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Predicted function of 1fx7A_1



Proteins Structurally Close to the Query Protein

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

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RankPDB
Hit
TM-scoreRMSDaIDENaCov.Download
Alignment
12x4hA10.890.790.2740.939model1_2x4hA1.pdb.gz
26jbxA0.861.050.1770.939model1_6jbxA.pdb.gz
32h09A0.861.560.2730.970model1_2h09A.pdb.gz
42f5cA0.861.130.3060.939model1_2f5cA.pdb.gz
53ecoA0.851.430.2340.970model1_3ecoA.pdb.gz
64o6jA0.851.310.1900.924model1_4o6jA.pdb.gz
75eriA0.851.370.1450.939model1_5eriA.pdb.gz
81lj9A0.851.370.2100.939model1_1lj9A.pdb.gz
93oopA0.841.490.2260.939model1_3oopA.pdb.gz
102fxaB0.801.400.2500.909model1_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)RMSDa is the RMSD between residues that are structurally aligned by TM-align.
(d)IDENa 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


GOsearchresult_final_MF.svg
Molecular Function (MF)
GO termCscoreGOName
GO:00037000.85transcription factor activity, sequence-specific DNA binding
GO:19013630.84heterocyclic compound binding
GO:00971590.84organic cyclic compound binding
GO:00036770.80DNA binding
GO:00468720.73metal ion binding
GO:00469140.71transition metal ion binding
GO:00469830.68protein dimerization activity
GO:00009750.64regulatory region DNA binding

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.
(a)CscoreGO is the confidence score of predicted GO terms. CscoreGO 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 CscoreGO:
[0.4,0.5)[0.5,0.6)[0.6,0.7)[0.7,0.8)[0.8,0.9)[0.9,1.0]

GOsearchresult_final_BP.svg
Biological Process (BP)
GO termCscoreGOName
GO:00063550.92regulation of transcription, DNA-templated
GO:00099870.84cellular process
GO:00081520.78metabolic process
GO:00717040.71organic substance metabolic process
GO:00442370.71cellular metabolic process
GO:00446990.61single-organism process
GO:00090580.61biosynthetic process
GO:00442380.60primary metabolic process
GO:00068070.60nitrogen compound metabolic process
GO:00442490.59cellular biosynthetic process
GO:19015760.56organic substance biosynthetic process
GO:00447630.54single-organism cellular process

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.
(a)CscoreGO is the confidence score of predicted GO terms. CscoreGO 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 CscoreGO:
[0.4,0.5)[0.5,0.6)[0.6,0.7)[0.7,0.8)[0.8,0.9)[0.9,1.0]

GOsearchresult_final_CC.svg
Cellular Component (CC)
GO termCscoreGOName
GO:00444241.00intracellular part
GO:00057370.89cytoplasm
GO:00160200.72membrane
GO:00058860.62plasma membrane

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.
(a)CscoreGO is the confidence score of predicted GO terms. CscoreGO 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 CscoreGO:
[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

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RankCscoreECPDB
Hit
TM-scoreRMSDaIDENaCov.EC NumberPredicted Active Site Residues
10.1571leaA0.8121.700.2421.0003.4.21.88 NA
20.0601ak4A0.4774.140.0920.8945.2.1.8 NA
30.0603k2cC0.4863.760.1090.8795.2.1.8 NA
40.0603f9kI0.4833.070.1000.7582.7.7.49 NA
50.0601ox7B0.5013.380.0830.8183.5.4.1 NA

 Click on the radio buttons to visualize predicted active site residues.
(a)CscoreEC is the confidence score for the Enzyme Commission (EC) number prediction. CscoreEC 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)RMSDa is the RMSD between residues that are structurally aligned by TM-align.
(d)IDENa 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

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to view
RankCscoreLBPDB
Hit
TM-scoreRMSDaIDENaCov.BS-scoreLig. NameDownload
Complex
Predicted binding site residues
10.053q5fA0.8311.510.2380.9550.50QNAcomplex1.pdb.gz38,39,42
20.051dpuA0.8001.840.1850.9851.13IIIcomplex2.pdb.gz49,50,51,52,53,55,56,57,59,65

  Click on the radio buttons to visualize predicted binding site and residues.
(a)CscoreLB is the confidence score of predicted binding site. CscoreLB 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)RMSDa the RMSD between residues that are structurally aligned by TM-align.
(e)IDENa 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.
  • yangzhanglabumich.edu | (734) 647-1549 | 100 Washtenaw Avenue, Ann Arbor, MI 48109-2218