[Home] [Server] [About] [Statistics] [Annotation]

I-TASSER results for job id Rv2083

[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
10.06 3 2ckjC FES Rep, Mult 84,85,89,91,103,106,107
20.04 2 2ckjA FES Rep, Mult 81,82,83,84,86,88,91,93
30.04 2 3wubA ZN Rep, Mult 64,68
40.04 2 4il6H CLA Rep, Mult 35,39,42
50.04 2 1vdfB CL Rep, Mult 35,38
60.04 2 2ckjB FES Rep, Mult 162,164,166,167,169
70.02 1 1yklG DHB Rep, Mult 190,191
80.02 1 1c9uB CA Rep, Mult 190,191,289
90.02 1 1fbmD RTL Rep, Mult 28,35
100.02 1 2vqgA ZN Rep, Mult 57,61
110.02 1 3vh7E MG Rep, Mult 26,29
120.02 1 1cq1A CA Rep, Mult 180,190,191
130.02 1 3ucpA MG Rep, Mult 160,163,166
140.02 1 1yo8A CA Rep, Mult 244,246,253,255
150.02 1 3l36A DTR Rep, Mult 43,44
160.02 1 1aklA CA Rep, Mult 203,204,205,207,217,218,219,222
170.02 1 1satA CA Rep, Mult 259,260,261,263,284
180.02 1 3zvwC MG Rep, Mult 251,252
190.02 1 2z8xA CA Rep, Mult 169,170,171,178,179,180,183

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
10.0603b9jC0.3426.190.0160.5641.17.3.2,1.17.1.4NA
20.0601q16A0.3697.160.0630.6851.7.99.4NA
30.0603lxuX0.3396.710.0360.5893.4.14.10NA
40.0602np0A0.3596.270.0550.5923.4.24.69NA
50.0601fo4A0.3516.360.0180.5861.17.1.4NA
60.0602fy3A0.3456.550.0510.5862.3.1.6NA
70.0603cskA0.3406.760.0420.5893.4.14.4NA
80.0602occN0.3265.390.0380.4781.9.3.1147,153
90.0601jqnA0.3406.550.0180.5864.1.1.31NA
100.0601t3tA0.3436.560.0360.5836.3.5.355,59
110.0602vuaA0.2726.170.0340.4403.4.24.69NA
120.0602uv8G0.3486.740.0370.6052.3.1.86NA
130.0603ikmD0.3366.480.0510.5702.7.7.7150
140.0601m56A0.3365.670.0470.5101.9.3.1NA
150.0603hhsA0.3466.420.0270.5801.14.18.1NA
160.0602axqA0.3386.790.0540.5991.5.1.10NA
170.0601occA0.3345.650.0500.5001.9.3.159
180.0601gthA0.3617.200.0400.6811.3.1.2NA
190.0601t7nA0.3666.070.0410.5862.3.1.7NA

(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
00.060.3457.300.030.653aibC GO:0005576 GO:0005975 GO:0009250 GO:0016740 GO:0016757 GO:0046527 GO:0047849
10.060.3327.110.030.614aygA GO:0005975 GO:0009250 GO:0016740 GO:0016757 GO:0046527 GO:0046872 GO:0047849
20.060.3036.260.040.505d3qB GO:0000166 GO:0001917 GO:0002031 GO:0003924 GO:0005525 GO:0005737 GO:0005794 GO:0005856 GO:0005874 GO:0005886 GO:0006897 GO:0006898 GO:0007032 GO:0007605 GO:0008021 GO:0008022 GO:0008344 GO:0016787 GO:0019901 GO:0030117 GO:0031623 GO:0031749 GO:0032403 GO:0042802 GO:0043196 GO:0043209 GO:0043234 GO:0044822 GO:0045202 GO:0046983 GO:0048013 GO:0050998 GO:0051262 GO:0051932 GO:0070062 GO:0072583 GO:1901998 GO:1903423
30.060.3706.790.040.664amcA GO:0005975 GO:0009250 GO:0016740 GO:0016757 GO:0046527 GO:0046872 GO:0047849
40.060.2617.000.040.475do8B GO:0003824 GO:0005975
50.060.3197.260.040.613ttoA GO:0005975 GO:0009250 GO:0016740 GO:0016757 GO:0046527 GO:0046872 GO:0047849
60.060.2666.080.050.423k1dA GO:0003824 GO:0003844 GO:0004553 GO:0005886 GO:0005975 GO:0005977 GO:0005978 GO:0009250 GO:0016740 GO:0016757 GO:0040007 GO:0043169 GO:0045227
70.060.2756.760.040.472h0vA GO:0008127 GO:0016491 GO:0046872 GO:0051213 GO:0055114
80.060.2816.370.040.473ueqA GO:0003824 GO:0005576 GO:0005975 GO:0016740 GO:0016757 GO:0047669
90.060.2306.550.040.392bibA GO:0046872
100.060.2376.890.030.435e70B GO:0003824 GO:0003844 GO:0004553 GO:0005975 GO:0005977 GO:0005978 GO:0016740 GO:0016757 GO:0043169
110.060.2706.490.060.461jdaA GO:0003824 GO:0005576 GO:0005975 GO:0005983 GO:0008152 GO:0016787 GO:0016798 GO:0030246 GO:0033910 GO:0043169 GO:0046872 GO:2001070
120.060.2836.810.040.495e70C GO:0003824 GO:0003844 GO:0004553 GO:0005975 GO:0005977 GO:0005978 GO:0016740 GO:0016757 GO:0043169
130.060.2306.210.010.395a2aA GO:0003824 GO:0004556 GO:0005975 GO:0008152 GO:0016020 GO:0016021 GO:0016787 GO:0016798
140.060.2696.550.040.443bsgA GO:0003824 GO:0004556 GO:0005509 GO:0005576 GO:0005615 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0043169 GO:0046872
150.060.2327.220.040.443bh4A GO:0003824 GO:0004553 GO:0004556 GO:0005509 GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0046872
160.060.2247.190.020.411hvxA GO:0003824 GO:0004553 GO:0004556 GO:0005509 GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0046872
170.060.2556.990.060.474h8vA GO:0003824 GO:0005975 GO:0046872
180.060.2506.900.050.454z7cA GO:0000166 GO:0004163 GO:0005524 GO:0005829 GO:0006629 GO:0008299 GO:0016829 GO:0016831 GO:0019287


Consensus prediction of GO terms
 
Molecular Function GO:0016758
GO-Score 0.36
Biological Processes GO:0033692 GO:0006073
GO-Score 0.36 0.36
Cellular Component GO:0008021 GO:0005794 GO:0043196 GO:0005874 GO:0005886 GO:0030117 GO:0001917 GO:0070062 GO:0043209
GO-Score 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06

(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.