D-I-TASSER Q2VYF4

D-I-TASSER results for Q2VYF4

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

Summary of the Protein

Uniprot ID: Q2VYF4
Protein Name: LETM1 domain-containing protein LETM2, mitochondrial
Gene Name: LETM2

Input Sequence in FASTA format

>Q2VYF4 (491 residues)
MAFYSYNSVLAIARTRFPSHFVHPTCSSYSPSCAFLHLPDSHLNKTCMKNYESKKYSDPS
QPGNTVLHPGTRLIQKLHTSTCWLQEVPGKPQLEQATKHPQVTSPQATKETGMEIKEGKQ
SYRQKIMDELKYYYNGFYLLWIDAKVAARMVWRLLHGQVLTRRERRRLLRTCVDFFRLVP
FMVFLIVPFMEFLLPVFLKLFPEMLPSTFESESKKEEKQKKKMAVKLELAKFLQETMTEM
ARRNRAKMGDASTQLSSYVKQVQTGHKPSTKEIVRFSKLFEDQLALEHLDRPQLVALCKL
LELQTFGTNNLLRFQLLMKLKSIKADDEIIAKEGVTALSVSELQAACRARGMRSLGLTEE
QLRQQLTEWQDLHLKENVPPSLLLLSRTFYLIDVKPKPIEIPLSGEAPKTDILVELPTFT
ESKENMVDLAPQLKGTKDEDFIQPPPVTSSPITPSTPISLPKGPITSSEEPTLQAKSQMT
AQNSKASSKGA

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	Q2VYF4-D1	1-491	491		MAFYSYNSVLAIARTRFPSHFVHPTCSSYSPSCAFLHLPDSHLNKTCMKNYESKKYSDPSQPGNTVLHPGTRLIQKLHTSTCWLQEVPGKPQLEQATKHPQVTSPQATKETGMEIKEGKQSYRQKIMDELKYYYNGFYLLWIDAKVAARMVWRLLHGQVLTRRERRRLLRTCVDFFRLVPFMVFLIVPFMEFLLPVFLKLFPEMLPSTFESESKKEEKQKKKMAVKLELAKFLQETMTEMARRNRAKMGDASTQLSSYVKQVQTGHKPSTKEIVRFSKLFEDQLALEHLDRPQLVALCKLLELQTFGTNNLLRFQLLMKLKSIKADDEIIAKEGVTALSVSELQAACRARGMRSLGLTEEQLRQQLTEWQDLHLKENVPPSLLLLSRTFYLIDVKPKPIEIPLSGEAPKTDILVELPTFTESKENMVDLAPQLKGTKDEDFIQPPPVTSSPITPSTPISLPKGPITSSEEPTLQAKSQMTAQNSKASSKGA

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.575

(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	6tdvA	0.42	4.73	0.150	0.544	model1_6tdvA.pdb.gz
2	8ap7E	0.41	5.10	0.080	0.523	model1_8ap7E.pdb.gz
3	7k10A	0.36	7.11	0.068	0.583	model1_7k10A.pdb.gz
4	6emkA	0.36	7.25	0.022	0.601	model1_6emkA.pdb.gz
5	5h64A	0.36	6.98	0.036	0.576	model1_5h64A.pdb.gz
6	7pw4A	0.36	7.33	0.054	0.593	model1_7pw4A.pdb.gz
7	6bcuA	0.36	7.26	0.056	0.587	model1_6bcuA.pdb.gz
8	5yz0A	0.36	6.78	0.049	0.560	model1_5yz0A.pdb.gz
9	5fvmA	0.35	7.35	0.041	0.585	model1_5fvmA.pdb.gz
10	6jxaA	0.34	6.92	0.044	0.540	model1_6jxaA.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:0005509	0.46	calcium ion binding
GO:0005432	0.40	calcium:sodium antiporter activity
GO:0003824	0.39	catalytic activity
GO:0052813	0.38	phosphatidylinositol bisphosphate kinase activity
GO:0052742	0.38	phosphatidylinositol kinase activity
GO:0035639	0.38	purine ribonucleoside triphosphate binding
GO:0035004	0.38	phosphatidylinositol 3-kinase activity
GO:0032559	0.38	adenyl ribonucleotide binding
GO:0032550	0.38	purine ribonucleoside binding
GO:0016307	0.38	phosphatidylinositol phosphate 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	0.81	cellular process
GO:0044763	0.80	single-organism cellular process
GO:1902589	0.75	single-organism organelle organization
GO:0007005	0.74	mitochondrion organization
GO:0007006	0.54	mitochondrial membrane organization
GO:0006810	0.54	transport

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:0043231	1.00	intracellular membrane-bounded organelle
GO:0016020	1.00	membrane
GO:0005634	0.98	nucleus
GO:0044444	0.95	cytoplasmic part
GO:0044425	0.84	membrane part
GO:0005942	0.82	phosphatidylinositol 3-kinase complex
GO:0044446	0.70	intracellular organelle part
GO:0031090	0.65	organelle membrane
GO:0005739	0.63	mitochondrion
GO:0031966	0.57	mitochondrial membrane
GO:0005886	0.52	plasma 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	0.060	2uv8G	0.260	7.72	0.034	0.434	2.3.1.86	NA
2	0.060	2fxhA	0.303	7.54	0.050	0.501	1.11.1.7 1.11.1.6	NA
3	0.060	1ffuB	0.277	7.58	0.053	0.464	1.2.99.2	NA
4	0.060	2vdcA	0.307	7.97	0.041	0.536	1.4.1.13	NA
5	0.060	1rs0A	0.248	7.45	0.057	0.413	3.4.21.47	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	0.01	1zw3A	0.184	5.96	0.063	0.265	0.23	III	complex1.pdb.gz	139,145,146,149,150,153,156
2	0.01	1ea0B	0.310	8.00	0.032	0.546	0.12	FMN	complex2.pdb.gz	170,346,347
3	0.01	1ofdA	0.311	8.13	0.037	0.562	0.27	F3S	complex3.pdb.gz	170,173,174,207
4	0.01	1xwjA	0.189	6.18	0.038	0.275	0.20	III	complex4.pdb.gz	136,139,140,144,147,148,150,151,154,183,185
5	0.01	2gwwA	0.179	6.27	0.038	0.267	0.36	III	complex5.pdb.gz	76,138,141,142,145,148,149,152,156
6	0.01	2hsqA	0.183	6.08	0.048	0.265	0.24	III	complex6.pdb.gz	77,136,139,140,146,147,150,153
7	0.01	1rkcA	0.184	6.04	0.051	0.269	0.22	III	complex7.pdb.gz	129,136,139,140,150,157
8	0.01	1rke0	0.188	6.30	0.043	0.277	0.18	III	complex8.pdb.gz	136,140,143,146,147,150,151,154,159
9	0.01	1ofdB	0.313	8.01	0.039	0.560	0.23	F3S	complex9.pdb.gz	139,141,142,144
10	0.01	3s90A	0.160	5.34	0.040	0.216	0.25	III	complex10.pdb.gz	78,81,139,142,143,146,149,150,153,156,171

	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.