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I-TASSER results for job id Rv0658c

[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 3s8gA OLC Rep, Mult 189,194,201
20.05 3 2nwlA ASP Rep, Mult 150,195,196,201,212,215,216,219
30.05 3 2nwwA TB1 Rep, Mult 148,210,213,214,217
40.05 3 4x23F III Rep, Mult 148,151,152,155
50.05 3 1f51D MG Rep, Mult 216,220
60.04 2 3u32L DCW Rep, Mult 21,59,153,158
70.02 1 4ev6E MG Rep, Mult 25,181
80.02 1 3mk7A CA Rep, Mult 180,184,188
90.02 1 3bz1X CLA Rep, Mult 156,157,160,161
100.02 1 3qblA 22B Rep, Mult 23,27,58,153
110.02 1 3gjcA BOG Rep, Mult 201,204
120.02 1 3aebC EPH Rep, Mult 139,181
130.02 1 3mk7D CA Rep, Mult 162,170,172,177
140.02 1 1e86A CMO Rep, Mult 25,28,154
150.02 1 2y00A 2CV Rep, Mult 31,34,51,58
160.02 1 5etzA 22B Rep, Mult 27,50,51,54,153,157

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
10.0601w27A0.3945.750.0310.6724.3.1.24NA
20.0601j36A0.3926.410.0420.7143.4.15.1NA
30.0603hjbA0.4485.760.0730.7315.3.1.9NA
40.0602p0mA0.3946.250.0660.6931.13.11.33NA
50.0602wu8A0.4325.760.0890.7235.3.1.9NA
60.0603czoB0.4225.060.0630.6514.3.1.3NA
70.0601b8fA0.3925.280.0580.6224.3.1.3NA
80.0602yr4A0.3945.840.0590.6551.13.12.9NA
90.0603bkkA0.3995.780.0420.6553.4.15.1NA
100.0601ygeA0.4126.350.0480.7561.13.11.12NA
110.0601wgzA0.4125.170.0500.6513.4.24.66NA
120.0601ci8A0.3966.100.0650.7063.1.1.1NA
130.0602vkzG0.3956.110.0620.6982.3.1.38,3.1.2.14NA
140.0602o2dB0.4355.740.0640.7315.3.1.9NA
150.0602uv8G0.3945.990.0680.6932.3.1.86NA
160.0601no3A0.3916.600.0560.7351.13.11.12NA
170.0602pgiA0.3915.510.0570.6225.3.1.9154
180.0601i1iP0.4085.820.0590.6983.4.24.1624
190.0601pgjA0.4065.090.0740.6091.1.1.44NA

(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
00.300.8181.810.150.894cadI GO:0004175 GO:0004662 GO:0005886 GO:0005887 GO:0006508 GO:0008233 GO:0016020 GO:0016021 GO:0016787 GO:0071586
10.070.4855.250.060.732ww9A GO:0005048 GO:0005783 GO:0005789 GO:0006614 GO:0006810 GO:0008320 GO:0015031 GO:0016020 GO:0016021 GO:0071261 GO:0071806
20.070.4675.610.070.754qfhB GO:0004347 GO:0006094 GO:0006096 GO:0016853
30.070.4645.410.050.722yxrA GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0065002
40.070.4295.690.060.714em6A GO:0004347 GO:0005737 GO:0006094 GO:0006096 GO:0016853
50.070.4355.740.060.732o2dB GO:0004347 GO:0005777 GO:0006094 GO:0006096 GO:0016853 GO:0020015
60.070.4375.810.060.711iriA GO:0001525 GO:0001701 GO:0001707 GO:0004347 GO:0005125 GO:0005576 GO:0005615 GO:0005654 GO:0005737 GO:0005829 GO:0005886 GO:0005975 GO:0006094 GO:0006096 GO:0006959 GO:0007599 GO:0007611 GO:0008083 GO:0016020 GO:0016853 GO:0016866 GO:0019242 GO:0031625 GO:0034101 GO:0042593 GO:0043005 GO:0043154 GO:0043209 GO:0043524 GO:0046185 GO:0048029 GO:0051156 GO:0060170 GO:0061621 GO:0070062
70.070.4405.790.060.724wmjB GO:0004347 GO:0006094 GO:0006096 GO:0016853
80.070.4485.760.070.733hjbA GO:0004347 GO:0005737 GO:0006094 GO:0006096 GO:0016853
90.070.4325.760.090.722wu8A GO:0004347 GO:0005737 GO:0005886 GO:0006094 GO:0006096 GO:0016853 GO:0040007
100.070.4365.780.040.743nbuB GO:0004347 GO:0005737 GO:0005829 GO:0006094 GO:0006096 GO:0016853 GO:0034599 GO:0042802
110.070.4405.580.060.713ljkA GO:0004347 GO:0005737 GO:0006094 GO:0006096 GO:0016853
120.070.4335.670.060.711q50A GO:0004347 GO:0005737 GO:0006094 GO:0006096 GO:0016853
130.070.4385.520.050.713pr3A GO:0004347 GO:0006094 GO:0006096 GO:0006098 GO:0016853
140.060.3865.950.070.663dl8G GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0043952 GO:0065002
150.060.3875.120.090.591zzgA GO:0004347 GO:0005737 GO:0006094 GO:0006096 GO:0016853
160.060.2936.460.040.553ff1A GO:0004347 GO:0005737 GO:0006094 GO:0006096 GO:0016853
170.060.3826.010.060.663dinC GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0043952 GO:0065002
180.060.4625.390.050.723bo0A GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0065002


Consensus prediction of GO terms
 
Molecular Function GO:0004661 GO:0070011
GO-Score 0.59 0.59
Biological Processes GO:0080120 GO:0016485
GO-Score 0.59 0.59
Cellular Component GO:0031226 GO:0016021
GO-Score 0.59 0.39

(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.