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I-TASSER results for job id Rv0036c

[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
10.56 7 1rxqD GLU Rep, Mult 39,47,80,138,142
20.15 3 2rd9A NI Rep, Mult 43,142,146

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
10.0602fhbA0.4095.940.0660.6813.2.1.41NA
20.0603i39X0.4625.290.0720.7081.2.99.2NA
30.0602nyaF0.4266.120.0380.7511.7.99.4134
40.0601occA0.4135.680.0410.6541.9.3.1225
50.0601ogyI0.4326.070.0470.7511.7.99.4165
60.0602xaaA0.4135.870.0640.6811.1.1.117
70.0603ce6A0.4105.500.0700.6343.3.1.1212
80.0601jqkF0.4665.450.0680.7201.2.99.2NA
90.0601uufA0.4055.940.0410.6811.-.-.-142
100.0603h6oC0.4135.480.0520.6542.7.1.40NA
110.0601h0hA0.4566.010.0380.7781.2.1.2NA
120.0601cdoA0.4076.140.0500.7041.1.1.1NA
130.0603i4cC0.3755.840.0840.6191.1.1.1NA
140.0601ry2A0.4146.060.0180.7046.2.1.146
150.0601bf2A0.4036.280.0510.7163.2.1.68NA
160.0602g50D0.4045.620.0430.6382.7.1.40211
170.0602eerB0.4106.030.0370.6971.1.1.124
180.0602nyaA0.4265.970.0340.7321.7.99.4NA
190.0602fhcA0.4106.110.0600.7043.2.1.4113,162,214

(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
00.520.8641.330.150.902nsfA GO:0046872
10.070.4762.980.120.571rxqB GO:0005737 GO:0008270 GO:0016787 GO:0046872
20.070.5145.630.090.794x8bA GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0046872 GO:0052699 GO:0055114
30.070.4902.810.080.575cogB GO:0005634 GO:0005737 GO:0006312
40.060.2756.480.040.512q17E GO:0046872
50.060.2916.080.070.505dn1A GO:0000105 GO:0000162 GO:0003824 GO:0003949 GO:0004640 GO:0005622 GO:0005737 GO:0008152 GO:0008652 GO:0009073 GO:0016853
60.060.3385.720.070.552akzA GO:0000015 GO:0000287 GO:0001917 GO:0004634 GO:0005615 GO:0005622 GO:0005737 GO:0005829 GO:0005886 GO:0006094 GO:0006096 GO:0016020 GO:0016829 GO:0043025 GO:0043204 GO:0043209 GO:0046872 GO:0061621 GO:0070062
70.060.2915.830.040.483amgB GO:0004553 GO:0005576 GO:0005975 GO:0006073 GO:0008152 GO:0008422 GO:0009251 GO:0009986 GO:0016787 GO:0016798
80.060.3316.270.010.582x7gA GO:0000166 GO:0000245 GO:0000287 GO:0001525 GO:0004672 GO:0004674 GO:0005524 GO:0005634 GO:0005654 GO:0005730 GO:0005737 GO:0006397 GO:0006468 GO:0008284 GO:0008380 GO:0010628 GO:0016301 GO:0016310 GO:0016740 GO:0030154 GO:0035063 GO:0035556 GO:0043525 GO:0044822 GO:0045070 GO:0045071 GO:0045087 GO:0045787 GO:0048024 GO:0071889
90.060.3176.090.050.543b8gA GO:0004042 GO:0005737 GO:0006526 GO:0008080 GO:0008652 GO:0016740 GO:0016746
100.060.3415.580.030.543fwnA GO:0004616 GO:0005829 GO:0006098 GO:0016491 GO:0019521 GO:0042802 GO:0042803 GO:0055114
110.060.2756.580.070.511y1hX GO:0005783 GO:0005788 GO:0006687 GO:0016491 GO:0042803 GO:0043687 GO:0046872 GO:0055114
120.060.2435.320.030.382pqgA GO:0005737 GO:0006952 GO:0016787 GO:0017148 GO:0030598
130.060.2726.420.020.484a82A GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0042626 GO:0055085
140.060.2826.130.050.494hkaA GO:0004833 GO:0006569 GO:0006727 GO:0016491 GO:0019441 GO:0019442 GO:0020037 GO:0046872 GO:0048072 GO:0051213 GO:0055114 GO:0070189 GO:1901216
150.060.2756.730.060.521y4jB GO:0005783 GO:0005788 GO:0043687 GO:0046872
160.060.2636.690.050.492y3cA GO:0046872
170.060.2426.270.030.424meeA GO:0005576 GO:0007155 GO:0009279 GO:0009405 GO:0009986 GO:0016020 GO:0016021 GO:0019867 GO:0042597
180.060.2666.120.050.452pqiB GO:0006952 GO:0016787 GO:0017148 GO:0030598
190.060.2315.830.080.394gh8A GO:0004146 GO:0005829 GO:0006545 GO:0006730 GO:0009165 GO:0016491 GO:0031427 GO:0042493 GO:0046654 GO:0046677 GO:0050661 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0046872
GO-Score 0.61
Biological Processes GO:0055114 GO:0052699 GO:0006312
GO-Score 0.07 0.07 0.07
Cellular Component GO:0005737 GO:0005634
GO-Score 0.13 0.07

(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.