D-I-TASSER Q96NY9

D-I-TASSER results for Q96NY9

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

Summary of the Protein

Uniprot ID: Q96NY9
Protein Name: Crossover junction endonuclease MUS81
Gene Name: MUS81

Input Sequence in FASTA format

>Q96NY9 (551 residues)
MAAPVRLGRKRPLPACPNPLFVRWLTEWRDEATRSRRRTRFVFQKALRSLRRYPLPLRSG
KEAKILQHFGDGLCRMLDERLQRHRTSGGDHAPDSPSGENSPAPQGRLAEVQDSSMPVPA
QPKAGGSGSYWPARHSGARVILLVLYREHLNPNGHHFLTKEELLQRCAQKSPRVAPGSAR
PWPALRSLLHRNLVLRTHQPARYSLTPEGLELAQKLAESEGLSLLNVGIGPKEPPGEETA
VPGAASAELASEAGVQQQPLELRPGEYRVLLCVDIGETRGGGHRPELLRELQRLHVTHTV
RKLHVGDFVWVAQETNPRDPANPGELVLDHIVERKRLDDLCSSIIDGRFREQKFRLKRCG
LERRVYLVEEHGSVHNLSLPESTLLQAVTNTQVIDGFFVKRTADIKESAAYLALLTRGLQ
RLYQGHTLRSRPWGTPGNPESGAMTSPNPLCSLLTFSDFNAGAIKNKAQSVREVFARQLM
QVRGVSGEKAAALVDRYSTPASLLAAYDACATPKEQETLLSTIKCGRLQRNLGPALSRTL
SQLYCSYGPLT

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 AttentionPotential. 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	Q96NY9-D1	1-238	238		MAAPVRLGRKRPLPACPNPLFVRWLTEWRDEATRSRRRTRFVFQKALRSLRRYPLPLRSGKEAKILQHFGDGLCRMLDERLQRHRTSGGDHAPDSPSGENSPAPQGRLAEVQDSSMPVPAQPKAGGSGSYWPARHSGARVILLVLYREHLNPNGHHFLTKEELLQRCAQKSPRVAPGSARPWPALRSLLHRNLVLRTHQPARYSLTPEGLELAQKLAESEGLSLLNVGIGPKEPPGEE
2	Q96NY9-D2	239-469	231		TAVPGAASAELASEAGVQQQPLELRPGEYRVLLCVDIGETRGGGHRPELLRELQRLHVTHTVRKLHVGDFVWVAQETNPRDPANPGELVLDHIVERKRLDDLCSSIIDGRFREQKFRLKRCGLERRVYLVEEHGSVHNLSLPESTLLQAVTNTQVIDGFFVKRTADIKESAAYLALLTRGLQRLYQGHTLRSRPWGTPGNPESGAMTSPNPLCSLLTFSDFNAGAIKNKAQ
3	Q96NY9-D3	470-551	82		SVREVFARQLMQVRGVSGEKAAALVDRYSTPASLLAAYDACATPKEQETLLSTIKCGRLQRNLGPALSRTLSQLYCSYGPLT

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.74

(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 AttentionPotential, 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	2zivA	0.48	1.88	0.647	0.499	model1_2zivA.pdb.gz
2	2zixA	0.45	2.56	0.941	0.490	model1_2zixA.pdb.gz
3	4bedA	0.39	7.49	0.030	0.613	model1_4bedA.pdb.gz
4	2xt6A	0.38	7.34	0.040	0.597	model1_2xt6A.pdb.gz
5	5cskA	0.38	7.95	0.054	0.632	model1_5cskA.pdb.gz
6	6eqoA	0.38	7.92	0.035	0.630	model1_6eqoA.pdb.gz
7	6lvfB	0.37	7.45	0.053	0.592	model1_6lvfB.pdb.gz
8	5julA	0.36	7.24	0.041	0.570	model1_5julA.pdb.gz
9	6hqvA	0.36	7.35	0.039	0.568	model1_6hqvA.pdb.gz
10	7bdiB	0.36	7.52	0.060	0.577	model1_7bdiB.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	0.71	catalytic activity
GO:0016787	0.68	hydrolase activity
GO:0004518	0.66	nuclease activity
GO:0004520	0.64	endodeoxyribonuclease activity
GO:0016889	0.63	endodeoxyribonuclease activity, producing 3'-phosphomonoesters
GO:1901363	0.52	heterocyclic compound binding
GO:0097159	0.52	organic cyclic compound binding
GO:0048257	0.50	3'-flap endonuclease 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	0.96	cellular process
GO:0071704	0.89	organic substance metabolic process
GO:0044238	0.89	primary metabolic process
GO:0044237	0.89	cellular metabolic process
GO:0044260	0.88	cellular macromolecule metabolic process
GO:0006139	0.88	nucleobase-containing compound metabolic process
GO:0090304	0.87	nucleic acid metabolic process
GO:0006259	0.86	DNA metabolic process
GO:0051716	0.85	cellular response to stimulus
GO:0006281	0.83	DNA repair
GO:0044265	0.65	cellular macromolecule catabolic process
GO:0034655	0.65	nucleobase-containing compound catabolic process
GO:0090305	0.64	nucleic acid phosphodiester bond hydrolysis
GO:0000737	0.63	DNA catabolic process, endonucleolytic
GO:0072429	0.58	response to intra-S DNA damage checkpoint signaling

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:0043229	1.00	intracellular organelle
GO:0043231	0.96	intracellular membrane-bounded organelle
GO:0005634	0.94	nucleus
GO:0044446	0.90	intracellular organelle part
GO:0044428	0.89	nuclear part
GO:0043232	0.84	intracellular non-membrane-bounded organelle
GO:0005730	0.77	nucleolus

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	1z0hB	0.232	7.54	0.047	0.381	3.4.24.69	NA
2	0.060	2rd0A	0.314	7.77	0.036	0.521	2.7.1.153	NA
3	0.060	2ckjA	0.316	7.88	0.049	0.530	1.17.1.4 1.17.3.2	NA
4	0.060	1rs0A	0.240	7.48	0.054	0.390	3.4.21.47	282
5	0.060	1vbgA	0.331	7.40	0.047	0.524	2.7.9.1	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	2uvaG	0.353	7.97	0.030	0.595	0.13	FMN	complex1.pdb.gz	306,309,310,360,361
2	0.01	3cmvD	0.279	7.83	0.042	0.459	0.26	ANP	complex2.pdb.gz	276,280,281,284,285,286,301
3	0.01	2uv8G	0.354	7.84	0.038	0.590	0.18	FMN	complex3.pdb.gz	274,328,329
4	0.01	2np0A	0.328	8.07	0.033	0.566	0.26	III	complex4.pdb.gz	272,274,308,396,397
5	0.01	2y0pB	0.264	7.43	0.037	0.421	0.19	ACO	complex5.pdb.gz	333,353,354,355
6	0.01	1i1eA	0.353	7.86	0.039	0.586	0.34	DM2	complex6.pdb.gz	276,306,307
7	0.01	3cmvE	0.259	8.23	0.028	0.448	0.17	ANP	complex7.pdb.gz	304,307,351,360
8	0.01	3cmtA	0.341	8.15	0.035	0.588	0.17	ALF	complex8.pdb.gz	277,278,281
9	0.01	2vkzG	0.352	7.79	0.040	0.586	0.13	FMN	complex9.pdb.gz	307,333,334
10	0.01	3cmvF	0.257	7.67	0.029	0.423	0.24	ANP	complex10.pdb.gz	274,276,277,278,279

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.