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I-TASSER results for job id Rv1196

[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
10.12 4 1pprM PID Rep, Mult 25,29
20.06 2 4g7hD MG Rep, Mult 32,33,35
30.06 2 5ezmA MPG Rep, Mult 29,89
40.06 2 2cl8A BGC Rep, Mult 37,81
50.03 1 2wieA CVM Rep, Mult 97,101
60.03 1 2g38B MN Rep, Mult 150,153,154
70.03 1 3ar2A NA Rep, Mult 65,66,68,69
80.03 1 1l4aB III Rep, Mult 250,251,254,258,261,265
90.03 1 1shkA MG Rep, Mult 147,150
100.03 1 4zttF O Rep, Mult 32,35,84,87

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
10.0602w00B0.3036.240.0460.4603.1.21.3105
20.0602nztA0.3326.880.0370.5522.7.1.144
30.0603gtgB0.2986.670.0390.4882.7.7.6NA
40.0601j09A0.2726.370.0440.4276.1.1.17NA
50.0601ti2A0.3056.850.0340.5041.97.1.2NA
60.0602ivfA0.2886.550.0380.4601.17.99.2NA
70.0603c66A0.2836.220.0600.4452.7.7.19NA
80.0602qf7A0.3167.160.0420.5456.4.1.1NA
90.0603b8eA0.3536.340.0230.5523.6.3.9NA
100.0601jqnA0.2956.650.0320.4734.1.1.31NA
110.0602vumB0.2637.040.0180.4502.7.7.6NA
120.0601vlbA0.2947.020.0570.5041.2.99.7NA
130.0601ti6A0.3046.750.0310.4991.97.1.2NA
140.0602cseW0.3026.640.0440.4833.6.4.13NA
150.0603g61A0.3996.560.0570.6343.6.3.44NA
160.0601ii0B0.2955.760.0430.4273.6.3.16NA
170.0602d33A0.2926.730.0370.4786.3.2.2NA
180.0601e6yA0.2886.850.0550.4762.8.4.1NA
190.0601n1hA0.3026.980.0540.5062.7.7.4890,166

(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
00.060.3456.320.040.544m1mA GO:0000086 GO:0000166 GO:0002481 GO:0002485 GO:0002489 GO:0002591 GO:0005524 GO:0005886 GO:0006810 GO:0006855 GO:0008559 GO:0009986 GO:0015893 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0042623 GO:0042626 GO:0042908 GO:0046581 GO:0055085 GO:0070062 GO:0072089
10.060.3006.620.040.493b5xA GO:0000166 GO:0005319 GO:0005524 GO:0005886 GO:0006810 GO:0006869 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0034040 GO:0042626 GO:0043190 GO:0055085
20.060.3326.410.060.524f4cA GO:0000166 GO:0005524 GO:0006810 GO:0006855 GO:0008559 GO:0010038 GO:0015562 GO:0016020 GO:0016021 GO:0016324 GO:0016787 GO:0016887 GO:0042626 GO:0042908 GO:0045087 GO:0050829 GO:0055085 GO:0093002
30.060.2926.360.030.454q4aA GO:0000166 GO:0005524 GO:0006810 GO:0006869 GO:0016020 GO:0016021 GO:0016887 GO:0034040 GO:0042626 GO:0046872 GO:0055085
40.060.2946.520.030.474pl0B GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0016887 GO:0030153 GO:0042626 GO:0043213 GO:0055085
50.060.2846.420.030.443qf4B GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0016020 GO:0016021 GO:0016887 GO:0042626 GO:0055085
60.060.3156.340.040.493wmgA GO:0000166 GO:0005524 GO:0006810 GO:0016020 GO:0016021 GO:0016887 GO:0042626 GO:0055085
70.060.2716.780.030.453b5wA GO:0000166 GO:0005319 GO:0005524 GO:0005886 GO:0006810 GO:0006869 GO:0008144 GO:0008289 GO:0015437 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0034040 GO:0042626 GO:0043190 GO:0055085 GO:1901264
80.060.2776.930.030.464a82A GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0042626 GO:0055085
90.060.2696.400.050.423ux8A GO:0000166 GO:0003677 GO:0003824 GO:0004518 GO:0005524 GO:0005737 GO:0006281 GO:0006289 GO:0006974 GO:0008270 GO:0009380 GO:0009381 GO:0009432 GO:0016887 GO:0046872 GO:0090305
100.060.2296.460.040.363pihA GO:0000166 GO:0003677 GO:0003824 GO:0004518 GO:0005524 GO:0005737 GO:0006281 GO:0006289 GO:0006974 GO:0008270 GO:0009380 GO:0009381 GO:0009432 GO:0016887 GO:0046872 GO:0090305
110.060.2756.470.040.435c73A GO:0000166 GO:0005524 GO:0006810 GO:0016021 GO:0016887 GO:0042626 GO:0055085
120.060.2607.090.030.444ry2A GO:0005524 GO:0006508 GO:0006810 GO:0008233 GO:0008234 GO:0016020 GO:0016021 GO:0016887 GO:0022885 GO:0042626 GO:0043213 GO:0055085
130.060.2366.880.050.393j5sD GO:0000049 GO:0000166 GO:0003723 GO:0005524 GO:0005737 GO:0006412 GO:0006417 GO:0016887 GO:0019843 GO:0043022 GO:0045900
140.060.2287.020.070.392vf8B GO:0000166 GO:0003677 GO:0004518 GO:0005524 GO:0005737 GO:0006281 GO:0006289 GO:0006974 GO:0009380 GO:0009381 GO:0016887 GO:0046872 GO:0090305
150.060.2017.290.030.343fxgA GO:0003824 GO:0008152 GO:0046872
160.060.2166.770.030.353j9tP GO:0000221 GO:0000329 GO:0005773 GO:0005774 GO:0006810 GO:0006811 GO:0007035 GO:0015991 GO:0015992 GO:0016020 GO:0016820 GO:0046961
170.060.2127.130.030.363ozxB GO:0000054 GO:0000166 GO:0005506 GO:0005524 GO:0005623 GO:0005852 GO:0006413 GO:0006415 GO:0016887 GO:0043024
180.060.2316.630.080.373uwxA GO:0000166 GO:0003677 GO:0003824 GO:0004518 GO:0005524 GO:0005737 GO:0006281 GO:0006289 GO:0006974 GO:0008270 GO:0009380 GO:0009381 GO:0009432 GO:0016887 GO:0046872 GO:0090305


Consensus prediction of GO terms
 
Molecular Function GO:0032550 GO:0035639 GO:0043492 GO:0032559 GO:0015405 GO:0016820
GO-Score 0.56 0.56 0.56 0.56 0.56 0.56
Biological Processes GO:0044765 GO:0044763
GO-Score 0.56 0.56
Cellular Component GO:0031224 GO:0071944
GO-Score 0.45 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.