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

I-TASSER results for job id Rv2079

[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 4 2ckjD FES Rep, Mult 574,575,577,579,580,581,582,584,590
20.06 4 1fo4A FES Rep, Mult 303,304,484,485,486,497,499
30.05 3 1ea0A F3S Rep, Mult 446,447,448,450,451,452,453,464
40.03 2 1dmrA O Rep, Mult 412,460
50.03 2 5d92A 8K6 Rep, Mult 81,84,88
60.02 1 3ovnA MPV Rep, Mult 462,466
70.02 1 3np5A CA Rep, Mult 185,188
80.02 1 2qtsC MAL Rep, Mult 89,93
90.02 1 1hjsA EPE Rep, Mult 409,415,422
100.02 1 3or3A CA Rep, Mult 592,593
110.02 1 2bf0X CA Rep, Mult 134,137
120.02 1 1utzA PF3 Rep, Mult 572,573
130.02 1 3iovA CA Rep, Mult 97,101
140.02 1 2hl6A CXS Rep, Mult 323,372,459,460,572,591,592
150.02 1 1oczB HEA Rep, Mult 98,130
160.02 1 1y10C CA Rep, Mult 411,413
170.02 1 2zo4A ZN Rep, Mult 459,476,572,595
180.02 1 3eubS FES Rep, Mult 424,425,442,443,444,445,447
190.02 1 4fhvA MG Rep, Mult 462,463,479
200.02 1 1jwlA NUC Rep, Mult 265,269

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
10.0602gbcA0.3117.850.0400.4943.4.14.5,3.4.15.5NA
20.0601ofdA0.3558.150.0450.5821.4.7.1NA
30.0603cmmC0.3208.130.0520.5236.3.2.19249
40.0601fa9A0.3287.780.0490.5232.4.1.1NA
50.0602pdaA0.3247.880.0390.5181.2.7.1353,423
60.0601n1hA0.3248.270.0560.5302.7.7.48536
70.0601llwA0.3548.270.0550.5881.4.7.1NA
80.0602d5lA0.3167.830.0430.5033.4.14.-NA
90.0601ahpA0.3288.130.0440.5372.4.1.1NA
100.0601vlbA0.3058.640.0230.5201.2.99.7251
110.0603b9jC0.2438.690.0340.4161.17.3.2,1.17.1.4NA
120.0601dgjA0.3168.570.0550.5381.2.-.-266
130.0601bxrA0.3368.410.0610.5726.3.5.559
140.0601orvA0.3348.000.0370.5403.4.14.5NA
150.0601e1yA0.3198.160.0290.5202.4.1.1NA
160.0603b9jJ0.1946.150.0710.2651.17.1.4,1.17.3.2259,269
170.0602qllA0.3148.170.0380.5142.4.1.1NA
180.0602cqsA0.3397.990.0440.5462.4.1.20NA
190.0603ffzA0.3738.130.0520.6073.4.24.69NA

(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
00.210.7662.830.100.833eb7A GO:0005102 GO:0006952 GO:0009405 GO:0030435
10.200.7413.230.090.821ji6A GO:0005102 GO:0006952 GO:0009405 GO:0030435
20.130.7443.110.100.821dlcA GO:0005102 GO:0006952 GO:0009405 GO:0030435
30.120.7183.220.100.791ciyA GO:0005102 GO:0006952 GO:0009405 GO:0030435
40.110.7053.300.100.784w8jA GO:0005102 GO:0006952 GO:0009405 GO:0030435
50.110.7123.840.070.812c9kA GO:0005102 GO:0006952 GO:0009405 GO:0030435
60.100.6884.230.070.814moaA GO:0005102 GO:0006952 GO:0009405 GO:0030435
70.070.6384.740.080.771i5pA GO:0005102 GO:0006952 GO:0009405 GO:0030435
80.070.5804.700.080.704d8mA GO:0009405 GO:0030435
90.070.4883.960.080.573x0uA GO:0009405
100.060.2136.310.060.304bvkB GO:0016787
110.060.2067.300.030.323odpA GO:0005975 GO:0016853 GO:0030246
120.060.1746.180.050.243o38A GO:0004316 GO:0016491 GO:0055114 GO:0102132
130.060.1786.470.050.254p4oA GO:0003677 GO:0003887 GO:0005634 GO:0006281 GO:0034061 GO:0071897
140.060.2016.560.020.291g6oA GO:0000166 GO:0005524 GO:0005737 GO:0006810 GO:0009405
150.060.1596.630.040.234k3vB GO:0006810 GO:0007155 GO:0030001 GO:0046872
160.060.1616.130.030.221nlzC GO:0000166 GO:0005524 GO:0005737 GO:0006810 GO:0009405
170.060.1433.720.030.161yo7A GO:0006351 GO:0006355
180.060.1365.790.040.182hhiA GO:0005576 GO:0005618 GO:0009267


Consensus prediction of GO terms
 
Molecular Function GO:0005102
GO-Score 0.57
Biological Processes GO:0009405 GO:0030435 GO:0006952
GO-Score 0.57 0.57 0.57
Cellular Component
GO-Score

(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.