIPIGQAAKDYLNLHIMPTLLEGLTELCKQKPADPLIWLADWLLKNNPNKPKLCHHPIVEEPY

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.7071

(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	1s59A	0.66	1.75	0.265	0.703	model1_1s59A.pdb.gz
2	1zs6A	0.66	1.63	0.273	0.698	model1_1zs6A.pdb.gz
3	1f6tB	0.66	1.79	0.289	0.698	model1_1f6tB.pdb.gz
4	4uofA	0.66	1.55	0.255	0.693	model1_4uofA.pdb.gz
5	3ngsA	0.66	1.63	0.309	0.693	model1_3ngsA.pdb.gz
6	1w7wA	0.66	1.63	0.262	0.693	model1_1w7wA.pdb.gz
7	5u2iA	0.66	1.57	0.255	0.693	model1_5u2iA.pdb.gz
8	6agyA	0.65	1.60	0.272	0.689	model1_6agyA.pdb.gz
9	2dy9B	0.65	1.31	0.272	0.679	model1_2dy9B.pdb.gz
10	1ndlA	0.65	1.77	0.267	0.698	model1_1ndlA.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:0016740	1.00	transferase activity
GO:0016772	0.96	transferase activity, transferring phosphorus-containing groups
GO:0004550	0.95	nucleoside diphosphate kinase 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:0009987	0.88	cellular process
GO:0008152	0.83	metabolic process
GO:0044699	0.82	single-organism process
GO:0071704	0.78	organic substance metabolic process
GO:0044763	0.78	single-organism cellular process
GO:0044237	0.78	cellular metabolic process
GO:0044238	0.76	primary metabolic process
GO:0006807	0.75	nitrogen compound metabolic process
GO:0034641	0.74	cellular nitrogen compound metabolic process
GO:0044710	0.73	single-organism metabolic process
GO:0006139	0.72	nucleobase-containing compound metabolic process
GO:0044281	0.71	small molecule metabolic process
GO:0065007	0.68	biological regulation
GO:0050789	0.67	regulation of biological process
GO:1901576	0.66	organic substance biosynthetic process
GO:0055086	0.66	nucleobase-containing small molecule metabolic process
GO:0050794	0.66	regulation of cellular process
GO:0044249	0.66	cellular biosynthetic process
GO:0044271	0.65	cellular nitrogen compound biosynthetic process
GO:1901564	0.64	organonitrogen compound metabolic process
GO:0034654	0.62	nucleobase-containing compound biosynthetic process
GO:0019637	0.62	organophosphate metabolic process
GO:0006796	0.62	phosphate-containing compound metabolic process
GO:0009117	0.61	nucleotide metabolic process
GO:0090407	0.60	organophosphate biosynthetic process
GO:0044711	0.60	single-organism biosynthetic process
GO:0009142	0.59	nucleoside triphosphate biosynthetic process
GO:0006163	0.58	purine nucleotide metabolic process
GO:0006220	0.55	pyrimidine nucleotide metabolic process
GO:0042981	0.51	regulation of apoptotic process

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:0044424	0.81	intracellular part
GO:0005622	0.80	intracellular
GO:0044444	0.52	cytoplasmic 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

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	0.366	1zs6B	0.662	1.66	0.273	0.698	2.7.4.6	22,24,29,78,80,127
2	0.360	1s59A	0.664	1.75	0.265	0.703	2.7.4.6	22,29,73,96,98,123,127
3	0.321	1u8wD	0.635	1.79	0.265	0.679	2.7.4.6	39,127,143
4	0.312	1pkuL	0.636	2.00	0.259	0.689	2.7.4.6	22,24,117,127
5	0.306	1k44F	0.599	1.25	0.353	0.627	2.7.4.6	23,29,41,43,96

	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	0.65	1hiyB	0.657	1.52	0.291	0.689	1.22	3AN	complex1.pdb.gz	20,57,66,70,93,100,124
2	0.57	1mn7A	0.659	1.63	0.270	0.693	1.24	ABT	complex2.pdb.gz	20,58,61,66,70,93,100,114,121,124,127,128
3	0.39	3ngsC	0.648	1.76	0.309	0.693	0.88	PO4	complex3.pdb.gz	100,124,126,127
4	0.37	3fkbD	0.655	1.34	0.272	0.684	1.12	TNV	complex4.pdb.gz	20,57,60,66,93,114,121,122,124
5	0.35	1bhnD	0.658	1.63	0.282	0.693	0.84	UUU	complex5.pdb.gz	20,94,100,121,122,124,127
6	0.19	1b4sA	0.660	1.40	0.270	0.689	0.82	PO4	complex6.pdb.gz	20,57,58,127,128
7	0.05	2cwk0	0.648	1.30	0.277	0.674	0.96	III	complex7.pdb.gz	25,26,27,28,29,31,32,35,41,42,44,49,78,80

	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.