D-I-TASSER Q96B01

D-I-TASSER results for Q96B01

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

Summary of the Protein

Uniprot ID: Q96B01
Protein Name: RAD51-associated protein 1
Gene Name: RAD51AP1

Input Sequence in FASTA format

>Q96B01 (352 residues)
MVRPVRHKKPVNYSQFDHSDSDDDFVSATVPLNKKSRTAPKELKQDKPKPNLNNLRKEEI
PVQEKTPKKRLPEGTFSIPASAVPCTKMALDDKLYQRDLEVALALSVKELPTVTTNVQNS
QDKSIEKHGSSKIETMNKSPHISNCSVASDYLDLDKITVEDDVGGVQGKRKAASKAAAQQ
RKILLEGSDGDSANDTEPDFAPGEDSEDDSDFCESEDNDEDFSMRKSKVKEIKKKEVKVK
SPVEKKEKKSKSKCNALVTSVDSAPAAVKSESQSLPKKVSLSSDTTRKPLEIRSPSAESK
KPKWVPPAASGGSRSSSSPLVVVSVKSPNQSLRLGLSRLARVKPLHPNATST

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	Q96B01-D1	1-352	352		MVRPVRHKKPVNYSQFDHSDSDDDFVSATVPLNKKSRTAPKELKQDKPKPNLNNLRKEEIPVQEKTPKKRLPEGTFSIPASAVPCTKMALDDKLYQRDLEVALALSVKELPTVTTNVQNSQDKSIEKHGSSKIETMNKSPHISNCSVASDYLDLDKITVEDDVGGVQGKRKAASKAAAQQRKILLEGSDGDSANDTEPDFAPGEDSEDDSDFCESEDNDEDFSMRKSKVKEIKKKEVKVKSPVEKKEKKSKSKCNALVTSVDSAPAAVKSESQSLPKKVSLSSDTTRKPLEIRSPSAESKKPKWVPPAASGGSRSSSSPLVVVSVKSPNQSLRLGLSRLARVKPLHPNATST

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.2996

(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	7abiE	0.43	6.34	0.042	0.696	model1_7abiE.pdb.gz
2	5mrwA	0.40	6.70	0.048	0.665	model1_5mrwA.pdb.gz
3	5lqwX	0.40	6.50	0.042	0.662	model1_5lqwX.pdb.gz
4	7abir	0.40	6.08	0.032	0.617	model1_7abir.pdb.gz
5	7c72A	0.40	6.06	0.027	0.614	model1_7c72A.pdb.gz
6	4pkcA	0.39	6.85	0.048	0.673	model1_4pkcA.pdb.gz
7	6hq6A	0.39	7.12	0.033	0.699	model1_6hq6A.pdb.gz
8	6vr4A	0.39	7.07	0.064	0.696	model1_6vr4A.pdb.gz
9	1b25A	0.39	6.51	0.042	0.651	model1_1b25A.pdb.gz
10	5mzsA	0.39	6.35	0.061	0.625	model1_5mzsA.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:0003676	1.00	nucleic acid binding
GO:0003723	0.97	RNA binding
GO:0003677	0.97	DNA binding
GO:0003690	0.96	double-stranded DNA binding
GO:0003697	0.93	single-stranded 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:0050794	1.00	regulation of cellular process
GO:0009987	0.99	cellular process
GO:0060255	0.97	regulation of macromolecule metabolic process
GO:0048583	0.97	regulation of response to stimulus
GO:0019219	0.97	regulation of nucleobase-containing compound metabolic process
GO:0006259	0.94	DNA metabolic process
GO:0071479	0.93	cellular response to ionizing radiation
GO:0051052	0.93	regulation of DNA metabolic process
GO:0006310	0.93	DNA recombination
GO:0080134	0.90	regulation of response to stress
GO:0000018	0.90	regulation of DNA recombination
GO:0010569	0.89	regulation of double-strand break repair via homologous recombination
GO:0006950	0.62	response to stress
GO:0006974	0.61	cellular response to DNA damage stimulus
GO:0036297	0.60	interstrand cross-link repair
GO:0000724	0.60	double-strand break repair via homologous recombination
GO:0034645	0.58	cellular macromolecule biosynthetic process
GO:0034654	0.57	nucleobase-containing compound biosynthetic process
GO:0000732	0.56	strand displacement
GO:0000731	0.56	DNA synthesis involved in DNA repair

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:0005634	1.00	nucleus
GO:0044446	0.78	intracellular organelle part
GO:0032991	0.70	macromolecular complex
GO:0044427	0.69	chromosomal part
GO:0044428	0.66	nuclear part
GO:0000785	0.64	chromatin
GO:0044454	0.61	nuclear chromosome part
GO:0000790	0.60	nuclear chromatin
GO:0005654	0.59	nucleoplasm

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	2nyaA	0.361	7.08	0.053	0.639	1.7.99.4	NA
2	0.060	3cmmC	0.376	6.86	0.045	0.642	6.3.2.19	NA
3	0.060	1kv9A	0.367	6.45	0.057	0.599	1.1.99.-	24
4	0.060	2ri9B	0.316	7.01	0.043	0.543	3.2.1.113	NA
5	0.060	1lrwC	0.362	6.35	0.047	0.580	1.1.99.8	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:

No Binding sites was predicted

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues

	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.