D-I-TASSER A0A3B3IRV3

D-I-TASSER results for A0A3B3IRV3

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

Summary of the Protein

Uniprot ID: A0A3B3IRV3
Protein Name: Malignant T-cell-amplified sequence
Gene Name: MCTS2P

Input Sequence in FASTA format

>A0A3B3IRV3 (181 residues)
MFKKFDEKESVSNCIQLKTSVIKGIKSQLVEQFPGIEPWLNQIMPKKDPVKIVRCHEHTE
ILTVSGELLFFRQRKGPFCPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPG
AKLYPAAVDTIVAVTAEGKQHALCVGVMKMSAEDIEKVNKGIGIENIHYLNDGLWHMKTY
K

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	A0A3B3IRV3-D1	1-91	91		MFKKFDEKESVSNCIQLKTSVIKGIKSQLVEQFPGIEPWLNQIMPKKDPVKIVRCHEHTEILTVSGELLFFRQRKGPFCPTLRLLHKYPFI
2	A0A3B3IRV3-D2	92-181	90		LPHQQVDKGAIKFVLSGANIMCPGLTSPGAKLYPAAVDTIVAVTAEGKQHALCVGVMKMSAEDIEKVNKGIGIENIHYLNDGLWHMKTYK

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.85

(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	3r90A	0.91	2.10	0.928	0.995	model1_3r90A.pdb.gz
2	5oa30	0.90	1.95	0.226	0.972	model1_5oa30.pdb.gz
3	1zs7A	0.74	3.13	0.205	0.923	model1_1zs7A.pdb.gz
4	3d79A	0.73	2.54	0.262	0.884	model1_3d79A.pdb.gz
5	1q7hA	0.64	2.85	0.174	0.796	model1_1q7hA.pdb.gz
6	6em5l	0.64	3.20	0.109	0.812	model1_6em5l.pdb.gz
7	1sqwA	0.64	3.32	0.132	0.823	model1_1sqwA.pdb.gz
8	1it7A2	0.63	2.83	0.136	0.779	model1_1it7A2.pdb.gz
9	2rfkA	0.50	3.38	0.143	0.630	model1_2rfkA.pdb.gz
10	3u28A	0.48	3.91	0.103	0.608	model1_3u28A.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:1901363	1.00	heterocyclic compound binding
GO:0097159	1.00	organic cyclic compound binding
GO:0005525	0.97	GTP binding
GO:0003676	0.85	nucleic acid binding
GO:0003723	0.84	RNA binding
GO:0003743	0.75	translation initiation factor activity
GO:0016866	0.63	intramolecular transferase 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	0.91	cellular process
GO:0044237	0.83	cellular metabolic process
GO:0044763	0.74	single-organism cellular process
GO:0006413	0.69	translational initiation
GO:0002183	0.61	cytoplasmic translational initiation
GO:0071840	0.60	cellular component organization or biogenesis
GO:0045184	0.54	establishment of protein localization
GO:0071816	0.51	tail-anchored membrane protein insertion into ER membrane
GO:0043933	0.51	macromolecular complex subunit organization
GO:0032790	0.50	ribosome disassembly
GO:0002192	0.50	IRES-dependent translational initiation
GO:0001731	0.50	formation of translation preinitiation 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 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:0044444	0.99	cytoplasmic part
GO:0032991	0.81	macromolecular complex
GO:0044446	0.76	intracellular organelle part
GO:0005737	0.76	cytoplasm
GO:0030529	0.63	intracellular ribonucleoprotein complex
GO:0005829	0.61	cytosol

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	1ze1A	0.481	4.06	0.125	0.646	4.2.1.70	NA
2	0.060	1dleA	0.425	5.05	0.041	0.724	3.4.21.47	NA
3	0.060	1bdaA	0.425	5.28	0.065	0.724	3.4.21.68	NA
4	0.060	2ok5A	0.436	5.03	0.061	0.729	3.4.21.47	NA
5	0.060	1f1sA	0.425	5.28	0.046	0.729	4.2.2.1	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	0.04	3mqkA	0.512	3.46	0.130	0.641	1.06	RQA	complex1.pdb.gz	98,100,101,104,107,108,109,110,111,112,114,115,160,161,162
2	0.02	2j5tD	0.551	4.21	0.093	0.762	0.95	GLU	complex2.pdb.gz	98,100,101,104,108
3	0.02	3hjyA	0.500	3.60	0.118	0.646	0.64	RQA	complex3.pdb.gz	106,107,108
4	0.02	2j5tA	0.553	4.16	0.093	0.762	0.55	GLU	complex4.pdb.gz	132,134,164
5	0.02	1ze2B	0.412	4.73	0.101	0.635	0.76	RQA	complex5.pdb.gz	107,108,166,167,168

	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.