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I-TASSER results for job id Rv1816

[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
10.11 7 2uxhB QUE Rep, Mult 95,98,99,113,117,143,192,193,196,197,200
20.10 5 3lsrA QNA Rep, Mult 9,10,38,39,40,44,50,51,54
30.06 3 1jt0C QNA Rep, Mult 37,38,39,50,54,59,60
40.06 4 2uxiB G50 Rep, Mult 95,98,102,145,193,196,200
50.05 3 1jusA RHQ Rep, Mult 68,72,75,105,106,109,112,115,138,200,201
60.03 2 1zk80 III Rep, Mult 190,191,193,194,197,198,199,201,202,204,205,206,207,208,216,218,219,222,223,226,227,229,230
70.02 1 3p9tA TCL Rep, Mult 22,26,29,64,67
80.02 1 3lsjB COA Rep, Mult 145,224,227,228
90.02 1 5d1rA 56S Rep, Mult 132,136,139,142,143,189,190,193
100.02 1 1qvtA PRL Rep, Mult 68,71,72,75,115
110.02 1 5d1rB MG Rep, Mult 30,109,110,111,112
120.02 1 2nx40 III Rep, Mult 30,31,32,33,114,117,120,139,186,187,190,191,194,195,198,202,204,205,207,221,225,226
130.02 1 2np5C NDS Rep, Mult 106,107,109,113

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
10.0601ahpA0.4185.290.0780.6452.4.1.1NA
20.0602i2xA0.4575.310.0430.7182.1.1.9033
30.0601olsB0.4215.520.0510.7051.2.4.4NA
40.0603flcX0.4295.580.0710.7222.7.1.3083,196
50.0601ivhA0.4314.890.0560.6371.3.99.10114
60.0602qtcB0.4275.660.0760.7271.2.4.136,61
70.0601s76D0.3456.000.0410.5862.7.7.6NA
80.0601k87A0.4226.200.0440.7731.5.99.8112,115,118
90.0601um9B0.4205.430.0870.6971.2.4.4125
100.0601mswD0.3686.430.0300.6712.7.7.6NA
110.0601tiwA0.3365.450.0270.5301.5.1.12,1.5.99.8108
120.0603ii9C0.4305.020.0420.6371.3.99.797
130.0601ukwA0.4364.720.0650.6411.3.99.3NA
140.0602d0tB0.4226.240.0350.7561.13.11.52NA
150.0601umdB0.4225.390.0820.6921.2.4.427,46
160.0602azdB0.4184.950.0630.6242.4.1.1NA
170.0601u8xX0.4235.620.0330.6843.2.1.12237,63
180.0602b4kA0.3395.970.0510.5863.1.1.4372
190.0603mosA0.4215.330.0780.6792.2.1.1NA

(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
00.700.9400.651.000.955d1rA GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0016020 GO:0016021
10.440.7832.080.340.872oi8A GO:0003677 GO:0006351 GO:0006355
20.360.6723.200.170.843lsjA GO:0000976 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0045922
30.330.6173.310.140.773f1bA GO:0003677 GO:0006351 GO:0006355
40.300.7172.560.200.813on2B GO:0003677 GO:0006351 GO:0006355
50.290.6233.080.170.763cjdA GO:0003677 GO:0006351 GO:0006355
60.280.5683.550.150.722hxiB GO:0003677 GO:0006351 GO:0006355 GO:0045892
70.260.6113.310.120.783qkxA GO:0003677 GO:0006351 GO:0006355
80.260.6373.440.140.822uxhA GO:0003677 GO:0006351 GO:0006355
90.240.5654.300.130.793cwrA GO:0003677 GO:0006351 GO:0006355
100.240.6353.390.170.804gctC GO:0000976 GO:0003677 GO:0003700 GO:0005737 GO:0005829 GO:0006355 GO:0007049 GO:0009295 GO:0010974 GO:0043565 GO:0043590 GO:0051301 GO:0051302
110.230.6233.230.200.762hxoA GO:0003677 GO:0006351 GO:0006355 GO:0045892
120.220.6382.830.140.763dcfA GO:0003677 GO:0006351 GO:0006355
130.220.6223.470.130.803pasB GO:0003677 GO:0006351 GO:0006355
140.210.6183.090.220.764jl3C GO:0003677 GO:0006351 GO:0006355
150.210.6033.390.140.763zqgA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677 GO:0046872
160.200.6203.290.140.793he0C GO:0003677 GO:0006351 GO:0006355
170.200.5583.670.130.722iaiA GO:0003677 GO:0006351 GO:0006355
180.190.6213.180.140.773vprA GO:0003677 GO:0006351 GO:0006355 GO:0042802
190.180.6162.910.200.753bqyA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677
200.180.5513.940.120.743colA GO:0003677 GO:0006351 GO:0006355
210.180.6023.330.140.772zcnD GO:0003677 GO:0006351 GO:0006355
220.180.6113.280.090.753ccyA GO:0003677 GO:0006351 GO:0006355
230.180.5114.340.080.724za6A GO:0003677
240.170.5784.020.110.792rasB GO:0003677 GO:0006351 GO:0006355
250.170.5783.300.140.733zqfA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677 GO:0046872
260.160.5853.150.130.731z0xA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677
270.160.5453.920.150.723vvxA GO:0003677 GO:0006351 GO:0006355
280.160.5843.470.170.753b6aA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677
290.130.6693.180.140.813g7rB GO:0003677 GO:0003700 GO:0006351 GO:0006355
300.120.5773.790.080.763aqtB GO:0003677 GO:0006351 GO:0006355
310.090.6303.610.130.803c07A GO:0003677 GO:0006351 GO:0006355
320.090.5913.140.100.722eh3A GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0046872
330.070.6203.290.110.792zcxA GO:0003677 GO:0006351 GO:0006355


Consensus prediction of GO terms
 
Molecular Function GO:0003700 GO:0000976
GO-Score 0.81 0.36
Biological Processes GO:0006355 GO:0045922
GO-Score 0.95 0.36
Cellular Component GO:0016021 GO:0005829
GO-Score 0.70 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.