D-I-TASSER O43502

D-I-TASSER results for O43502

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

Summary of the Protein

Uniprot ID: O43502
Protein Name: DNA repair protein RAD51 homolog 3
Gene Name: RAD51C

Input Sequence in FASTA format

>O43502 (376 residues)
MRGKTFRFEMQRDLVSFPLSPAVRVKLVSAGFQTAEELLEVKPSELSKEVGISKAEALET
LQIIRRECLTNKPRYAGTSESHKKCTALELLEQEHTQGFIITFCSALDDILGGGVPLMKT
TEICGAPGVGKTQLCMQLAVDVQIPECFGGVAGEAVFIDTEGSFMVDRVVDLATACIQHL
QLIAEKHKGEEHRKALEDFTLDNILSHIYYFRCRDYTELLAQVYLLPDFLSEHSKVRLVI
VDGIAFPFRHDLDDLSLRTRLLNGLAQQMISLANNHRLAVILTNQMTTKIDRNQALLVPA
LGESWGHAATIRLIFHWDRKQRLATLYKSPSQKECTVLFQIKPQGFRDTVVTSACSLQTE
GSLSTRKRSRDPEEEL

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	O43502-D1	1-376	376		MRGKTFRFEMQRDLVSFPLSPAVRVKLVSAGFQTAEELLEVKPSELSKEVGISKAEALETLQIIRRECLTNKPRYAGTSESHKKCTALELLEQEHTQGFIITFCSALDDILGGGVPLMKTTEICGAPGVGKTQLCMQLAVDVQIPECFGGVAGEAVFIDTEGSFMVDRVVDLATACIQHLQLIAEKHKGEEHRKALEDFTLDNILSHIYYFRCRDYTELLAQVYLLPDFLSEHSKVRLVIVDGIAFPFRHDLDDLSLRTRLLNGLAQQMISLANNHRLAVILTNQMTTKIDRNQALLVPALGESWGHAATIRLIFHWDRKQRLATLYKSPSQKECTVLFQIKPQGFRDTVVTSACSLQTEGSLSTRKRSRDPEEEL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.7353

(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	7c9aA	0.76	2.15	0.293	0.817	model1_7c9aA.pdb.gz
2	1xu4A	0.76	1.75	0.299	0.800	model1_1xu4A.pdb.gz
3	1szpA	0.73	2.06	0.313	0.782	model1_1szpA.pdb.gz
4	1pznA	0.64	3.18	0.277	0.742	model1_1pznA.pdb.gz
5	4nmnA	0.59	4.16	0.112	0.718	model1_4nmnA.pdb.gz
6	2q6tA	0.59	3.95	0.132	0.718	model1_2q6tA.pdb.gz
7	3cmuA	0.59	3.98	0.148	0.697	model1_3cmuA.pdb.gz
8	4zc0A	0.58	3.98	0.127	0.705	model1_4zc0A.pdb.gz
9	2zjbA	0.58	2.20	0.295	0.622	model1_2zjbA.pdb.gz
10	2zucB	0.57	2.01	0.263	0.604	model1_2zucB.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:0003676	1.00	nucleic acid binding
GO:0016887	0.99	ATPase activity
GO:0003697	0.99	single-stranded DNA binding
GO:0003690	0.99	double-stranded DNA binding
GO:0000150	0.98	recombinase activity
GO:0008094	0.95	DNA-dependent ATPase activity
GO:0004520	0.93	endodeoxyribonuclease activity
GO:0000400	0.93	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:0090304	1.00	nucleic acid metabolic process
GO:0050896	1.00	response to stimulus
GO:0044260	1.00	cellular macromolecule metabolic process
GO:0016043	0.99	cellular component organization
GO:0006310	0.99	DNA recombination
GO:0022607	0.97	cellular component assembly
GO:0009314	0.96	response to radiation
GO:0000730	0.96	DNA recombinase assembly
GO:0042148	0.95	strand invasion
GO:0022402	0.95	cell cycle process
GO:0010212	0.95	response to ionizing radiation
GO:0006312	0.95	mitotic recombination
GO:1903046	0.94	meiotic cell cycle process
GO:0007131	0.91	reciprocal meiotic recombination
GO:0006996	0.69	organelle organization
GO:0051276	0.66	chromosome organization
GO:0070192	0.62	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:0044428	1.00	nuclear part
GO:0043226	0.81	organelle
GO:0043229	0.80	intracellular organelle
GO:0043232	0.69	intracellular non-membrane-bounded organelle
GO:0005654	0.68	nucleoplasm
GO:0005694	0.66	chromosome
GO:0000228	0.65	nuclear chromosome
GO:0000794	0.64	condensed nuclear chromosome

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	0.191	2zrpA	0.508	3.09	0.183	0.569	3.4.99.37	130,132,161,245,284
2	0.060	2f43B	0.509	4.49	0.094	0.644	3.6.3.14	258
3	0.060	1s46A	0.424	6.82	0.026	0.710	2.4.1.4	99,109,112
4	0.060	2g25A	0.425	6.09	0.028	0.644	1.2.4.1	NA
5	0.060	1skyB	0.510	4.44	0.091	0.641	3.6.3.14	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	0.67	2i1qA	0.754	1.51	0.298	0.785	1.25	ANP	complex1.pdb.gz	127,128,129,130,131,132,133,161,168,171,341,342,343
2	0.17	1n0wA	0.525	1.94	0.321	0.556	1.56	MG	complex2.pdb.gz	99,111,114
3	0.03	3k0cB	0.566	4.36	0.099	0.700	0.98	MG	complex3.pdb.gz	132,242,283

	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.