D-I-TASSER O00764

D-I-TASSER results for O00764

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

Summary of the Protein

Uniprot ID: O00764
Protein Name: Pyridoxal kinase
Gene Name: PDXK

Input Sequence in FASTA format

>O00764 (312 residues)
MEEECRVLSIQSHVIRGYVGNRAATFPLQVLGFEIDAVNSVQFSNHTGYAHWKGQVLNSD
ELQELYEGLRLNNMNKYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVLGDKW
DGEGSMYVPEDLLPVYKEKVVPLADIITPNQFEAELLSGRKIHSQEEALRVMDMLHSMGP
DTVVITSSDLPSPQGSNYLIVLGSQRRRNPAGSVVMERIRMDIRKVDAVFVGTGDLFAAM
LLAWTHKHPNNLKVACEKTVSTLHHVLQRTIQCAKAQAGEGVRPSPMQLELRMVQSKRDI
EDPEIVVQATVL

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	O00764-D1	1-145	145		MEEECRVLSIQSHVIRGYVGNRAATFPLQVLGFEIDAVNSVQFSNHTGYAHWKGQVLNSDELQELYEGLRLNNMNKYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVLGDKWDGEGSMYVPEDLLPVYKEKVVPLAD
2	O00764-D2	146-312	167		IITPNQFEAELLSGRKIHSQEEALRVMDMLHSMGPDTVVITSSDLPSPQGSNYLIVLGSQRRRNPAGSVVMERIRMDIRKVDAVFVGTGDLFAAMLLAWTHKHPNNLKVACEKTVSTLHHVLQRTIQCAKAQAGEGVRPSPMQLELRMVQSKRDIEDPEIVVQATVL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.973

(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	2f7kA	0.97	1.20	1.000	1.000	model1_2f7kA.pdb.gz
2	5b6aA	0.87	1.65	0.305	0.913	model1_5b6aA.pdb.gz
3	6k8zA	0.84	1.53	0.378	0.881	model1_6k8zA.pdb.gz
4	4s1hA	0.84	1.87	0.277	0.891	model1_4s1hA.pdb.gz
5	5trwA	0.84	1.45	0.325	0.878	model1_5trwA.pdb.gz
6	1vi9A	0.84	1.58	0.313	0.881	model1_1vi9A.pdb.gz
7	3zs7A	0.84	1.46	0.393	0.872	model1_3zs7A.pdb.gz
8	6su9A	0.83	2.16	0.298	0.904	model1_6su9A.pdb.gz
9	3mbjA	0.82	1.72	0.202	0.869	model1_3mbjA.pdb.gz
10	5zw9A	0.79	1.81	0.261	0.837	model1_5zw9A.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:0016301	1.00	kinase activity
GO:0016773	0.99	phosphotransferase activity, alcohol group as acceptor
GO:0008478	0.98	pyridoxal 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:1901576	1.00	organic substance biosynthetic process
GO:1901564	1.00	organonitrogen compound metabolic process
GO:1901360	1.00	organic cyclic compound metabolic process
GO:0046483	1.00	heterocycle metabolic process
GO:0044763	1.00	single-organism cellular process
GO:0044249	1.00	cellular biosynthetic process
GO:0034641	1.00	cellular nitrogen compound metabolic process
GO:0006767	1.00	water-soluble vitamin metabolic process
GO:0042816	0.98	vitamin B6 metabolic process
GO:0009443	0.98	pyridoxal 5'-phosphate 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	0.97	cytoplasmic part
GO:0005829	0.96	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	0.371	1jxiA	0.715	2.83	0.174	0.811	2.7.4.7	232
2	0.183	3hj6A	0.581	3.22	0.129	0.696	2.7.1.4	186,234,266
3	0.164	3h74A	0.782	2.25	0.179	0.859	2.7.1.35	NA
4	0.153	2i5bA	0.725	3.25	0.173	0.853	2.7.4.7	NA
5	0.099	1v8aA	0.629	3.11	0.178	0.750	2.7.1.50	232,234

	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	0.79	3keuA	0.970	0.58	1.000	0.978	1.94	PLP	complex1.pdb.gz	12,19,20,47,84,231,232,233,234,235
2	0.69	2yxuB	0.971	0.86	1.000	0.984	1.88	MPD	complex2.pdb.gz	12,19,46,47,84,235
3	0.65	1ygjA	0.975	0.92	0.867	0.990	2.00	RMC	complex3.pdb.gz	12,14,19,20,41,43,46,47,84,127,232,235
4	0.62	3fhxA	0.975	0.66	0.997	0.984	1.46	ATP	complex4.pdb.gz	113,118,127,150,153,186,187,224,225,226,228,233,267
5	0.46	1lhp0	0.945	1.22	0.863	0.965	1.86	III	complex5.pdb.gz	4,6,13,15,16,18,22,26,29,30,32,33,34,35,36,37,38,39,42,43,44,45,49,50,51,53,55,57,61,64,65,68,69,71,72,74,277,294,297,301
6	0.16	1jxiA	0.715	2.83	0.174	0.811	0.91	HMH	complex6.pdb.gz	12,13,20,45,235

	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.