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I-TASSER results for job id Rv3633

[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 3 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
10.41 38 5equD AKG Rep, Mult 74,116,118,125,128,130,148,161,200,202,211,215
20.25 25 3kv6D FE2 Rep, Mult 128,130,200
30.02 3 1uogA P1C Rep, Mult 114,128,130,146,148,161,194,200,202,215,217
40.01 1 3ouiA 42Z Rep, Mult 11,15,97,100,103,109,194

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
10.0912a1xA0.6043.370.1630.7181.14.11.18NA
20.0602ztgA0.3866.050.0280.6566.1.1.7NA
30.0603f93A0.3746.760.0440.6773.2.1.-247
40.0603hmjA0.3866.770.0690.6982.3.1.86NA
50.0603hhsB0.3656.410.0510.6321.14.18.1NA
60.0601ygbA0.3885.980.0200.6466.1.1.784
70.0601p8fA0.3656.510.0350.6461.1.1.42254
80.0601bk0A0.5263.800.1130.6561.21.3.1NA
90.0601gp6A0.5353.470.0880.6531.14.11.19NA
100.0602pqdA0.3665.780.0430.5672.5.1.19NA
110.0602ilmA0.5073.710.0780.6251.14.11.16128
120.0602de0X0.3946.160.0470.6462.4.1.68100
130.0603h09B0.3786.730.0600.6843.4.21.72NA
140.0601n1hA0.3856.470.0520.6732.7.7.48111
150.0603kv4A0.5074.930.0820.6981.14.11.27NA
160.0601unbA0.5194.120.0650.6731.14.20.1NA
170.0601t3tA0.4026.620.0440.7256.3.5.3NA
180.0601e5rB0.4263.160.0900.5021.14.11.28NA
190.0603dmsA0.3586.510.0240.6361.1.1.42254
200.0602zzgA0.3816.290.0480.6496.1.1.7123

(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
00.370.8831.370.210.924naoA GO:0046872
10.360.8561.890.220.925dapA GO:0051213 GO:0055114
20.340.8332.330.220.914y5sA GO:0016491 GO:0051213 GO:0055114 GO:1902181
30.290.6193.730.180.754q5oA GO:0016706 GO:0046872 GO:0055114
40.280.6443.680.170.793obzA GO:0016491 GO:0046872 GO:0051213 GO:0055114
50.280.6043.370.160.722a1xA GO:0001561 GO:0003824 GO:0005739 GO:0005777 GO:0005782 GO:0006631 GO:0006720 GO:0016491 GO:0031418 GO:0046872 GO:0048037 GO:0048244 GO:0051213 GO:0055114 GO:0097089
60.180.6153.560.140.744nmiA GO:0005506 GO:0016491 GO:0016706 GO:0019491 GO:0042400 GO:0046872 GO:0051213 GO:0055114
70.060.3286.520.060.574n5fA GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
80.060.2916.450.040.513hlfA GO:0016740 GO:0016746 GO:0016787 GO:0017000 GO:0030639 GO:0050832
90.060.2977.080.070.563vehB GO:0000287 GO:0004106 GO:0008909 GO:0009058 GO:0009697 GO:0016829 GO:0016833 GO:0016853 GO:0019540 GO:0043904 GO:0046872
100.060.2796.150.040.453qvfA GO:0000166 GO:0005524 GO:0016301 GO:0016310 GO:0016740
110.060.2926.200.060.494bkqA GO:0004318 GO:0006629 GO:0006631 GO:0006633 GO:0016491 GO:0051287 GO:0055114
120.060.2786.950.030.523ip4B GO:0000166 GO:0005524 GO:0006412 GO:0016874 GO:0016884 GO:0050567
130.060.2756.250.040.482f17A GO:0000166 GO:0004788 GO:0005524 GO:0006772 GO:0009229 GO:0016301 GO:0016310 GO:0016740 GO:0030975
140.060.2836.660.060.503txxB GO:0005737 GO:0006520 GO:0006596 GO:0016597 GO:0016740 GO:0016743 GO:0033388 GO:0033390 GO:0050231
150.060.2906.550.040.523wnbA GO:0003746 GO:0006414
160.060.2696.770.030.493im9A GO:0003824 GO:0004314 GO:0006629 GO:0006631 GO:0006633 GO:0008152 GO:0016740 GO:0016746
170.060.2416.760.020.444hacA GO:0000166 GO:0000287 GO:0004496 GO:0005524 GO:0005737 GO:0006629 GO:0008152 GO:0008299 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019287
180.060.3006.490.050.524c20B GO:0005737 GO:0005975 GO:0005996 GO:0006004 GO:0008736 GO:0016853 GO:0016861 GO:0019317 GO:0030145 GO:0042355 GO:0046872
190.060.3075.580.020.464qqaA GO:0009405 GO:0015485
200.060.2966.470.060.503bjxA GO:0019120


Consensus prediction of GO terms
 
Molecular Function GO:0051213 GO:0046872 GO:0016705
GO-Score 0.70 0.68 0.58
Biological Processes GO:0055114 GO:1902181
GO-Score 0.78 0.34
Cellular Component
GO-Score

(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.