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I-TASSER results for job id Rv2253

[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 4n6hA OLA Rep, Mult 8,11,12,15
20.07 4 1wc0B APC Rep, Mult 146,147,148,149,150,151,154
30.05 3 1wc1A TAT Rep, Mult 36,37,39,40,72,73
40.05 3 2kdxA ZN Rep, Mult 70,75,113,152
50.03 2 3cf4A SF4 Rep, Mult 31,32,33,34,35,36,37,70,72,76
60.03 2 1izlM CLA Rep, Mult 12,19
70.02 1 3du7A MG Rep, Mult 68,69,71,118,119
80.02 1 1ud9A ZN Rep, Mult 46,164
90.02 1 3a0bH CLA Rep, Mult 9,17
100.02 1 1wc1C TAT Rep, Mult 137,138,140,163
110.02 1 4cv7A CO Rep, Mult 144,157
120.02 1 2pe7A PDC Rep, Mult 92,93
130.02 1 1rneA NGA Rep, Mult 99,101
140.02 1 2ei3A MG Rep, Mult 95,117
150.02 1 3cf4A SF4 Rep, Mult 122,123,125,127,145,146,147,156
160.02 1 3m9iA 3PE Rep, Mult 19,50
170.02 1 2bw7B APC Rep, Mult 131,132,133,134,135,140
180.02 1 1l6mB DBH Rep, Mult 42,67,158

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
10.0602ivfA0.4044.910.0510.6831.17.99.2NA
20.0601yx2B0.4044.800.0750.6652.1.2.10NA
30.0603dt7A0.4035.340.0360.7134.1.1.32NA
40.0601pj6A0.4015.410.0630.7131.5.3.10NA
50.0601occA0.3715.260.0500.6351.9.3.1NA
60.0603hsiB0.3974.830.0500.6772.7.8.8NA
70.0601s9iA0.3756.200.0680.7782.7.12.2,2.7.1.37NA
80.0601ua2A0.4115.370.0400.7542.7.11.22,2.7.11.23NA
90.0601bi7A0.3046.060.0330.6112.7.11.22,2.7.1.-NA
100.0602qx1A0.3945.180.0890.7012.3.1.180NA
110.0601t3qB0.3945.600.0420.7311.3.99.17NA
120.0602w01A0.4084.930.0760.6894.6.1.25
130.0601rw9A0.4194.660.0900.6774.2.2.5NA
140.0602wz1A0.4025.270.0230.7074.6.1.25
150.0603eqdA0.3975.970.0670.7842.7.12.281,87
160.0602w96B0.3425.420.0450.5932.7.11.2286,88
170.0601ybtB0.4104.710.0670.6654.6.1.1NA
180.0603cf4A0.4225.530.0790.7661.2.99.276
190.0603girA0.4055.120.0770.6952.1.2.10132

(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
00.070.4265.630.100.814xakA GO:0009405 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0019064 GO:0033644 GO:0039663 GO:0044173 GO:0046718 GO:0046813 GO:0055036 GO:0061025
10.060.4225.560.060.804qzvB GO:0009405 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0033644 GO:0039663 GO:0044173 GO:0046718 GO:0046813 GO:0055036 GO:0061025
20.060.4405.310.040.773w6qA GO:0004503 GO:0005634 GO:0008152 GO:0016491 GO:0046872 GO:0055114
30.060.3545.380.040.651js8A GO:0005344 GO:0006810 GO:0008152 GO:0015671 GO:0016491 GO:0046872 GO:0055114
40.060.3435.610.020.652dd8S GO:0009405 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0020002 GO:0033644 GO:0039654 GO:0039663 GO:0044173 GO:0046718 GO:0046789 GO:0046813 GO:0055036 GO:0061025
50.060.3275.640.070.611gu6A GO:0005506 GO:0005509 GO:0006807 GO:0016491 GO:0016966 GO:0019645 GO:0020037 GO:0030288 GO:0042128 GO:0042279 GO:0042597 GO:0046872 GO:0055114
60.060.3425.460.070.623qjoA GO:0008152 GO:0016491 GO:0046872 GO:0055114
70.060.2835.400.070.514j3rA GO:0004097 GO:0008152 GO:0016491 GO:0046872 GO:0055114
80.060.3545.270.060.625a97C GO:0003723 GO:0019012 GO:0019013 GO:0019028 GO:0019029
90.060.3176.080.060.655i08A GO:0005198 GO:0009405 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0019064 GO:0033644 GO:0039663 GO:0044173 GO:0046718 GO:0046813 GO:0055036 GO:0061025
100.060.2805.560.010.505ce9A GO:0004097 GO:0004503 GO:0008152 GO:0016491 GO:0036263 GO:0046148 GO:0046872 GO:0055114
110.060.4135.570.040.784z11A GO:0004097 GO:0008152 GO:0016491 GO:0046148 GO:0046872 GO:0055114
120.060.2535.840.010.473awtA GO:0008152 GO:0016491 GO:0046872 GO:0055114
130.060.4065.800.080.803jclA GO:0009405 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0019064 GO:0033644 GO:0039663 GO:0044165 GO:0044173 GO:0044177 GO:0046718 GO:0046813 GO:0055036 GO:0061025
140.060.4305.230.070.754ouaB GO:0004503 GO:0008152 GO:0016491 GO:0046872 GO:0055114
150.060.3375.020.040.581lnlA GO:0005344 GO:0005576 GO:0005615 GO:0006810 GO:0008152 GO:0015671 GO:0016491 GO:0046872 GO:0055114
160.060.2945.350.040.534hd4A GO:0008152 GO:0016491 GO:0046872 GO:0055114
170.060.4325.310.060.773w6wA GO:0004503 GO:0005634 GO:0008152 GO:0016491 GO:0046872 GO:0055114
180.060.3055.540.040.562p3xA GO:0004097 GO:0008152 GO:0009507 GO:0009536 GO:0009543 GO:0009579 GO:0016491 GO:0046148 GO:0046872 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0046872 GO:0004503 GO:0046789 GO:0005344
GO-Score 0.12 0.07 0.06 0.06
Biological Processes GO:0044800 GO:0019062 GO:0046718
GO-Score 0.36 0.36 0.36
Cellular Component GO:0036338 GO:0033644 GO:0044172
GO-Score 0.36 0.36 0.36

(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.