Predicted function of 1fx7A_2

Proteins Structurally Close to the Query Protein

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	2x4hA	0.87	0.50	0.254	0.893	model1_2x4hA.pdb.gz
2	5cviA	0.85	1.35	0.370	0.973	model1_5cviA.pdb.gz
3	3hrsA	0.83	1.59	0.365	0.987	model1_3hrsA.pdb.gz
4	5zr4A	0.83	1.45	0.425	0.973	model1_5zr4A.pdb.gz
5	6o5cA1	0.83	1.58	0.392	0.987	model1_6o5cA1.pdb.gz
6	7b1vA	0.83	1.72	0.824	0.987	model1_7b1vA.pdb.gz
7	1fx7A	0.82	1.60	0.960	0.960	model1_1fx7A.pdb.gz
8	1c0wB	0.80	1.68	0.733	0.960	model1_1c0wB.pdb.gz
9	2f5cA	0.62	1.92	0.162	0.747	model1_2f5cA.pdb.gz
10	2h09A2	0.57	1.71	0.245	0.693	model1_2h09A2.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:0003700	0.92	transcription factor activity, sequence-specific DNA binding
GO:1901363	0.73	heterocyclic compound binding
GO:0097159	0.73	organic cyclic compound binding
GO:0003677	0.67	DNA binding
GO:0043167	0.60	ion binding
GO:0046872	0.59	metal ion binding
GO:0046983	0.57	protein dimerization activity
GO:0046914	0.56	transition metal ion 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:0006355 0.92 regulation of transcription, DNA-templated

GO:2000144 0.81 positive regulation of DNA-templated transcription, initiation

GO:0045892 0.81 negative regulation of transcription, DNA-templated

GO:0008152 0.75 metabolic process

GO:0009987 0.72 cellular process

GO:0044237 0.70 cellular metabolic process

GO:0071704 0.67 organic substance metabolic process

GO:0009058 0.61 biosynthetic process

GO:0044249 0.59 cellular biosynthetic process

GO:0006807 0.59 nitrogen compound metabolic process

GO:1901576 0.56 organic substance biosynthetic process

GO:0044238 0.55 primary metabolic 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:0044424 1.00 intracellular part

GO:0005737 0.83 cytoplasm

GO:0016020 0.52 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	1pv9A	0.489	3.10	0.095	0.707	3.4.13.9	NA
2	0.060	3efsA	0.460	3.68	0.061	0.773	6.3.4.15	NA
3	0.060	3enmD	0.490	3.77	0.028	0.760	2.7.12.2	NA
4	0.060	3daiA	0.484	3.41	0.028	0.733	3.6.1.3	NA
5	0.060	2dylA	0.480	3.16	0.043	0.707	2.7.12.2	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

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	0.03	1on20	0.620	1.89	0.169	0.747	0.90	III	complex1.pdb.gz	19,25,26,30,34,37,38,41,42,43,45,46,49,52,53,55

	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.

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Reference:

Xiaogen Zhou, XXXX, and Yang Zhang. automated multidomain protein structure prediction. to be submitted.

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