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I-TASSER results for job id Rv1975

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

 Input Sequence in FASTA format
 Predicted Secondary Structure
 Predicted Solvent Accessibility
 Predicted Normalized B-facotr
 Top 10 threading templates used by I-TASSER
 Top 5 final models predicted by I-TASSER

(For each target, I-TASSER simulations generate a large ensemble of structural conformations, called decoys. To select the final models, I-TASSER uses the SPICKER program to cluster all the decoys based on the pair-wise structure similarity, and reports up to five models which corresponds to the five largest structure clusters. The confidence of each model is quantitatively measured by C-score that is calculated based on the significance of threading template alignments and the convergence parameters of the structure assembly simulations. C-score is typically in the range of [-5, 2], where a C-score of higher value signifies a model with a high confidence and vice-versa. TM-score and RMSD are estimated based on C-score and protein length following the correlation observed between these qualities. Since the top 5 models are ranked by the cluster size, it is possible that the lower-rank models have a higher C-score in rare cases. Although the first model has a better quality in most cases, it is also possible that the lower-rank models have a better quality than the higher-rank models as seen in our benchmark tests. If the I-TASSER simulations converge, it is possible to have less than 5 clusters generated. This is usually an indication that the models have a good quality because of the converged simulations.)
 Proteins structureally close to the target in PDB (as identified by TM-align

(After the structure assembly simulation, I-TASSER uses the TM-align structural alignment program to match the first I-TASSER model to all structures in the PDB library. This section reports the top 10 proteins from the PDB that have the closest structural similarity, i.e. the highest TM-score, to the predicted I-TASSER model. Due to the structural similarity, these proteins often have similar function to the target. However, users are encouraged to use the data in the next section 'Predicted function using COACH' to infer the function of the target protein, since COACH has been extensively trained to derive biological functions from multi-source of sequence and structure features which has on average a higher accuracy than the function annotations derived only from the global structure comparison.)


 Predicted function using COACH

(This section reports biological annotations of the target protein by COACH based on the I-TASSER structure prediction. COACH is a meta-server approach that combines multiple function annotation results from the COFACTOR, TM-SITE and S-SITE programs.)


  Ligand binding sites

Rank C-score Cluster
size
PDB
Hit
Lig
Name
Download
Complex
Ligand Binding Site Residues
10.07 4 1hxpA U5P Rep, Mult 80,81,88,89,90,100
20.05 3 2cz8B FAD Rep, Mult 104,144,151,153
30.04 2 1gfnA C8E Rep, Mult 105,152
40.04 2 2h39B ADQ Rep, Mult 104,106,107,108,118
50.04 2 3kziA CLA Rep, Mult 37,41
60.04 2 4ac1X ZN Rep, Mult 78,124
70.02 1 3i9dW MG Rep, Mult 42,45
80.02 1 3qbmA MG Rep, Mult 130,133
90.02 1 2boqA CA Rep, Mult 69,81,83,85
100.02 1 1c4aA SF4 Rep, Mult 118,120,122,125,127,153,202
110.02 1 1swiC BNZ Rep, Mult 59,63
120.02 1 5eteA DIO Rep, Mult 59,100,138
130.02 1 1c4aA FES Rep, Mult 67,68,69,70,80,81,103
140.02 1 2wse3 CLA Rep, Mult 118,119,213
150.02 1 3v2d2 MG Rep, Mult 70,74
160.02 1 3kdpB III Rep, Mult 89,90
170.02 1 4fe1F CLA Rep, Mult 32,36
180.02 1 3u3uC EAH Rep, Mult 40,44,47,105,117,118,121,122,127,131,154
190.02 1 2fhbA GLC Rep, Mult 89,91,99,157

Download the all possible binding ligands and detailed prediction summary.
Download the templates clustering results.
(a)C-score is the confidence score of the prediction. C-score ranges [0-1], where a higher score indicates a more reliable prediction.
(b)Cluster size is the total number of templates in a cluster.
(c)Lig Name is name of possible binding ligand. Click the name to view its information in the BioLiP database.
(d)Rep is a single complex structure with the most representative ligand in the cluster, i.e., the one listed in the Lig Name column.
Mult is the complex structures with all potential binding ligands in the cluster.

  Enzyme Commission (EC) numbers and active sites

RankCscoreECPDB
Hit
TM-scoreRMSDaIDENaCovEC NumberActive Site Residues
10.0603d7uA0.3345.490.0410.5472.7.10.269
20.0602veoB0.4075.370.0560.6613.1.1.3NA
30.0601ofdA0.3785.990.0350.6561.4.7.1122
40.0602pffB0.3975.650.0670.6792.3.1.86114
50.0601h19A0.4065.040.0670.6383.3.2.6NA
60.0602qr5A0.4225.890.0480.7333.4.19.1NA
70.0602e3xA0.4145.140.0520.6383.4.24.58118,133
80.0601e6yA0.4054.580.0860.5882.8.4.1155
90.0602fhbA0.4105.790.0410.7063.2.1.41NA
100.0601hr9F0.3985.620.0440.6833.4.24.64115
110.0602wk5A0.3145.710.0420.5432.4.2.4NA
120.0602pffA0.4165.590.0550.7202.3.1.41,2.3.1.86NA
130.0602ecfA0.4056.180.0400.7423.4.14.5NA
140.0601hr6D0.4025.510.0390.6793.4.24.64NA
150.0601z84A0.4165.210.0510.6612.7.7.12NA
160.0601t3tA0.4325.850.0280.7566.3.5.381
170.0601kyaA0.3956.050.0350.7151.10.3.2NA
180.0601llwA0.3996.060.0340.7241.4.7.1122
190.0602gdkB0.4125.230.0440.6612.7.7.12153

(a)CscoreEC is the confidence score for the 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.

