D-I-TASSER Q2M2D7

D-I-TASSER results for Q2M2D7

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

Summary of the Protein

Uniprot ID: Q2M2D7
Protein Name: TBC1 domain family member 28
Gene Name: TBC1D28

Input Sequence in FASTA format

>Q2M2D7 (210 residues)
MEMDEDPDNLPAQGQGNIIITKYEQGHRAGAAVDLGHEQVDVRKYTNNLGIVHEMELPRV
SALEVKQRRKESKRTNKWQKMLADWTKYRSTKKLSQRVCKVIPLAVRGRALSLLLDIDKI
KSQNPGKYKVMKEKGKRSSRIIHCIQLDVSHTLQKHMMFIQRFGVKQQELCDILVAYSAY
NPVSIPGQRYSWYLCPYSQAWVSLGGVATS

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	Q2M2D7-D1	1-210	210		MEMDEDPDNLPAQGQGNIIITKYEQGHRAGAAVDLGHEQVDVRKYTNNLGIVHEMELPRVSALEVKQRRKESKRTNKWQKMLADWTKYRSTKKLSQRVCKVIPLAVRGRALSLLLDIDKIKSQNPGKYKVMKEKGKRSSRIIHCIQLDVSHTLQKHMMFIQRFGVKQQELCDILVAYSAYNPVSIPGQRYSWYLCPYSQAWVSLGGVATS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6318

(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	4p17A	0.71	1.33	0.178	0.748	model1_4p17A.pdb.gz
2	3qyeA	0.60	2.86	0.203	0.686	model1_3qyeA.pdb.gz
3	5tubA1	0.59	2.53	0.153	0.671	model1_5tubA1.pdb.gz
4	2g77A	0.57	2.46	0.176	0.662	model1_2g77A.pdb.gz
5	4hl4A	0.55	2.67	0.169	0.648	model1_4hl4A.pdb.gz
6	3hzjC	0.55	2.38	0.225	0.614	model1_3hzjC.pdb.gz
7	2qfzA1	0.54	2.45	0.168	0.624	model1_2qfzA1.pdb.gz
8	2qq8A	0.54	2.96	0.185	0.638	model1_2qq8A.pdb.gz
9	3qwlA	0.45	3.04	0.112	0.548	model1_3qwlA.pdb.gz
10	1hg4A	0.31	5.43	0.019	0.500	model1_1hg4A.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:0005096	0.99	GTPase activator activity
GO:0017137	0.96	Rab GTPase binding
GO:0097159	0.73	organic cyclic compound binding
GO:1901363	0.71	heterocyclic compound binding
GO:0036094	0.69	small molecule binding
GO:0032555	0.68	purine ribonucleotide binding
GO:0032550	0.68	purine ribonucleoside binding
GO:0035639	0.62	purine ribonucleoside triphosphate binding
GO:0032561	0.52	guanyl ribonucleotide 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:0065007	1.00	biological regulation
GO:0050794	0.99	regulation of cellular process
GO:0043087	0.98	regulation of GTPase activity
GO:0051128	0.97	regulation of cellular component organization
GO:0060627	0.96	regulation of vesicle-mediated transport
GO:0033043	0.96	regulation of organelle organization
GO:0015031	0.96	protein transport
GO:0090630	0.95	activation of GTPase activity
GO:0031338	0.95	regulation of vesicle fusion
GO:0006886	0.95	intracellular protein transport

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:0044464	1.00	cell part
GO:0012505	0.95	endomembrane system
GO:0005622	0.90	intracellular
GO:0044424	0.75	intracellular part
GO:0044444	0.58	cytoplasmic part

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	2h12E	0.397	6.50	0.055	0.795	2.3.3.1	48,110
2	0.060	2ifcC	0.407	6.40	0.049	0.781	2.3.3.1	NA
3	0.060	1ayxA	0.418	5.55	0.051	0.719	3.2.1.3	133
4	0.060	1o7xC	0.391	6.18	0.050	0.729	2.3.3.1	NA
5	0.060	3hwkE	0.396	6.14	0.070	0.729	2.3.3.1	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	0.07	3cscA	0.415	6.44	0.064	0.809	0.16	ACO	complex1.pdb.gz	98,102,106,107,108
2	0.01	1zcmA	0.281	5.86	0.047	0.505	0.29	C1N	complex2.pdb.gz	107,108,194,195
3	0.01	2nqiA	0.285	5.89	0.023	0.509	0.20	NQI	complex3.pdb.gz	107,108,166
4	0.01	1cscA	0.393	5.80	0.010	0.705	0.12	CMC	complex4.pdb.gz	108,199,200,201
5	0.01	3eqaA	0.414	5.57	0.057	0.710	0.18	UUU	complex5.pdb.gz	49,111,197
6	0.01	2ctsA	0.404	5.96	0.020	0.719	0.18	CIT	complex6.pdb.gz	49,107,166
7	0.01	1gahA	0.417	5.65	0.057	0.719	0.19	UUU	complex7.pdb.gz	48,49,74,79,107,108,109
8	0.01	3eqaA	0.414	5.57	0.057	0.710	0.13	GOL	complex8.pdb.gz	48,49,50
9	0.01	2r9eA	0.392	6.14	0.051	0.714	0.13	SDX	complex9.pdb.gz	50,103,107,201
10	0.01	2r26A	0.407	6.32	0.041	0.748	0.16	CMC	complex10.pdb.gz	47,48,49,74,105,107

	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.