D-I-TASSER Q13257

D-I-TASSER results for Q13257

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

Summary of the Protein

Uniprot ID: Q13257
Protein Name: Mitotic spindle assembly checkpoint protein MAD2A
Gene Name: MAD2L1

Input Sequence in FASTA format

>Q13257 (205 residues)
MALQLSREQGITLRGSAEIVAEFFSFGINSILYQRGIYPSETFTRVQKYGLTLLVTTDLE
LIKYLNNVVEQLKDWLYKCSVQKLVVVISNIESGEVLERWQFDIECDKTAKDDSAPREKS
QKAIQDEIRSVIRQITATVTFLPLLEVSCSFDLLIYTDKDLVVPEKWEESGPQFITNSEE
VRLRSFTTTIHKVNSMVAYKIPVND

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	Q13257-D1	1-205	205		MALQLSREQGITLRGSAEIVAEFFSFGINSILYQRGIYPSETFTRVQKYGLTLLVTTDLELIKYLNNVVEQLKDWLYKCSVQKLVVVISNIESGEVLERWQFDIECDKTAKDDSAPREKSQKAIQDEIRSVIRQITATVTFLPLLEVSCSFDLLIYTDKDLVVPEKWEESGPQFITNSEEVRLRSFTTTIHKVNSMVAYKIPVND

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.9042

(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	2v64A	0.99	0.45	0.995	0.995	model1_2v64A.pdb.gz
2	4aezB	0.85	1.31	0.483	0.878	model1_4aezB.pdb.gz
3	3abeC	0.83	1.90	0.216	0.902	model1_3abeC.pdb.gz
4	4tzlA	0.80	2.96	0.109	0.946	model1_4tzlA.pdb.gz
5	4trkA	0.79	2.69	0.113	0.917	model1_4trkA.pdb.gz
6	6v8pD	0.67	1.91	0.191	0.742	model1_6v8pD.pdb.gz
7	5c50B	0.66	3.16	0.133	0.805	model1_5c50B.pdb.gz
8	4yk8B	0.66	3.65	0.117	0.834	model1_4yk8B.pdb.gz
9	4wzgA	0.59	3.38	0.117	0.727	model1_4wzgA.pdb.gz
10	4j2gA	0.57	2.90	0.163	0.688	model1_4j2gA.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:0097159	0.45	organic cyclic compound binding
GO:1901363	0.44	heterocyclic compound binding
GO:0042802	0.39	identical protein binding
GO:0046983	0.36	protein dimerization activity
GO:0042803	0.35	protein homodimerization 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	0.99	cellular process
GO:0065007	0.97	biological regulation
GO:0050789	0.97	regulation of biological process
GO:0050794	0.96	regulation of cellular process
GO:0048523	0.93	negative regulation of cellular process
GO:0051726	0.81	regulation of cell cycle
GO:0022402	0.81	cell cycle process
GO:0051128	0.80	regulation of cellular component organization
GO:1903047	0.78	mitotic cell cycle process
GO:0007346	0.78	regulation of mitotic cell cycle
GO:0000075	0.78	cell cycle checkpoint
GO:0007093	0.75	mitotic cell cycle checkpoint
GO:0010564	0.68	regulation of cell cycle process
GO:0030071	0.67	regulation of mitotic metaphase/anaphase transition
GO:0016043	0.58	cellular component organization
GO:0051129	0.56	negative regulation of cellular component organization
GO:0007094	0.54	mitotic spindle assembly checkpoint
GO:0060255	0.52	regulation of macromolecule metabolic process
GO:0080090	0.51	regulation of primary metabolic process
GO:0050790	0.51	regulation of catalytic activity
GO:0048518	0.51	positive regulation of biological process
GO:0031323	0.51	regulation of cellular metabolic process
GO:0048522	0.50	positive regulation of cellular process
GO:0006996	0.50	organelle organization

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	0.98	intracellular organelle part
GO:0043229	0.97	intracellular organelle
GO:0043234	0.94	protein complex
GO:0043232	0.93	intracellular non-membrane-bounded organelle
GO:0044428	0.82	nuclear part
GO:0044430	0.77	cytoskeletal part
GO:0044427	0.76	chromosomal part
GO:0043227	0.75	membrane-bounded organelle
GO:0000776	0.75	kinetochore
GO:0043231	0.74	intracellular membrane-bounded organelle
GO:0005634	0.73	nucleus

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	3ic1A	0.396	5.70	0.068	0.722	3.5.1.18	NA
2	0.060	1gu6A	0.379	5.93	0.044	0.678	1.7.2.2	NA
3	0.060	2j2fA	0.400	5.63	0.051	0.688	1.14.19.2 1.14.99.6	NA
4	0.060	2fhbA	0.383	4.44	0.069	0.546	3.2.1.41	NA
5	0.060	1tlbA	0.420	5.35	0.037	0.693	1.3.3.3	131

	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	0.82	2v64C	0.988	0.47	0.995	0.995	2.00	III	complex1.pdb.gz	38,58,60,64,67,68,83,85,99,151,152,153,154,155,156,157,159,163,166,167,168,169,170,171,172
	2	0.07	3abeC	0.826	1.90	0.216	0.902	0.99	III	complex2.pdb.gz	36,37,38,41,42,58,61,64,148,149,151,153,154,155,156,157,159

	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.