D-I-TASSER P51570

D-I-TASSER results for P51570

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

Summary of the Protein

Uniprot ID: P51570
Protein Name: Galactokinase
Gene Name: GALK1

Input Sequence in FASTA format

>P51570 (392 residues)
MAALRQPQVAELLAEARRAFREEFGAEPELAVSAPGRVNLIGEHTDYNQGLVLPMALELM
TVLVGSPRKDGLVSLLTTSEGADEPQRLQFPLPTAQRSLEPGTPRWANYVKGVIQYYPAA
PLPGFSAVVVSSVPLGGGLSSSASLEVATYTFLQQLCPDSGTIAARAQVCQQAEHSFAGM
PCGIMDQFISLMGQKGHALLIDCRSLETSLVPLSDPKLAVLITNSNVRHSLASSEYPVRR
RQCEEVARALGKESLREVQLEELEAARDLVSKEGFRRARHVVGEIRRTAQAAAALRRGDY
RAFGRLMVESHRSLRDDYEVSCPELDQLVEAALAVPGVYGSRMTGGGFGGCTVTLLEASA
APHAMRHIQEHYGGTATFYLSQAADGAKVLCL

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	P51570-D1	1-37,55-197,382-392	191		MAALRQPQVAELLAEARRAFREEFGAEPELAVSAPGRMALELMTVLVGSPRKDGLVSLLTTSEGADEPQRLQFPLPTAQRSLEPGTPRWANYVKGVIQYYPAAPLPGFSAVVVSSVPLGGGLSSSASLEVATYTFLQQLCPDSGTIAARAQVCQQAEHSFAGMPCGIMDQFISLMGQKGHQAADGAKVLCL
2	P51570-D2	38-54,198-381	201		VNLIGEHTDYNQGLVLPALLIDCRSLETSLVPLSDPKLAVLITNSNVRHSLASSEYPVRRRQCEEVARALGKESLREVQLEELEAARDLVSKEGFRRARHVVGEIRRTAQAAAALRRGDYRAFGRLMVESHRSLRDDYEVSCPELDQLVEAALAVPGVYGSRMTGGGFGGCTVTLLEASAAPHAMRHIQEHYGGTATFYLS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.9342

(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	1wuuA	0.96	0.91	0.990	0.975	model1_1wuuA.pdb.gz
2	6tepA	0.92	1.87	0.351	0.975	model1_6tepA.pdb.gz
3	1pieA	0.92	1.66	0.347	0.957	model1_1pieA.pdb.gz
4	2aj4A	0.91	2.17	0.276	0.972	model1_2aj4A.pdb.gz
5	2a2dA	0.89	2.21	0.306	0.954	model1_2a2dA.pdb.gz
6	2deiA	0.84	1.65	0.352	0.878	model1_2deiA.pdb.gz
7	4uskA	0.74	2.60	0.192	0.824	model1_4uskA.pdb.gz
8	1kkhA	0.70	2.95	0.188	0.788	model1_1kkhA.pdb.gz
9	4hacA	0.68	2.91	0.227	0.765	model1_4hacA.pdb.gz
10	2r3vA	0.68	3.85	0.237	0.827	model1_2r3vA.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:0016772	0.98	transferase activity, transferring phosphorus-containing groups
GO:0016301	0.95	kinase activity
GO:0016773	0.94	phosphotransferase activity, alcohol group as acceptor
GO:0019200	0.91	carbohydrate kinase activity
GO:0004335	0.89	galactokinase activity
GO:1901363	0.61	heterocyclic compound binding
GO:0097159	0.61	organic cyclic compound binding
GO:0036094	0.58	small molecule binding
GO:0097367	0.57	carbohydrate derivative binding
GO:0000166	0.57	nucleotide binding
GO:0035639	0.56	purine ribonucleoside triphosphate binding
GO:0032555	0.56	purine ribonucleotide binding
GO:0032550	0.56	purine ribonucleoside binding
GO:0005524	0.55	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:0071704	1.00	organic substance metabolic process
GO:0044238	1.00	primary metabolic process
GO:0044699	0.96	single-organism process
GO:0044710	0.95	single-organism metabolic process
GO:0044281	0.94	small molecule metabolic process
GO:0005975	0.94	carbohydrate metabolic process
GO:0019318	0.87	hexose metabolic process
GO:0006012	0.86	galactose metabolic process
GO:0009987	0.66	cellular process
GO:0044237	0.54	cellular metabolic 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:0044424	1.00	intracellular part
GO:0005737	0.82	cytoplasm
GO:0044444	0.68	cytoplasmic part
GO:0043226	0.64	organelle
GO:0043227	0.62	membrane-bounded organelle
GO:0005829	0.56	cytosol
GO:0016020	0.52	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	0.558	1s4eF	0.838	1.77	0.359	0.880	2.7.1.6	231,233
2	0.353	2aj4A	0.909	2.17	0.276	0.972	2.7.1.6	47,109,138,141,175,179,236
3	0.283	3hulA	0.618	2.87	0.168	0.699	2.7.1.39	59,134,138,142,174
4	0.226	2hfuA	0.672	3.30	0.165	0.783	2.7.1.36	142,186,230,232,350
5	0.208	2r3vA	0.675	3.85	0.237	0.827	2.7.1.36	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	0.77	1wuuA	0.981	0.90	0.990	0.995	1.87	GLA	complex1.pdb.gz	37,43,44,46,47,182,183,185,186,236,345,346
2	0.61	1wuuD	0.983	0.80	0.995	0.995	1.82	ANP	complex2.pdb.gz	37,77,106,109,129,135,136,137,138,140,141,142,145,345,346
3	0.47	1pieA	0.916	1.66	0.347	0.957	1.83	PO4	complex3.pdb.gz	37,138,139,140,186,346
4	0.30	1s4eG	0.613	1.78	0.373	0.643	1.18	GLA	complex4.pdb.gz	43,44,46,182,183,346
5	0.17	2oi2A	0.616	3.30	0.196	0.717	0.84	DP6	complex5.pdb.gz	37,44,46,47,140,186,345,346

	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.