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I-TASSER results for job id Rv2059

[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
10.50 28 3hh8A FE Rep, Mult 137,197,261,286,343
20.02 1 1a9x1 III Rep, Mult 143,144,146,147,170,171
30.02 1 3u7qB IMD Rep, Mult 127,128,148,149,152
40.02 1 3u7qD IMD Rep, Mult 278,279,280,298,302
50.02 1 1xvlC MN Rep, Mult 137,197,261,326
60.02 1 3u7qD IMD Rep, Mult 315,318,319,322

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
10.0601m34A0.4226.090.0670.5971.18.6.1NA
20.0601fp4B0.4205.610.0400.5541.18.6.1NA
30.0601ofdA0.3467.750.0340.5911.4.7.1NA
40.0602pmgB0.3436.500.0650.5095.4.2.2136,320
50.0601t3tA0.3927.490.0780.6366.3.5.3324
60.0602w00B0.3717.010.0450.5733.1.21.3357
70.0602vdcF0.3827.880.0500.6481.4.1.13115
80.0602d1rA0.3587.260.0650.5791.13.12.7NA
90.0601mioB0.4115.310.0650.5341.18.6.1319
100.0603gpbA0.3536.250.0330.5052.4.1.1NA
110.0602qllA0.3476.300.0400.5052.4.1.1NA
120.0601qh8A0.4206.100.0850.6011.18.6.1204,212
130.0601fa9A0.3476.280.0330.4992.4.1.1NA
140.0601h1lB0.4185.380.0660.5461.18.6.1NA
150.0601l5hA0.4015.410.0910.5361.18.6.1NA
160.0602jfgA0.3626.420.0700.5306.3.2.9NA
170.0602cseW0.3597.350.0480.5713.6.4.13NA
180.0601kfqB0.3616.780.0420.5505.4.2.2237
190.0602vdcA0.4077.160.0590.6421.4.1.13NA

(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
00.160.4612.800.160.502o1eA GO:0005886 GO:0006810 GO:0006811 GO:0006829 GO:0007155 GO:0010043 GO:0016020 GO:0030001 GO:0046872
10.150.4682.310.170.505afsA GO:0006810 GO:0007155 GO:0030001 GO:0046872
20.140.4782.070.190.504xrvB GO:0006810 GO:0007155 GO:0030001 GO:0046872
30.120.4921.670.170.513cx3A GO:0005886 GO:0006810 GO:0007155 GO:0010043 GO:0030001 GO:0046872
40.110.4842.220.190.515i4kA GO:0005886 GO:0006810 GO:0007155 GO:0010043 GO:0016020 GO:0030001 GO:0046872
50.100.4322.040.240.464irmC GO:0005886 GO:0006810 GO:0007155 GO:0010043 GO:0030001 GO:0046872
60.080.4792.250.170.514k3vB GO:0006810 GO:0007155 GO:0030001 GO:0046872
70.080.4513.030.160.502xy4A GO:0005886 GO:0010043 GO:0030001 GO:0046872
80.070.4872.130.160.521k0fA GO:0006810 GO:0006811 GO:0006829 GO:0007155 GO:0030001 GO:0042597 GO:0046872
90.070.4982.100.210.531xvlA GO:0005886 GO:0006810 GO:0007155 GO:0010043 GO:0030001 GO:0046872
100.070.4941.350.180.514h0fA GO:0006810 GO:0007155 GO:0030001 GO:0046872
110.070.4862.310.160.521pszA GO:0005886 GO:0006810 GO:0007155 GO:0016020 GO:0030001 GO:0046872
120.070.4812.020.150.513mfqA GO:0006810 GO:0007155 GO:0030001 GO:0046872
130.070.4852.190.160.513hh8A GO:0005886 GO:0006810 GO:0006811 GO:0006825 GO:0006829 GO:0007155 GO:0016020 GO:0030001 GO:0046872 GO:0055072
140.070.4772.340.170.514oxqA GO:0006810 GO:0007155 GO:0030001 GO:0046872
150.070.4662.120.200.501pq4B GO:0005886 GO:0010043 GO:0030001 GO:0046872
160.060.4452.330.170.474k3vA GO:0006810 GO:0007155 GO:0030001 GO:0046872
170.060.2907.010.060.454whbA GO:0016787 GO:0016810
180.060.2466.250.070.354gcmB GO:0004791 GO:0005737 GO:0016491 GO:0019430 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0046872
GO-Score 0.52
Biological Processes GO:0007155 GO:0010043 GO:0070838 GO:0000041
GO-Score 0.52 0.34 0.32 0.32
Cellular Component GO:0005886
GO-Score 0.34

(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.