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I-TASSER results for job id Rv3015c

[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
10.45 19 1xdjA ZN Rep, Mult 215,217,237,306
20.30 10 1u1hA MET Rep, Mult 10,11,12,42,48,111,168,170,215,217,306,307
30.09 6 1xr2B C2F Rep, Mult 46,65,69,70,121,174
40.01 1 2inf0 III Rep, Mult 132,173,174,238,266,272,278,306
50.01 1 3cyv0 III Rep, Mult 132,174,176,238,277
60.01 1 1u1hA ZN Rep, Mult 224,228

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
10.2671xi3A0.4613.510.1000.5642.5.1.3235
20.2582infA0.7213.370.0890.8554.1.1.3747
30.2561j93A0.7093.490.1100.8584.1.1.3747
40.1821tqxA0.4803.910.0630.6025.1.3.1NA
50.1452infC0.7223.450.0920.8584.1.1.37NA
60.1213cyvA0.7313.330.1130.8614.1.1.3747
70.1021j2wA0.4793.390.1120.5794.1.2.4NA
80.0951nsjA0.4663.580.0890.5645.3.1.24NA
90.0932v81A0.4733.510.1190.5764.1.2.21NA
100.0751vcvA0.5003.300.1100.5944.1.2.4NA
110.0673f4wA0.4813.630.1210.5914.1.2.-7,214
120.0672czfA0.4663.780.0460.5824.1.1.23NA
130.0671xi3B0.4613.550.0990.5672.5.1.3319
140.0671w0mA0.4873.660.1320.5965.3.1.1NA
150.0662cz5A0.4763.550.0620.5794.1.1.23220
160.0661mxsA0.4683.580.0890.5704.1.2.14NA
170.0662h6rB0.4693.500.0730.5705.3.1.1NA
180.0661mzhA0.4893.820.0670.6084.1.2.4NA
190.0601o7aA0.6464.410.0410.8463.2.1.5286,87
200.0602pbgA0.6483.980.0500.8283.2.1.85NA
210.0602e9lA0.6454.010.0600.8343.2.1.21NA
220.0601kwgA0.6424.110.1060.8313.2.1.23NA
230.0601gowA0.6434.420.0640.8553.2.1.23NA
240.0601uroA0.7253.460.1090.8644.1.1.37308
250.0601c7sA0.6644.880.0770.8993.2.1.52NA
260.0601veoA0.6494.000.0820.8313.2.1.2NA
270.0601b90A0.6494.170.0740.8403.2.1.2NA
280.0601bgaA0.6444.110.0700.8343.2.1.21NA
290.0601gnxA0.6464.040.0990.8283.2.1.21NA
300.0601fa2A0.6534.310.0550.8583.2.1.2NA
310.0602ejaA0.7083.530.1310.8524.1.1.3747
320.0603bq5A0.8541.700.1640.9052.1.1.14NA
330.0602gjxA0.6454.460.0440.8493.2.1.5286,87
340.0601t7lA0.8661.690.1650.9172.1.1.14NA
350.0602nq5A0.8101.650.1700.8552.1.1.14NA
360.0601qbaA0.6624.940.0710.8993.2.1.52NA
370.0603cmjA0.6483.920.1080.8223.2.1.21NA

