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I-TASSER results for job id Rv3181c

[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 3pm1A ET Rep, Mult 48,76,80,86,92,120,123
20.07 4 1jt0A QNA Rep, Mult 9,10,23,27,32,33
30.05 3 3aqtB RCO Rep, Mult 53,69,72,73,76,97,98,101,119
40.05 3 1jt0C QNA Rep, Mult 76,119,120,121,122,125,126
50.03 2 1rkwA PNT Rep, Mult 44,47,48,52,72,76,79,80,83,98,119,122,123
60.02 1 3dc7B MG Rep, Mult 142,143
70.02 1 3lxvN CO3 Rep, Mult 84,86
80.02 1 2i5jB GLC Rep, Mult 53,71
90.02 1 1j79B NCD Rep, Mult 129,136
100.02 1 4dlmA ZN Rep, Mult 77,126
110.02 1 2ivzA CA Rep, Mult 66,67
120.02 1 3d6aA MG Rep, Mult 109,110
130.02 1 1efkA NAD Rep, Mult 81,82
140.02 1 1c1yB CA Rep, Mult 86,88
150.02 1 3c9iE XE Rep, Mult 89,104
160.02 1 1ovrC MN Rep, Mult 67,71
170.02 1 3leeD B65 Rep, Mult 66,70,73,74,77,80,81,141,145
180.02 1 3zqlB QNA Rep, Mult 22,24,25,28,29

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
10.0602fhbA0.4965.000.0830.8733.2.1.41NA
20.0601kwgA0.4934.730.0780.8133.2.1.2371
30.0601uokA0.5154.690.0360.8403.2.1.10NA
40.0602qllA0.5094.280.0440.8002.4.1.173
50.0601ahpA0.5264.030.0590.8072.4.1.1NA
60.0602iz1B0.4934.390.0620.7601.1.1.44NA
70.0602gfiA0.4874.850.0630.8403.1.3.8NA
80.0601fa9A0.5194.220.0510.8202.4.1.1NA
90.0601rboB0.4863.780.0750.6934.1.1.39NA
100.0601yewB0.5113.830.0240.7331.14.13.2572
110.0601e1yA0.4165.380.0150.7932.4.1.1NA
120.0601fa2A0.4864.850.0430.8073.2.1.2NA
130.0602c4mC0.5174.120.0290.7932.4.1.173
140.0601svdA0.4784.070.0830.7004.1.1.39NA
150.0602weiA0.3595.120.0210.6532.7.1.17123
160.0603ikmD0.4894.760.0860.7602.7.7.7NA
170.0602fhcA0.4895.110.0490.8403.2.1.41NA
180.0601s46A0.4775.370.0790.8802.4.1.451
190.0602zf5Y0.4814.710.0740.7932.7.1.30NA

