D-I-TASSER Q14565

D-I-TASSER results for Q14565

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

Summary of the Protein

Uniprot ID: Q14565
Protein Name: Meiotic recombination protein DMC1/LIM15 homolog
Gene Name: DMC1

Input Sequence in FASTA format

>Q14565 (340 residues)
MKEDQVVAEEPGFQDEEESLFQDIDLLQKHGINVADIKKLKSVGICTIKGIQMTTRRALC
NVKGLSEAKVDKIKEAANKLIEPGFLTAFEYSEKRKMVFHITTGSQEFDKLLGGGIESMA
ITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRDIADRFNVD
HDAVLDNVLYARAYTSEHQMELLDYVAAKFHEEAGIFKLLIIDSIMALFRVDFSGRGELA
ERQQKLAQMLSRLQKISEEYNVAVFVTNQMTADPGATMTFQADPKKPIGGHILAHASTTR
ISLRKGRGELRIAKIYDSPEMPENEATFAITAGGIGDAKE

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	Q14565-D1	1-340	340		MKEDQVVAEEPGFQDEEESLFQDIDLLQKHGINVADIKKLKSVGICTIKGIQMTTRRALCNVKGLSEAKVDKIKEAANKLIEPGFLTAFEYSEKRKMVFHITTGSQEFDKLLGGGIESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRDIADRFNVDHDAVLDNVLYARAYTSEHQMELLDYVAAKFHEEAGIFKLLIIDSIMALFRVDFSGRGELAERQQKLAQMLSRLQKISEEYNVAVFVTNQMTADPGATMTFQADPKKPIGGHILAHASTTRISLRKGRGELRIAKIYDSPEMPENEATFAITAGGIGDAKE

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.871

(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	7ej6B	0.88	1.79	0.548	0.923	model1_7ej6B.pdb.gz
2	7ejcA	0.87	1.61	0.539	0.912	model1_7ejcA.pdb.gz
3	1xu4A	0.81	2.51	0.368	0.891	model1_1xu4A.pdb.gz
4	1szpA	0.79	2.28	0.488	0.868	model1_1szpA.pdb.gz
5	1pznA	0.74	3.07	0.453	0.850	model1_1pznA.pdb.gz
6	8fazC	0.69	2.69	0.289	0.756	model1_8fazC.pdb.gz
7	8fazD	0.68	2.95	0.184	0.762	model1_8fazD.pdb.gz
8	2zjbA	0.68	1.27	0.967	0.703	model1_2zjbA.pdb.gz
9	8gjaB	0.68	3.03	0.247	0.765	model1_8gjaB.pdb.gz
10	3cmuA	0.66	3.23	0.191	0.759	model1_3cmuA.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:0003824	1.00	catalytic activity
GO:0016887	0.99	ATPase activity
GO:0003697	0.99	single-stranded DNA binding
GO:0003690	0.99	double-stranded DNA binding
GO:0000150	0.97	recombinase activity
GO:0008094	0.91	DNA-dependent ATPase activity
GO:0004520	0.88	endodeoxyribonuclease activity
GO:0000400	0.88	four-way junction DNA 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:0009987	1.00	cellular process
GO:0050896	0.99	response to stimulus
GO:0006259	0.99	DNA metabolic process
GO:0016043	0.98	cellular component organization
GO:0006310	0.98	DNA recombination
GO:0022607	0.97	cellular component assembly
GO:0000730	0.96	DNA recombinase assembly
GO:0010212	0.95	response to ionizing radiation
GO:0042148	0.94	strand invasion
GO:0006312	0.94	mitotic recombination
GO:0022402	0.88	cell cycle process
GO:1903046	0.87	meiotic cell cycle process
GO:0007131	0.85	reciprocal meiotic recombination
GO:0006996	0.71	organelle organization
GO:0051276	0.69	chromosome organization
GO:0070192	0.66	chromosome organization involved in meiotic cell cycle

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:0044446	0.97	intracellular organelle part
GO:0044428	0.96	nuclear part
GO:0043226	0.88	organelle
GO:0043229	0.87	intracellular organelle
GO:0043232	0.75	intracellular non-membrane-bounded organelle
GO:0005654	0.73	nucleoplasm
GO:0000228	0.73	nuclear chromosome
GO:0000794	0.71	condensed nuclear chromosome
GO:0043227	0.51	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	0.226	2zrpA	0.564	2.75	0.229	0.626	3.4.99.37	131,133,162,289,304
2	0.060	1fx0B	0.567	3.94	0.116	0.700	3.6.3.14	NA
3	0.060	3crvA	0.423	5.38	0.055	0.629	3.6.4.12	NA
4	0.060	1r9jB	0.419	5.57	0.031	0.618	2.2.1.1	NA
5	0.060	3i62A	0.435	5.02	0.053	0.618	3.6.4.13	133

	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	0.80	3ew9A	0.804	2.42	0.380	0.882	1.55	ANP	complex1.pdb.gz	128,129,131,132,133,134,169,172,330,331
2	0.31	2zrcA	0.574	2.94	0.213	0.647	1.38	PO4	complex2.pdb.gz	127,129,130,131,132,133
3	0.30	1n0wA	0.589	1.89	0.581	0.618	1.76	MG	complex3.pdb.gz	100,112,115
4	0.17	1cr1A	0.544	3.12	0.147	0.629	0.89	TTP	complex4.pdb.gz	126,127,128,130,131,132,133,134,269,305,330

	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.