(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
00.560.8641.750.190.921u1hA GO:0003871 GO:0005507 GO:0005737 GO:0005774 GO:0005777 GO:0005794 GO:0005829 GO:0005886 GO:0008168 GO:0008270 GO:0008652 GO:0008705 GO:0009086 GO:0009506 GO:0009507 GO:0009570 GO:0009651 GO:0010043 GO:0016020 GO:0016740 GO:0032259 GO:0046686 GO:0046872 GO:0048046 GO:0050667
10.490.8541.700.160.913bq5A GO:0003871 GO:0005576 GO:0005829 GO:0008168 GO:0008270 GO:0008652 GO:0008705 GO:0009086 GO:0016740 GO:0032259 GO:0046872 GO:0050667
20.490.8661.690.170.921t7lA GO:0003871 GO:0005576 GO:0005829 GO:0008168 GO:0008270 GO:0008652 GO:0008705 GO:0009086 GO:0016740 GO:0032259 GO:0046872 GO:0050667
30.470.7783.030.110.893ppfA GO:0003871 GO:0006555 GO:0008168 GO:0008270 GO:0008652 GO:0009086 GO:0009277 GO:0009986 GO:0016740 GO:0030446 GO:0032259 GO:0034605 GO:0044416 GO:0046872
40.460.8641.630.170.913t0cA GO:0003871 GO:0008168 GO:0008270 GO:0008652 GO:0009086 GO:0016740 GO:0032259 GO:0046872
50.370.8222.050.190.893ppcB GO:0003871 GO:0006555 GO:0008168 GO:0008270 GO:0008652 GO:0009086 GO:0009277 GO:0009986 GO:0016740 GO:0030446 GO:0032259 GO:0034605 GO:0044416 GO:0046872
60.330.8572.030.180.934ztxA GO:0003871 GO:0008168 GO:0008270 GO:0008652 GO:0009086 GO:0016740 GO:0032259
70.280.7552.800.150.851ypxA GO:0003871 GO:0005576 GO:0005829 GO:0008270 GO:0008705 GO:0009086 GO:0032259 GO:0050667
80.160.8302.310.190.914qquA GO:0003871 GO:0006555 GO:0008168 GO:0008270 GO:0008652 GO:0009086 GO:0009277 GO:0009986 GO:0016740 GO:0030446 GO:0032259 GO:0034605 GO:0044416 GO:0046872
90.150.8012.450.160.883rpdA GO:0003871 GO:0008168 GO:0008270 GO:0009086 GO:0016740 GO:0032259
100.070.5904.580.040.803emcA GO:0000272 GO:0004553 GO:0005737 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0031176 GO:0045493
110.070.5134.600.060.683thuA GO:0000287 GO:0003824 GO:0005975 GO:0008152 GO:0008927 GO:0009063 GO:0016052 GO:0016829 GO:0046872
120.060.4176.130.070.663ooqF GO:0016787 GO:0016810 GO:0019239
130.060.3106.760.040.544v38A GO:0016740 GO:0016757
140.060.3116.820.040.542ii6A GO:0016740 GO:0016757
150.060.2786.980.060.491jhdA GO:0000103 GO:0000166 GO:0004781 GO:0005524 GO:0016740 GO:0016779 GO:0070814
160.060.2797.110.050.504dnxA GO:0000103 GO:0000166 GO:0004781 GO:0005524 GO:0016740 GO:0016779 GO:0070814
170.060.2684.170.060.353ewqA GO:0001172 GO:0003723 GO:0003968 GO:0004197 GO:0006508 GO:0008233 GO:0008234 GO:0008242 GO:0008270 GO:0016020 GO:0016021 GO:0016032 GO:0016740 GO:0016787 GO:0019079 GO:0019082 GO:0030430 GO:0030683 GO:0033644 GO:0036459 GO:0039503 GO:0039520 GO:0039548 GO:0039648 GO:0044220 GO:0046872
180.060.2826.960.050.502cy8A GO:0003824 GO:0008483 GO:0016740 GO:0030170


Consensus prediction of GO terms
 
Molecular Function GO:0003871 GO:0008270 GO:0008705 GO:0005507
GO-Score 0.97 0.97 0.89 0.56
Biological Processes GO:0032259 GO:0009086 GO:0050667 GO:0010043 GO:0046686 GO:0009651 GO:0044416 GO:0034605
GO-Score 0.97 0.97 0.89 0.56 0.56 0.56 0.47 0.47
Cellular Component GO:0005829 GO:0005774 GO:0009506 GO:0009570 GO:0005794 GO:0048046 GO:0005886 GO:0005777 GO:0030446 GO:0009986
GO-Score 0.89 0.56 0.56 0.56 0.56 0.56 0.56 0.56 0.47 0.47

(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.