D-I-TASSER P16422

D-I-TASSER results for P16422

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

Summary of the Protein

Uniprot ID: P16422
Protein Name: Epithelial cell adhesion molecule
Gene Name: EPCAM

Input Sequence in FASTA format

>P16422 (314 residues)
MAPPQVLAFGLLLAAATATFAAAQEECVCENYKLAVNCFVNNNRQCQCTSVGAQNTVICS
KLAAKCLVMKAEMNGSKLGRRAKPEGALQNNDGLYDPDCDESGLFKAKQCNGTSMCWCVN
TAGVRRTDKDTEITCSERVRTYWIIIELKHKAREKPYDSKSLRTALQKEITTRYQLDPKF
ITSILYENNVITIDLVQNSSQKTQNDVDIADVAYYFEKDVKGESLFHSKKMDLTVNGEQL
DLDPGQTLIYYVDEKAPEFSMQGLKAGVIAVIVVVVIAVVAGIVVLVISRKKRMAKYEKA
EIKEMGEMHRELNA

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	P16422-D1	1-314	314		MAPPQVLAFGLLLAAATATFAAAQEECVCENYKLAVNCFVNNNRQCQCTSVGAQNTVICSKLAAKCLVMKAEMNGSKLGRRAKPEGALQNNDGLYDPDCDESGLFKAKQCNGTSMCWCVNTAGVRRTDKDTEITCSERVRTYWIIIELKHKAREKPYDSKSLRTALQKEITTRYQLDPKFITSILYENNVITIDLVQNSSQKTQNDVDIADVAYYFEKDVKGESLFHSKKMDLTVNGEQLDLDPGQTLIYYVDEKAPEFSMQGLKAGVIAVIVVVVIAVVAGIVVLVISRKKRMAKYEKAEIKEMGEMHRELNA

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5997

(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	4mzvA	0.77	0.39	0.979	0.771	model1_4mzvA.pdb.gz
2	3o6xA	0.45	5.81	0.035	0.707	model1_3o6xA.pdb.gz
3	7cqlA	0.45	5.07	0.053	0.640	model1_7cqlA.pdb.gz
4	3qajA	0.45	5.14	0.047	0.653	model1_3qajA.pdb.gz
5	3ng0A	0.45	5.34	0.052	0.659	model1_3ng0A.pdb.gz
6	1f1hL	0.44	5.21	0.060	0.653	model1_1f1hL.pdb.gz
7	6pewD	0.44	5.44	0.042	0.659	model1_6pewD.pdb.gz
8	3pflA	0.44	6.30	0.052	0.733	model1_3pflA.pdb.gz
9	2y8nA	0.44	6.41	0.049	0.745	model1_2y8nA.pdb.gz
10	4hppA	0.44	5.33	0.058	0.646	model1_4hppA.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:0098641	0.92	cadherin binding involved in cell-cell adhesion

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	0.89	biological regulation
GO:0050789	0.88	regulation of biological process
GO:0050794	0.87	regulation of cellular process
GO:0048518	0.72	positive regulation of biological process
GO:0048522	0.71	positive regulation of cellular process
GO:0007155	0.57	cell adhesion
GO:0098609	0.56	cell-cell adhesion
GO:0044699	0.52	single-organism process
GO:0048519	0.51	negative regulation of biological process
GO:0048523	0.50	negative regulation of cellular process

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:0044459	0.98	plasma membrane part
GO:0016021	0.85	integral component of membrane
GO:0005887	0.84	integral component of plasma membrane
GO:0044424	0.62	intracellular part
GO:0016020	0.61	membrane
GO:0005923	0.54	bicellular tight junction

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	1bgvA	0.411	6.78	0.045	0.729	1.4.1.2	70,100
2	0.060	2pffD	0.419	6.85	0.043	0.742	2.3.1.86	NA
3	0.060	1w6jA	0.384	7.07	0.028	0.694	5.4.99.7	NA
4	0.060	1ygeA	0.352	6.25	0.028	0.573	1.13.11.12	NA
5	0.060	2iukA	0.388	6.59	0.030	0.669	1.13.11.12	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	2f7rA	0.369	6.83	0.058	0.653	0.15	SK3	complex1.pdb.gz	52,72,96,97,98
2	0.01	1mzoA	0.442	6.37	0.051	0.736	0.13	PYR	complex2.pdb.gz	34,35,69
3	0.01	1h17A	0.445	6.55	0.053	0.780	0.28	COA	complex3.pdb.gz	51,52,94
4	0.01	3o6xB	0.449	5.82	0.050	0.698	0.13	ADP	complex4.pdb.gz	103,123,125
5	0.01	2yajA	0.439	6.50	0.055	0.752	0.15	4HP	complex5.pdb.gz	125,211,215,216,218
6	0.01	1h16A	0.442	6.46	0.047	0.752	0.22	COA	complex6.pdb.gz	53,54,70,71,74,75
7	0.01	1f1hA	0.442	5.25	0.065	0.646	0.16	ADP	complex7.pdb.gz	48,51,65
8	0.01	1h18B	0.422	6.71	0.042	0.736	0.21	PYR	complex8.pdb.gz	34,70,75
9	0.01	1h78A	0.402	6.24	0.034	0.662	0.37	DCP	complex9.pdb.gz	71,72,73,74,77
10	0.01	1fpyA	0.445	5.23	0.060	0.653	0.16	PPQ	complex10.pdb.gz	93,123,125,127

	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.