D-I-TASSER O95727

D-I-TASSER results for O95727

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

Summary of the Protein

Uniprot ID: O95727
Protein Name: Cytotoxic and regulatory T-cell molecule
Gene Name: CRTAM

Input Sequence in FASTA format

>O95727 (393 residues)
MWWRVLSLLAWFPLQEASLTNHTETITVEEGQTLTLKCVTSLRKNSSLQWLTPSGFTIFL
NEYPALKNSKYQLLHHSANQLSITVPNVTLQDEGVYKCLHYSDSVSTKEVKVIVLATPFK
PILEASVIRKQNGEEHVVLMCSTMRSKPPPQITWLLGNSMEVSGGTLHEFETDGKKCNTT
STLIIHTYGKNSTVDCIIRHRGLQGRKLVAPFRFEDLVTDEETASDALERNSLSSQDPQQ
PTSTVSVTEDSSTSEIDKEEKEQTTQDPDLTTEANPQYLGLARKKSGILLLTLVSFLIFI
LFIIVQLFIMKLRKAHVIWKKENEVSEHTLESYRSRSNNEETSSEEKNGQSSHPMRCMNY
ITKLYSEAKTKRKENVQHSKLEEKHIQVPESIV

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	O95727-D1	1-115	115		MWWRVLSLLAWFPLQEASLTNHTETITVEEGQTLTLKCVTSLRKNSSLQWLTPSGFTIFLNEYPALKNSKYQLLHHSANQLSITVPNVTLQDEGVYKCLHYSDSVSTKEVKVIVL
2	O95727-D2	116-287	172		ATPFKPILEASVIRKQNGEEHVVLMCSTMRSKPPPQITWLLGNSMEVSGGTLHEFETDGKKCNTTSTLIIHTYGKNSTVDCIIRHRGLQGRKLVAPFRFEDLVTDEETASDALERNSLSSQDPQQPTSTVSVTEDSSTSEIDKEEKEQTTQDPDLTTEANPQYLGLARKKSG
3	O95727-D3	288-393	106		ILLLTLVSFLIFILFIIVQLFIMKLRKAHVIWKKENEVSEHTLESYRSRSNNEETSSEEKNGQSSHPMRCMNYITKLYSEAKTKRKENVQHSKLEEKHIQVPESIV

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	4ofyD	0.54	4.49	0.097	0.679	model1_4ofyD.pdb.gz
2	5zo1A	0.50	3.15	0.190	0.565	model1_5zo1A.pdb.gz
3	6efzA	0.50	3.49	0.139	0.575	model1_6efzA.pdb.gz
4	3alpA	0.50	3.73	0.134	0.583	model1_3alpA.pdb.gz
5	6iaaA	0.49	5.02	0.111	0.644	model1_6iaaA.pdb.gz
6	6efyA	0.48	3.66	0.139	0.570	model1_6efyA.pdb.gz
7	4fomA	0.47	4.03	0.121	0.583	model1_4fomA.pdb.gz
8	6dldA	0.47	3.97	0.148	0.560	model1_6dldA.pdb.gz
9	4of8A	0.47	2.20	0.187	0.504	model1_4of8A.pdb.gz
10	6eg0B	0.46	4.50	0.121	0.590	model1_6eg0B.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:0005102	0.87	receptor binding
GO:0050839	0.86	cell adhesion molecule binding
GO:0004872	0.86	receptor activity
GO:0042802	0.85	identical protein binding
GO:0046983	0.84	protein dimerization activity
GO:0042803	0.83	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:0044699	0.96	single-organism process
GO:0009987	0.92	cellular process
GO:0044763	0.91	single-organism cellular process
GO:0022610	0.87	biological adhesion
GO:0007155	0.86	cell adhesion
GO:0098609	0.84	cell-cell adhesion
GO:0098742	0.83	cell-cell adhesion via plasma-membrane adhesion molecules
GO:0007156	0.82	homophilic cell adhesion via plasma membrane adhesion molecules
GO:0008037	0.80	cell recognition
GO:0007157	0.79	heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules
GO:0065007	0.73	biological regulation
GO:0050789	0.72	regulation of biological process
GO:0048518	0.60	positive regulation of biological process
GO:0048583	0.58	regulation of response to stimulus
GO:0048584	0.55	positive regulation of response to stimulus
GO:0080134	0.53	regulation of response to stress
GO:0002684	0.52	positive regulation of immune system process
GO:0050778	0.51	positive regulation of immune response
GO:0045954	0.50	positive regulation of natural killer cell mediated cytotoxicity

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	0.99	cell part
GO:0044425	0.89	membrane part
GO:0030054	0.87	cell junction
GO:0016021	0.87	integral component of membrane
GO:0044459	0.86	plasma membrane part
GO:0005911	0.86	cell-cell junction
GO:0005887	0.85	integral component of plasma membrane
GO:0005913	0.84	cell-cell adherens junction
GO:0016020	0.51	membrane

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	2q3zA	0.377	6.63	0.058	0.601	2.3.2.13	NA
2	0.060	3k1dA	0.324	7.13	0.024	0.552	2.4.1.18	NA
3	0.060	1y2mB	0.328	6.41	0.032	0.509	4.3.1.24	NA
4	0.060	2nziA	0.357	3.94	0.114	0.440	2.7.11.1	31
5	0.060	1ej6A	0.340	7.38	0.061	0.598	2.7.7.50	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	2l7uA	0.211	3.16	0.211	0.242	0.60	III	complex1.pdb.gz	51,52,53,95,97,98,99,107,108,109,111,113
2	0.01	2vraB	0.404	2.73	0.133	0.453	0.44	UUU	complex2.pdb.gz	34,35,36,37,112
3	0.01	1a4kB	0.281	5.39	0.084	0.402	0.50	FRA	complex3.pdb.gz	29,32,94
4	0.01	1c5cH	0.263	3.23	0.112	0.298	0.67	TK4	complex4.pdb.gz	31,88,90,91
5	0.01	3agvB	0.253	4.23	0.063	0.308	0.48	UUU	complex5.pdb.gz	31,32,34,85,94
6	0.01	3agvA	0.240	3.80	0.109	0.285	0.42	UUU	complex6.pdb.gz	31,32,34,85
7	0.01	1ncg0	0.175	3.65	0.024	0.209	0.44	III	complex7.pdb.gz	32,33,34,35,36,37,94,95,96,109,110,112
8	0.01	3d6gB	0.243	3.65	0.094	0.285	0.46	X12	complex8.pdb.gz	28,30,94
9	0.01	2gj73	0.252	4.13	0.071	0.303	0.42	III	complex9.pdb.gz	28,29,30,31,32,33,34,84,85,94,202
10	0.01	2if70	0.359	3.46	0.076	0.430	0.42	III	complex10.pdb.gz	48,52,54,55,58,65,66,107

	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.