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I-TASSER results for job id Rv0910

[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 4 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
10.23 14 3nmnA PYV Rep, Mult 53,64,66,79,81,85,87,89,126,130,131
20.09 5 4n3eW 2AN Rep, Mult 6,8,10,17,21,23,79,93,106
30.03 2 2e3rB 18C Rep, Mult 21,27,31,33,52,54,55,57,60,81,87,106,110,116,122,123,126,127,130,131,134
40.02 1 2flhC ZEA Rep, Mult 21,23,53,64,66,79,93
50.02 1 1s5lK CLA Rep, Mult 11,12
60.02 1 2gkdA NUC Rep, Mult 118,121,122
70.02 1 3tvqA DQH Rep, Mult 56,62,64,81,86,118,122,123,126
80.02 1 2z9yA DDR Rep, Mult 21,27,30,54,64,80,106,110,130,134
90.02 1 3kv7B ACT Rep, Mult 29,48
100.02 1 2gkdA NUC Rep, Mult 124,125
110.02 1 2flhA ZEA Rep, Mult 22,68,72
120.02 1 1txcB 2AN Rep, Mult 50,67,82,87,88

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
10.0672vq5A0.6513.900.0810.9384.2.1.7824,48,92
20.0602ihwA0.5394.550.0450.8402.3.1.168NA
30.0601q23B0.5074.950.0450.8542.3.1.28NA
40.0601kfqB0.4973.930.0990.7505.4.2.2NA
50.0603b9jC0.4884.680.0360.7991.17.3.2,1.17.1.4NA
60.0603kvnX0.5014.630.0300.8063.1.1.174
70.0601sczA0.5254.550.0300.8332.3.1.61NA
80.0603l60A0.5524.410.0600.8472.3.1.12NA
90.0603igyB0.5104.760.0950.8545.4.2.1NA
100.0601z01A0.6144.360.0790.9581.14.13.61NA
110.0601wqlA0.6033.940.0610.9101.14.12.-23
120.0602de6B0.6004.390.0570.9511.14.12.-20
130.0601vlbA0.4864.880.0490.8331.2.99.7NA
140.0602b1xA0.6173.910.0580.9171.14.12.12NA
150.0602e1qA0.5164.950.0490.8751.17.3.2,1.17.1.4NA
160.0601yaaB0.5074.630.0730.8122.6.1.139
170.0602ckjA0.4865.220.0700.8681.17.1.4,1.17.3.2NA
180.0601uliC0.6024.140.0680.9101.14.12.1823
190.0603b9jI0.2744.910.0650.4651.17.1.4,1.17.3.2NA
200.0601eadA0.5264.490.0850.8262.3.1.12NA

(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
00.230.6783.390.140.924n0gC GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
10.190.6863.550.110.964c94A GO:0006952 GO:0009607
20.170.6953.390.110.964q0kA GO:0006952 GO:0009607 GO:0009740
30.160.6813.710.080.974c9iA GO:0006952 GO:0009607
40.150.6913.480.110.962flhB GO:0006952 GO:0009607
50.120.7223.020.130.943k3kA GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042802 GO:0042803 GO:0043086 GO:0080163
60.120.7253.320.110.985i8fA GO:0006952 GO:0009607
70.120.6703.940.110.974m9bA GO:0006952 GO:0009607
80.110.7083.190.150.943nefA GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
90.110.6713.800.110.962wqlA GO:0006952 GO:0009607
100.110.6783.880.090.971tw0A GO:0006952 GO:0009607
110.110.6793.760.110.944gy9A GO:0006952 GO:0009607 GO:0009736 GO:0009877
120.110.7023.500.120.964oicA GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0009738 GO:0010427 GO:0043086 GO:0080163
130.100.6833.700.100.971e09A GO:0006952 GO:0009607
140.100.7093.380.130.953kdhA GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
150.100.6873.450.130.943rt0C GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
160.100.6713.810.090.962vneA GO:0006952 GO:0009607 GO:0009820 GO:0016829 GO:0050474
170.100.6913.460.140.943ojiB GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
180.100.6683.690.090.965amwA GO:0006952 GO:0009607


Consensus prediction of GO terms
 
Molecular Function GO:0019888 GO:0060089 GO:0046983 GO:0033293 GO:0019212 GO:0042562 GO:0042802
GO-Score 0.47 0.47 0.47 0.47 0.47 0.47 0.47
Biological Processes GO:0009607 GO:0006952 GO:0043666 GO:0071215 GO:0044092 GO:0010476
GO-Score 0.52 0.52 0.47 0.47 0.47 0.35
Cellular Component GO:0043231 GO:0071944 GO:0016020
GO-Score 0.47 0.47 0.35

(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.