(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
00.310.9201.180.130.973bniA GO:0003677 GO:0006351 GO:0006355
10.230.7122.970.130.952qibA GO:0003677 GO:0003700 GO:0006351 GO:0006355
20.210.6973.160.120.923b6aA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677
30.180.6973.200.120.932genA GO:0003677 GO:0003700 GO:0006351 GO:0006355
40.160.7083.020.150.953mnlA GO:0000976 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0042803
50.150.7053.180.080.963c07A GO:0003677 GO:0006351 GO:0006355
60.140.6593.140.110.904hkuA GO:0003677 GO:0006351 GO:0006355
70.140.7493.040.060.963whcA GO:0003677 GO:0005737 GO:0006351 GO:0006355 GO:0006629 GO:0006631 GO:0016042
80.120.7172.870.130.933bjbB GO:0003677 GO:0006351 GO:0006355
90.120.6713.660.080.953zqgA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677 GO:0046872
100.120.6233.360.090.853vuqC GO:0003677 GO:0006351 GO:0006355
110.120.6913.330.080.944yzeA GO:0000976 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0045892
120.120.6793.090.080.903htaA GO:0003677 GO:0006351 GO:0006355
130.110.7113.080.090.932hxoA GO:0003677 GO:0006351 GO:0006355 GO:0045892
140.110.6473.630.080.953bhqA GO:0003677 GO:0006351 GO:0006355
150.110.7103.330.090.953bqyA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677
160.110.6783.550.050.972id6A GO:0003677 GO:0006351 GO:0006355
170.110.7013.280.100.953lhqA GO:0003677 GO:0003700 GO:0006351 GO:0006355
180.100.6833.210.140.935d18A GO:0003677 GO:0006351 GO:0006355
190.100.6983.260.110.954auxA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677 GO:0046872
200.100.6903.140.090.941sgmA GO:0003677 GO:0006351 GO:0006355
210.100.6863.300.090.953on4A GO:0003677 GO:0006351 GO:0006355
220.100.6913.380.060.942vprA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677 GO:0046872
230.100.6603.460.090.914pxiB GO:0003677 GO:0006351 GO:0006355
240.090.6044.020.070.932oerB GO:0003677 GO:0006351 GO:0006355
250.080.6593.520.070.911z0xA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677
260.070.6533.050.120.894jl3C GO:0003677 GO:0006351 GO:0006355
270.070.6473.610.080.932eh3A GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0046872
280.070.6683.350.070.893b81A GO:0003677 GO:0006351 GO:0006355
290.070.6643.490.080.913zqfA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677 GO:0046872
300.070.6473.150.070.892dg8B GO:0003677 GO:0006351 GO:0006355
310.070.6623.310.090.883vp5A GO:0003677 GO:0006351 GO:0006355 GO:0046872
320.070.6313.890.060.933vprA GO:0003677 GO:0006351 GO:0006355 GO:0042802
330.070.6493.630.120.933f1bA GO:0003677 GO:0006351 GO:0006355
340.070.6443.470.090.932hyjA GO:0003677 GO:0003700 GO:0006351 GO:0006355
350.070.6533.420.090.912zcnD GO:0003677 GO:0006351 GO:0006355
360.070.6763.110.120.923qbmA GO:0003677 GO:0003700 GO:0006351 GO:0006355
370.070.6653.160.120.935d1wD GO:0003677 GO:0006351 GO:0006355
380.070.6683.540.080.933p9tA GO:0003677 GO:0006351 GO:0006355
390.070.6213.560.100.893t6nA GO:0003677 GO:0003700 GO:0006351 GO:0006355
400.070.5973.930.070.912np3B GO:0003677 GO:0006351 GO:0006355
410.070.6203.480.050.874aciB GO:0000287 GO:0003677 GO:0006351 GO:0006355 GO:0046872
420.070.6593.340.130.923dcfA GO:0003677 GO:0006351 GO:0006355
430.070.6413.820.110.933he0C GO:0003677 GO:0006351 GO:0006355
440.070.6093.690.070.893geuA GO:0003677 GO:0006351 GO:0006355
450.070.6184.140.090.933colA GO:0003677 GO:0006351 GO:0006355
460.070.6413.680.090.914me9A GO:0003677 GO:0006351 GO:0006355
470.070.5713.420.160.792qwtA GO:0003677 GO:0006351 GO:0006355
480.070.6293.920.090.932fbqA GO:0000976 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0044212 GO:0045893 GO:0050714
490.070.6013.860.090.922dg7A GO:0003677 GO:0006351 GO:0006355
500.070.6183.990.100.943himB GO:0003677 GO:0006351 GO:0006355
510.070.5964.310.060.902ibdA GO:0003677 GO:0006351 GO:0006355
520.070.5973.530.090.842qkoB GO:0003677 GO:0006351 GO:0006355
530.070.6184.160.080.953nrgA GO:0003677 GO:0003700 GO:0006351 GO:0006355


Consensus prediction of GO terms
 
Molecular Function GO:0003700 GO:1990837 GO:0044212 GO:0042802 GO:0046983
GO-Score 0.47 0.31 0.31 0.31 0.31
Biological Processes GO:0006355 GO:0010629 GO:1903507 GO:0042221 GO:2000113
GO-Score 0.71 0.42 0.42 0.42 0.42
Cellular Component GO:0044444
GO-Score 0.31

(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.