Predicted function of 1fx7A_1

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	2x4hA1	0.89	0.79	0.274	0.939	model1_2x4hA1.pdb.gz
2	6jbxA	0.86	1.05	0.177	0.939	model1_6jbxA.pdb.gz
3	2h09A	0.86	1.56	0.273	0.970	model1_2h09A.pdb.gz
4	2f5cA	0.86	1.13	0.306	0.939	model1_2f5cA.pdb.gz
5	3ecoA	0.85	1.43	0.234	0.970	model1_3ecoA.pdb.gz
6	4o6jA	0.85	1.31	0.190	0.924	model1_4o6jA.pdb.gz
7	5eriA	0.85	1.37	0.145	0.939	model1_5eriA.pdb.gz
8	1lj9A	0.85	1.37	0.210	0.939	model1_1lj9A.pdb.gz
9	3oopA	0.84	1.49	0.226	0.939	model1_3oopA.pdb.gz
10	2fxaB	0.80	1.40	0.250	0.909	model1_2fxaB.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	0.85	transcription factor activity, sequence-specific DNA binding
GO:1901363	0.84	heterocyclic compound binding
GO:0097159	0.84	organic cyclic compound binding
GO:0003677	0.80	DNA binding
GO:0046872	0.73	metal ion binding
GO:0046914	0.71	transition metal ion binding
GO:0046983	0.68	protein dimerization activity
GO:0000975	0.64	regulatory region DNA 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:0009987 0.84 cellular process

GO:0008152 0.78 metabolic process

GO:0071704 0.71 organic substance metabolic process

GO:0044237 0.71 cellular metabolic process

GO:0044699 0.61 single-organism process

GO:0009058 0.61 biosynthetic process

GO:0044238 0.60 primary metabolic process

GO:0006807 0.60 nitrogen compound metabolic process

GO:0044249 0.59 cellular biosynthetic process

GO:1901576 0.56 organic substance biosynthetic process

GO:0044763 0.54 single-organism 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:0044424 1.00 intracellular part

GO:0005737 0.89 cytoplasm

GO:0016020 0.72 membrane

GO:0005886 0.62 plasma 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	0.157	1leaA	0.812	1.70	0.242	1.000	3.4.21.88	NA
2	0.060	1ak4A	0.477	4.14	0.092	0.894	5.2.1.8	NA
3	0.060	3k2cC	0.486	3.76	0.109	0.879	5.2.1.8	NA
4	0.060	3f9kI	0.483	3.07	0.100	0.758	2.7.7.49	NA
5	0.060	1ox7B	0.501	3.38	0.083	0.818	3.5.4.1	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

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	0.05	3q5fA	0.831	1.51	0.238	0.955	0.50	QNA	complex1.pdb.gz	38,39,42
	2	0.05	1dpuA	0.800	1.84	0.185	0.985	1.13	III	complex2.pdb.gz	49,50,51,52,53,55,56,57,59,65

	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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