D-I-TASSER P13995

D-I-TASSER results for P13995

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

Summary of the Protein

Uniprot ID: P13995
Protein Name: Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial
Gene Name: MTHFD2

Input Sequence in FASTA format

>P13995 (350 residues)
MAATSLMSALAARLLQPAHSCSLRLRPFHLAAVRNEAVVISGRKLAQQIKQEVRQEVEEW
VASGNKRPHLSVILVGENPASHSYVLNKTRAAAVVGINSETIMKPASISEEELLNLINKL
NNDDNVDGLLVQLPLPEHIDERRICNAVSPDKDVDGFHVINVGRMCLDQYSMLPATPWGV
WEIIKRTGIPTLGKNVVVAGRSKNVGMPIAMLLHTDGAHERPGGDATVTISHRYTPKEQL
KKHTILADIVISAAGIPNLITADMIKEGAAVIDVGINRVHDPVTAKPKLVGDVDFEGVRQ
KAGYITPVPGGVGPMTVAMLMKNTIIAAKKVLRLEEREVLKSKELGVATN

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	P13995-D1	1-40,175-307	173		MAATSLMSALAARLLQPAHSCSLRLRPFHLAAVRNEAVVIATPWGVWEIIKRTGIPTLGKNVVVAGRSKNVGMPIAMLLHTDGAHERPGGDATVTISHRYTPKEQLKKHTILADIVISAAGIPNLITADMIKEGAAVIDVGINRVHDPVTAKPKLVGDVDFEGVRQKAGYITP
2	P13995-D2	41-174,308-350	177		SGRKLAQQIKQEVRQEVEEWVASGNKRPHLSVILVGENPASHSYVLNKTRAAAVVGINSETIMKPASISEEELLNLINKLNNDDNVDGLLVQLPLPEHIDERRICNAVSPDKDVDGFHVINVGRMCLDQYSMLPVPGGVGPMTVAMLMKNTIIAAKKVLRLEEREVLKSKELGVATN

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.863

(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	5tc4A	0.83	0.36	1.000	0.834	model1_5tc4A.pdb.gz
2	5zf1A	0.81	1.01	0.557	0.820	model1_5zf1A.pdb.gz
3	4cjxA	0.79	1.97	0.416	0.834	model1_4cjxA.pdb.gz
4	6apeA	0.79	1.34	0.433	0.811	model1_6apeA.pdb.gz
5	3l07B	0.78	1.50	0.479	0.811	model1_3l07B.pdb.gz
6	4a26A	0.78	2.05	0.435	0.834	model1_4a26A.pdb.gz
7	1b0aA	0.78	1.75	0.481	0.814	model1_1b0aA.pdb.gz
8	6v6yA	0.78	1.08	0.466	0.791	model1_6v6yA.pdb.gz
9	3p2oA	0.77	1.22	0.475	0.789	model1_3p2oA.pdb.gz
10	1diaB	0.77	2.08	0.405	0.826	model1_1diaB.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:0004488	0.99	methylenetetrahydrofolate dehydrogenase (NADP+) activity
GO:0004477	0.99	methenyltetrahydrofolate cyclohydrolase activity
GO:0016879	0.57	ligase activity, forming carbon-nitrogen bonds
GO:0004329	0.56	formate-tetrahydrofolate ligase 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:0006730	1.00	one-carbon metabolic process
GO:0071704	0.57	organic substance 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:0005829	1.00	cytosol
GO:0043226	0.59	organelle
GO:0043229	0.56	intracellular organelle
GO:0043227	0.56	membrane-bounded organelle
GO:0043231	0.53	intracellular membrane-bounded organelle

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	0.606	1b0aA	0.776	1.75	0.481	0.814	1.5.1.5 3.5.4.9	88
2	0.481	1diaB	0.768	2.08	0.405	0.826	1.5.1.5 3.5.4.9	84,133,155,176,203,205,253,276,317
3	0.199	1a4iB	0.767	2.10	0.405	0.826	1.5.1.5 3.5.4.9	88
4	0.192	3l07B	0.780	1.50	0.479	0.811	3.5.4.9 1.5.1.5	88
5	0.156	2c2xA	0.761	1.61	0.421	0.800	1.5.1.5 3.5.4.9	88

	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	0.27	3p2oB	0.782	1.27	0.473	0.803	1.36	NAD	complex1.pdb.gz	84,176,200,201,202,205,232,233,253,254,255,259,274,275,276,313,316
2	0.25	1digA	0.778	1.34	0.411	0.800	1.65	L37	complex2.pdb.gz	88,276,310,311,313,314,317
3	0.25	1diaA	0.778	1.34	0.411	0.800	1.56	L24	complex3.pdb.gz	84,87,88,132,133,309,310,313,314,317
4	0.11	1b0a0	0.776	1.75	0.481	0.814	0.96	III	complex4.pdb.gz	157,159,160,163,164,166,167,168,203,207,211,230,231,232,234,235

	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.