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I-TASSER results for job id Rv3127

[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
10.37 35 3gh8A FMN Rep, Mult 115,116,117,119,265,266,267,268,311
20.33 32 1f5vA FMN Rep, Mult 13,14,15,17,56,57,60
30.01 1 3gh8C UUU Rep, Mult 115,116,117,119,165,169,178,181,188,221,265,266,267,268,311

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
10.0663gh8A0.4583.450.1280.5441.-.-.-119
20.0601kqbA0.3933.380.1570.4621.6.6.-141
30.0602cf2C0.3496.520.0490.5672.3.1.85NA
40.0603l4uA0.3436.710.0340.5873.2.1.20,3.2.1.3NA
50.0601ti2A0.3446.800.0190.5871.97.1.2NA
60.0602iukA0.3645.950.0420.5581.13.11.12NA
70.0601noxA0.3912.800.2040.4421.6.99.311,13,17,19,21,36
80.0601fo4A0.3766.700.0350.6341.17.1.4NA
90.0601v5yA0.4003.140.1060.4651.6.99.-NA
100.0603b9jI0.1765.520.0450.2621.17.1.4,1.17.3.265
110.0601vlbA0.3606.470.0490.5841.2.99.7296
120.0601ofdA0.3537.040.0630.6221.4.7.1NA
130.0601zchA0.4102.860.1250.4651.5.1.29113,250,252
140.0601dgjA0.3556.340.0530.5701.2.-.-289
150.0603bg3A0.3286.370.0350.5266.4.1.1NA
160.0603gb5A0.4143.080.1470.4771.-.-.-113,116,254,260,264,266
170.0601ogyI0.3447.150.0490.6161.7.99.413
180.0601rqgA0.3456.390.0270.5586.1.1.10NA
190.0603fg3A0.3656.120.0410.5704.2.1.92,1.13.11.40NA
200.0601ds7A0.3943.450.1500.4651.5.1.34,1.6.99.7NA

(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
00.560.9080.980.470.922ymvA GO:0016491 GO:0055114
10.210.4343.460.110.513eo8A GO:0000166 GO:0016491 GO:0055114
20.210.4273.010.130.494dn2A GO:0000166 GO:0016491 GO:0055114
30.200.4073.080.170.473e39A GO:0000166 GO:0016491 GO:0055114
40.190.4362.950.120.493gfaA GO:0000166 GO:0016491 GO:0055114
50.170.4053.880.100.484eo3A GO:0000166 GO:0016209 GO:0016491 GO:0055114 GO:0098869
60.160.4613.440.130.553tnzA GO:0004447 GO:0016020 GO:0016021 GO:0016491 GO:0055114 GO:0098869
70.160.4583.450.140.544ttcA GO:0004447 GO:0005886 GO:0006590 GO:0016020 GO:0016021 GO:0016491 GO:0055114 GO:0098869
80.130.4103.360.150.482i7hA GO:0000166 GO:0016491 GO:0055114
90.110.4173.190.150.494ttbA GO:0004447 GO:0005886 GO:0006590 GO:0016020 GO:0016021 GO:0016491 GO:0055114 GO:0098869
100.110.4043.330.130.482hayD GO:0000166 GO:0016491 GO:0055114
110.080.4292.930.130.493ek3A GO:0000166 GO:0016491 GO:0055114
120.080.4583.720.180.562wzvB GO:0000166 GO:0010181 GO:0016491 GO:0042802 GO:0042803 GO:0050661 GO:0055114 GO:2001039
130.070.3942.720.140.443ge6A GO:0000166 GO:0016491 GO:0055114
140.070.4593.900.160.563gr3A GO:0016491 GO:0055114
150.070.4513.730.120.542isjA GO:0000166 GO:0009236 GO:0016491 GO:0016705 GO:0055114
160.060.3943.660.150.472freA GO:0000166 GO:0016491 GO:0055114
170.060.4143.080.150.483gb5A GO:0004447 GO:0016020 GO:0016021 GO:0016491 GO:0055114 GO:0098869
180.060.4062.790.180.461bkjA GO:0008218 GO:0016491 GO:0052873 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0016491 GO:0000166
GO-Score 0.82 0.60
Biological Processes GO:0055114
GO-Score 0.82
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.