  Gene Ontology (GO) terms

Homologous GO templates in PDB 
RankCscoreGOTM-scoreRMSDaIDENaCovPDB HitAssociated GO Terms
00.150.4953.440.140.602vznA GO:0005576
10.100.4793.150.190.574aiwA GO:0000139 GO:0005576 GO:0005794 GO:0010634 GO:0010718 GO:0016020 GO:0042803 GO:0070062 GO:0070374
20.080.4923.370.130.601qnxA GO:0005576
30.070.4723.690.100.603mz8A GO:0005576
40.070.4773.780.090.601wvrA GO:0005576
50.070.4743.710.080.611rc9A GO:0005576
60.070.4873.380.100.613q2uA GO:0005576 GO:0005886 GO:0016020 GO:0016021
70.070.4673.390.090.574nuiA GO:0005576 GO:0046872
80.060.4673.370.100.572ddbB GO:0005576 GO:0046872
90.060.4303.170.100.521cfeA GO:0005576 GO:0006952 GO:0009607 GO:0031640 GO:0050832
100.060.4993.910.090.633nt8A GO:0005576
110.060.3054.090.020.424jgoB GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0005524 GO:0005622 GO:0005886 GO:0007165 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0018106 GO:0023014 GO:0030435
120.060.3065.780.040.535er8A GO:0003824 GO:0004311 GO:0008152 GO:0008299 GO:0016740 GO:0016829 GO:0046872
130.060.2434.920.050.382khcA GO:0000166 GO:0000381 GO:0002121 GO:0003676 GO:0003723 GO:0003729 GO:0003730 GO:0005634 GO:0005737 GO:0006378 GO:0007281 GO:0007286 GO:0007319 GO:0007476 GO:0014881 GO:0016604 GO:0017148 GO:0030727 GO:0031536 GO:0031965 GO:0036099 GO:0042078 GO:0043186 GO:0045214 GO:0046011 GO:0048477 GO:2000738
140.060.2494.970.070.384ffuI GO:0016491 GO:0055114
150.060.2334.460.060.341c2nA GO:0009055 GO:0015979 GO:0020037 GO:0046872 GO:0055114
160.060.2244.800.050.334yuuQ2 GO:0005509 GO:0009523 GO:0009654 GO:0015979 GO:0019898
170.060.2034.990.030.324a53A GO:0000932 GO:0003729 GO:0005737 GO:0010494 GO:0031087 GO:0033962
180.060.2004.260.040.281q38A GO:0001525 GO:0001775 GO:0001932 GO:0002020 GO:0002576 GO:0002931 GO:0005178 GO:0005518 GO:0005576 GO:0005577 GO:0005578 GO:0005604 GO:0005605 GO:0005615 GO:0005793 GO:0006953 GO:0007044 GO:0007155 GO:0007160 GO:0007161 GO:0008201 GO:0008284 GO:0008347 GO:0008360 GO:0009611 GO:0010193 GO:0010628 GO:0010952 GO:0016324 GO:0016504 GO:0018149 GO:0022617 GO:0030198 GO:0030335 GO:0031012 GO:0031093 GO:0033622 GO:0034446 GO:0035924 GO:0035987 GO:0036120 GO:0042060 GO:0042802 GO:0043066 GO:0045340 GO:0045773 GO:0048146 GO:0050900 GO:0050921 GO:0051384 GO:0070062 GO:0070372 GO:0071222 GO:0071288 GO:0071333 GO:0071347 GO:0071380 GO:0071560 GO:0071773 GO:0072562 GO:1904237 GO:2001202


Consensus prediction of GO terms
 
Molecular Function GO:0042803
GO-Score 0.10
Biological Processes GO:0010718 GO:0010634 GO:0070374
GO-Score 0.10 0.10 0.10
Cellular Component GO:0005576
GO-Score 0.38

(a)CscoreGO is a combined measure for evaluating global and local similarity between query and template protein. It's range is [0-1] and higher values indicate more confident predictions.
(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.
(f)The second table shows a consensus GO terms amongst the top scoring templates. The GO-Score associated with each prediction is defined as the average weight of the GO term, where the weights are assigned based on CscoreGO of the template.

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]



Please cite the following articles when you use the I-TASSER server:
1. J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8, 2015.
2. J Yang, Y Zhang. I-TASSER server: new development for protein structure and function predictions, Nucleic Acids Research, 43: W174-W181, 2015.
3.A Roy, A Kucukural, Y Zhang. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols, 5: 725-738, 2010.
4.Y Zhang. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9: 40, 2008.