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I-TASSER results for job id Rv2619c

[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
10.35 86 3al6D AKG Rep, Mult 26,42,50,53,55,59,61,68,92,94,104,106
20.23 54 2vqaA MN Rep, Mult 53,55,59,92
30.00 1 1zzbA S0H Rep, Mult 26,28,53,55,92

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
10.0953elnA0.7342.840.1740.9491.13.11.2053,61
20.0831zvfA0.6652.830.1160.8721.13.11.653,56
30.0761fi2A0.6952.890.1350.8721.2.3.4NA
40.0752eteA0.6953.120.1360.8971.2.3.4NA
50.0661yfxA0.6752.630.1610.8631.13.11.6NA
60.0603balD0.6823.000.0990.8721.13.11.50105
70.0601fmd20.5333.200.0940.7353.4.22.46NA
80.0602ixhA0.5722.540.0750.6845.1.3.1353,88,92
90.0602qnkA0.6962.820.1300.9231.13.11.664,80
100.0601x8eA0.6943.110.1040.8975.3.1.985,104
110.0603cl4A0.5303.470.0430.7613.1.1.5385,89
120.0601pmiA0.6942.490.1110.8725.3.1.8NA
130.0602yu1A0.7413.240.1030.9661.14.11.27NA
140.0601unbA0.6383.330.1130.8971.14.20.1NA
150.0602ilmA0.7062.860.1030.8891.14.11.1652
160.0603eqeA0.7332.450.1320.9061.13.11.2053,63,87,101
170.0601bk0A0.6553.240.0860.9231.21.3.1NA
180.0603lm8A0.5683.430.0510.8292.7.6.292,102
190.0601qwrA0.6183.060.0870.8295.3.1.8NA
200.0601uofA0.5833.440.1100.8381.14.20.1NA
210.0603bu7B0.7602.660.1370.9571.13.11.473
220.0602a1xA0.6453.610.0700.9491.14.11.1848
230.0603f93A0.5674.090.0520.8723.2.1.-83
240.0601h1iB0.6983.220.1370.9231.13.11.24NA

(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
00.420.6672.630.110.821o4tA GO:0030145 GO:0033609 GO:0042802 GO:0042803 GO:0046564 GO:0046872
10.280.7252.480.160.914b29A GO:0046872 GO:0047869
20.280.7822.510.140.963nl1A GO:0046872 GO:0051213 GO:0055114
30.250.6892.650.130.851lr5A GO:0004872 GO:0005783 GO:0005788 GO:0008270 GO:0009734 GO:0010011 GO:0046872
40.220.6832.560.100.833h50A GO:0046872
50.210.6452.460.120.803jzvA GO:0046872
60.190.6632.870.140.853kgzA GO:0046872
70.180.5034.010.130.761zrrA GO:0005506 GO:0008652 GO:0009086 GO:0010308 GO:0010309 GO:0016151 GO:0016491 GO:0019284 GO:0019509 GO:0046872 GO:0051213 GO:0055114
80.160.6432.710.110.833ht2A GO:0016301 GO:0016310 GO:0046872
90.140.7602.660.140.963bu7B GO:0006725 GO:0016491 GO:0046872 GO:0047922 GO:0051213 GO:0055114
100.110.7612.730.120.972d40A GO:0046872 GO:0051213 GO:0055114
110.100.7022.820.130.932qnkA GO:0000334 GO:0005506 GO:0005737 GO:0005829 GO:0006569 GO:0008198 GO:0009055 GO:0009435 GO:0010043 GO:0016491 GO:0019363 GO:0019805 GO:0034354 GO:0043420 GO:0046686 GO:0046872 GO:0046874 GO:0051213 GO:0055114 GO:0070050 GO:0070062
120.090.7152.960.110.914metA GO:0005737 GO:0016829 GO:0016831 GO:0030288 GO:0033609 GO:0045735 GO:0046564 GO:0046872
130.090.7122.860.130.933fe5A GO:0000334 GO:0005506 GO:0005737 GO:0005829 GO:0006569 GO:0008198 GO:0009435 GO:0010043 GO:0016491 GO:0019363 GO:0019805 GO:0034354 GO:0043420 GO:0046686 GO:0046872 GO:0046874 GO:0051213 GO:0055114 GO:0070050 GO:0070062
140.090.7112.850.130.922h0vA GO:0008127 GO:0016491 GO:0046872 GO:0051213 GO:0055114
150.080.6252.840.070.821qwrA GO:0004476 GO:0005975 GO:0008270 GO:0016853 GO:0046872
160.070.7012.530.100.883h9aA GO:0005506 GO:0005737 GO:0016853 GO:0016863 GO:0017000 GO:0046872 GO:0050897
170.070.6652.830.120.871zvfA GO:0000334 GO:0005506 GO:0005634 GO:0005737 GO:0006569 GO:0008198 GO:0009435 GO:0016491 GO:0019363 GO:0019805 GO:0034354 GO:0043420 GO:0046872 GO:0046874 GO:0051213 GO:0055114
180.070.7492.820.110.964qmaA GO:0005506 GO:0016702 GO:0046872 GO:0051213 GO:0055114
190.070.5263.170.100.704qgnA GO:0005506 GO:0005634 GO:0005737 GO:0005829 GO:0005886 GO:0008652 GO:0009086 GO:0010309 GO:0016020 GO:0016491 GO:0019509 GO:0046872 GO:0051213 GO:0055114
200.070.5353.460.100.754qglA GO:0005506 GO:0008652 GO:0009086 GO:0010308 GO:0010309 GO:0016151 GO:0016491 GO:0016701 GO:0019284 GO:0019509 GO:0046872 GO:0051213 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0016846 GO:0016491 GO:0060089 GO:0042562 GO:0030145 GO:0046564 GO:0042803
GO-Score 0.56 0.55 0.50 0.50 0.42 0.42 0.42
Biological Processes GO:0009755 GO:0071365 GO:0033609
GO-Score 0.50 0.50 0.42
Cellular Component GO:0070013 GO:0044432
GO-Score 0.50 0.50

(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.