D-I-TASSER Q9UI95

D-I-TASSER results for Q9UI95

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Summary of the Protein

Uniprot ID: Q9UI95
Protein Name: Mitotic spindle assembly checkpoint protein MAD2B
Gene Name: MAD2L2

Input Sequence in FASTA format

>Q9UI95 (211 residues)
MTTLTRQDLNFGQVVADVLCEFLEVAVHLILYVREVYPVGIFQKRKKYNVPVQMSCHPEL
NQYIQDTLHCVKPLLEKNDVEKVVVVILDKEHRPVEKFVFEITQPPLLSISSDSLLSHVE
QLLRAFILKISVCDAVLDHNPPGCTFTVLVHTREAATRNMEKIQVIKDFPWILADEQDVH
MHDPRLIPLKTMTSDILKMQLYVEERAHKGS

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	Q9UI95-D1	1-211	211		MTTLTRQDLNFGQVVADVLCEFLEVAVHLILYVREVYPVGIFQKRKKYNVPVQMSCHPELNQYIQDTLHCVKPLLEKNDVEKVVVVILDKEHRPVEKFVFEITQPPLLSISSDSLLSHVEQLLRAFILKISVCDAVLDHNPPGCTFTVLVHTREAATRNMEKIQVIKDFPWILADEQDVHMHDPRLIPLKTMTSDILKMQLYVEERAHKGS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.832

(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	3abeC	0.90	1.09	0.985	0.929	model1_3abeC.pdb.gz
2	2v64A	0.81	2.13	0.211	0.900	model1_2v64A.pdb.gz
3	4aezB	0.79	1.67	0.229	0.848	model1_4aezB.pdb.gz
4	4tzlA	0.74	2.91	0.085	0.896	model1_4tzlA.pdb.gz
5	4trkA	0.74	2.98	0.127	0.886	model1_4trkA.pdb.gz
6	8j69A	0.72	2.94	0.129	0.886	model1_8j69A.pdb.gz
7	6v8pD	0.64	1.98	0.238	0.716	model1_6v8pD.pdb.gz
8	5c50B	0.63	3.32	0.115	0.782	model1_5c50B.pdb.gz
9	4yk8B	0.63	3.41	0.065	0.791	model1_4yk8B.pdb.gz
10	4wzgA	0.58	3.28	0.111	0.706	model1_4wzgA.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:0019899	0.56	enzyme binding
GO:0019901	0.55	protein kinase binding
GO:0008432	0.54	JUN kinase 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:0009987	0.98	cellular process
GO:0050794	0.97	regulation of cellular process
GO:0048523	0.93	negative regulation of cellular process
GO:0050896	0.86	response to stimulus
GO:0006950	0.85	response to stress
GO:0080090	0.83	regulation of primary metabolic process
GO:0060255	0.83	regulation of macromolecule metabolic process
GO:0050790	0.83	regulation of catalytic activity
GO:0048518	0.83	positive regulation of biological process
GO:0031323	0.83	regulation of cellular metabolic process
GO:0048522	0.82	positive regulation of cellular process
GO:0033554	0.82	cellular response to stress
GO:0032268	0.82	regulation of cellular protein metabolic process
GO:1904666	0.81	regulation of ubiquitin protein ligase activity
GO:0006974	0.81	cellular response to DNA damage stimulus
GO:0042176	0.80	regulation of protein catabolic process
GO:0031325	0.80	positive regulation of cellular metabolic process
GO:0031324	0.80	negative regulation of cellular metabolic process
GO:0010604	0.80	positive regulation of macromolecule metabolic process
GO:1904667	0.79	negative regulation of ubiquitin protein ligase activity
GO:0042177	0.79	negative regulation of protein catabolic process
GO:0031401	0.79	positive regulation of protein modification process
GO:0008152	0.78	metabolic process
GO:0071704	0.77	organic substance metabolic process
GO:0044238	0.77	primary metabolic process
GO:0045893	0.76	positive regulation of transcription, DNA-templated
GO:0044260	0.76	cellular macromolecule metabolic process
GO:0007165	0.76	signal transduction
GO:0001934	0.76	positive regulation of protein phosphorylation
GO:0042772	0.75	DNA damage response, signal transduction resulting in transcription
GO:0033138	0.75	positive regulation of peptidyl-serine phosphorylation
GO:0051128	0.74	regulation of cellular component organization
GO:0090304	0.66	nucleic acid metabolic process
GO:0006259	0.64	DNA metabolic process
GO:0006281	0.61	DNA repair
GO:0006302	0.58	double-strand break repair
GO:0001558	0.58	regulation of cell growth

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:0044422	0.99	organelle part
GO:0044446	0.98	intracellular organelle part
GO:0043229	0.98	intracellular organelle
GO:0043234	0.97	protein complex
GO:0043232	0.96	intracellular non-membrane-bounded organelle
GO:0044428	0.94	nuclear part
GO:0044430	0.90	cytoskeletal part
GO:0005634	0.90	nucleus
GO:0005819	0.82	spindle
GO:1990234	0.80	transferase complex
GO:0005680	0.79	anaphase-promoting complex
GO:0042575	0.77	DNA polymerase complex
GO:0016035	0.76	zeta DNA polymerase complex

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	3ee4A	0.404	5.53	0.051	0.682	1.17.4.1	NA
2	0.060	3fwnA	0.396	5.75	0.030	0.697	1.1.1.44	NA
3	0.060	1ampA	0.413	5.91	0.036	0.735	3.4.11.10	NA
4	0.060	1ca1A	0.387	5.55	0.045	0.640	3.1.4.3	NA
5	0.060	3b8cA	0.420	5.25	0.060	0.678	3.6.3.6	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:

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
	1	0.50	3abeC	0.902	1.09	0.985	0.929	1.95	III	complex1.pdb.gz	35,36,37,40,41,57,60,63,143,144,146,148,149,150,151,152,154,163,169,170,171,172,174,178,179

	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.