Predicted function of 1fx7A_3

Proteins Structurally Close to the Query Protein

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

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	1bi2A	0.78	1.94	0.214	0.910	model1_1bi2A.pdb.gz
2	1fx7A	0.77	2.28	0.932	0.966	model1_1fx7A.pdb.gz
3	4o6jA	0.72	2.09	0.175	0.876	model1_4o6jA.pdb.gz
4	3hrsA	0.68	2.58	0.138	0.876	model1_3hrsA.pdb.gz
5	1qw1A	0.62	3.19	0.190	0.899	model1_1qw1A.pdb.gz
6	3rfuA3	0.35	4.22	0.107	0.640	model1_3rfuA3.pdb.gz
7	2h09A	0.31	4.14	0.047	0.517	model1_2h09A.pdb.gz
8	2fuaA1	0.31	4.63	0.052	0.629	model1_2fuaA1.pdb.gz
9	4b8xA	0.31	3.77	0.050	0.494	model1_4b8xA.pdb.gz
10	1cn4B	0.31	3.79	0.015	0.528	model1_1cn4B.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:0043167	0.68	ion binding
GO:0046872	0.67	metal ion binding
GO:0046914	0.65	transition metal ion binding
GO:1901363	0.59	heterocyclic compound binding
GO:0097159	0.59	organic cyclic compound binding
GO:0001071	0.52	nucleic acid binding transcription factor activity

Download full result of the above consensus prediction.

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(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:0008152 0.88 metabolic process

GO:0009987 0.87 cellular process

GO:0044237 0.86 cellular metabolic process

GO:0071704 0.84 organic substance metabolic process

GO:0009058 0.82 biosynthetic process

GO:0044249 0.81 cellular biosynthetic process

GO:0006807 0.81 nitrogen compound metabolic process

GO:1901576 0.79 organic substance biosynthetic process

GO:0044238 0.79 primary metabolic process

GO:0034641 0.75 cellular nitrogen compound metabolic process

GO:1901360 0.74 organic cyclic compound metabolic process

GO:0046483 0.74 heterocycle metabolic process

GO:0006725 0.74 cellular aromatic compound metabolic process

GO:1901362 0.72 organic cyclic compound biosynthetic process

GO:0044271 0.72 cellular nitrogen compound biosynthetic process

GO:0019438 0.72 aromatic compound biosynthetic process

GO:0018130 0.71 heterocycle biosynthetic process

GO:0044260 0.70 cellular macromolecule metabolic process

GO:0006139 0.70 nucleobase-containing compound metabolic process

GO:0090304 0.69 nucleic acid metabolic process

GO:0009059 0.69 macromolecule biosynthetic process

GO:0034645 0.67 cellular macromolecule biosynthetic process

GO:0032774 0.67 RNA biosynthetic process

GO:0006351 0.65 transcription, DNA-templated

GO:0080090 0.53 regulation of primary metabolic process

GO:0031323 0.53 regulation of cellular metabolic process

GO:2000112 0.52 regulation of cellular macromolecule biosynthetic process

GO:1903506 0.52 regulation of nucleic acid-templated transcription

GO:0010468 0.52 regulation of gene expression

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 0.95 cell part

GO:0044424 0.86 intracellular part

GO:0005737 0.71 cytoplasm

GO:0016020 0.67 membrane

GO:0005886 0.50 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

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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	1aecA	0.476	3.68	0.101	0.753	3.4.22.14	NA
2	0.060	1icfA	0.309	5.03	0.029	0.674	3.4.22.15	NA
3	0.060	3bc3B	0.309	5.13	0.029	0.697	3.4.22.15	47
4	0.060	2djfB	0.316	4.77	0.043	0.629	3.4.14.1	70
5	0.060	1pjjA	0.467	3.98	0.072	0.809	3.2.2.23	70

	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

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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	0.01	2i0iA	0.315	3.90	0.118	0.494	0.51	III	complex1.pdb.gz	24,25,47,48,69,72

	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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