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

I-TASSER results for job id Rv0615

[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
10.22 48 1sofH HEM Rep, Mult 34,37,38,41,59,63,66,67
20.08 17 3qvdA FE Rep, Mult 33,36,65
30.05 10 4uxzC 79M Rep, Mult 37,40,41,44
40.04 10 2xquE CVM Rep, Mult 29,32,33,36
50.03 7 3wmn2 BCL Rep, Mult 42,46
60.03 7 4fbyX CLA Rep, Mult 31,32,35,39
70.03 7 1brrC ARC Rep, Mult 2,9,10,41
80.03 6 3dk4A GSH Rep, Mult 39,42,43
90.01 2 4zzcA XE Rep, Mult 2,5,41,44
100.01 3 3ze3A 78N Rep, Mult 13,17,26
110.00 1 2q9eB MTN Rep, Mult 9,13,16,31,38
120.00 1 3dezA SO4 Rep, Mult 69,73
130.00 1 1u8vC FAD Rep, Mult 32,64,65,67
140.00 1 3a7kA CL Rep, Mult 24,27
150.00 1 3d1lB MPR Rep, Mult 32,51,65
160.00 1 1izlB CLA Rep, Mult 4,6,10
170.00 1 1oroA SO4 Rep, Mult 73,77

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
10.0602e9fB0.5802.730.2030.8504.3.2.1NA
20.0603i9wA0.5742.320.0390.7752.7.13.37,30,38
30.0601k04A0.5922.370.1170.8382.7.10.258,61,67,69
40.0603jz4A0.5743.780.0750.9251.2.1.1665
50.0603d4sA0.6113.560.1040.9253.2.1.1758
60.0601t90D0.5793.720.1030.9121.2.1.276
70.0601jswB0.5842.760.0630.8254.3.1.1NA
80.0603djlA0.5813.550.0630.9751.3.99.-NA
90.0603gtdA0.5852.720.0380.8254.2.1.2NA
100.0601jtnA0.3564.610.0870.7503.2.1.17NA
110.0603cf4A0.6082.680.0910.8501.2.99.2NA
120.0601siqA0.5742.750.0630.8501.3.99.736
130.0603ii9C0.5882.840.0750.8631.3.99.738
140.0602fenD0.5832.640.0760.8255.5.1.2NA
150.0603c20B0.6032.740.0900.8752.7.2.411
160.0602g2dA0.5932.330.0800.8002.5.1.17NA
170.0603ek1A0.5733.730.1010.9251.2.1.16NA
180.0602z8yD0.6372.140.0260.8251.2.7.4,1.2.99.261
190.0602wpnB0.5773.090.0380.8381.12.7.267

(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
00.100.4613.350.100.764iwbA GO:0044780
10.100.5503.380.110.841jqiA GO:0000062 GO:0003995 GO:0004085 GO:0005739 GO:0005759 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0009055 GO:0016491 GO:0016627 GO:0031966 GO:0033539 GO:0042594 GO:0046359 GO:0050660 GO:0051289 GO:0051384 GO:0055088 GO:0055114
20.090.5592.730.040.853pfdC GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
30.070.4813.700.080.812ebaA GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
40.070.6042.570.060.855iduC GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
50.070.5652.490.090.802z1qB GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
60.070.5253.580.080.902uxwA GO:0000062 GO:0001659 GO:0003995 GO:0004466 GO:0005634 GO:0005730 GO:0005737 GO:0005739 GO:0005743 GO:0005759 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0009055 GO:0015980 GO:0016020 GO:0016491 GO:0016627 GO:0017099 GO:0030855 GO:0033539 GO:0036498 GO:0042645 GO:0042760 GO:0045717 GO:0046322 GO:0050660 GO:0052890 GO:0055088 GO:0055114 GO:0090181
70.070.5562.700.110.824irnA GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
80.070.5462.780.130.843r7kA GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
90.070.5332.920.100.843mddA GO:0000062 GO:0001889 GO:0003995 GO:0005739 GO:0005759 GO:0005777 GO:0005978 GO:0006082 GO:0006111 GO:0006629 GO:0006631 GO:0006635 GO:0007507 GO:0008152 GO:0009055 GO:0009409 GO:0009437 GO:0009791 GO:0016491 GO:0016627 GO:0019254 GO:0033539 GO:0042594 GO:0050660 GO:0051791 GO:0052890 GO:0055007 GO:0055088 GO:0055114 GO:0070991
100.070.4863.650.040.853owaC GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
110.070.5482.550.090.821ukwA GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
120.070.5932.680.140.843nf4A GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
130.070.6012.600.070.855jscA GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
140.070.5742.700.040.842ix6A GO:0000062 GO:0003995 GO:0003997 GO:0005777 GO:0005829 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0009055 GO:0009514 GO:0009793 GO:0016491 GO:0016627 GO:0033539 GO:0046459 GO:0050660 GO:0052890 GO:0055088 GO:0055114
150.070.5452.680.090.822pg0A GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
160.070.5452.800.140.824m9aB GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
170.070.5163.280.140.823mpiC GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0019439 GO:0050660 GO:0055114
180.070.5712.770.060.852r0mA GO:0000062 GO:0003995 GO:0004361 GO:0005739 GO:0005759 GO:0006554 GO:0006568 GO:0006637 GO:0008152 GO:0009055 GO:0016491 GO:0016627 GO:0019395 GO:0033539 GO:0046949 GO:0050660 GO:0052890 GO:0055088 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0016627 GO:0050662 GO:0000166
GO-Score 0.59 0.59 0.59
Biological Processes GO:0044710
GO-Score 0.59
Cellular Component GO:0005759 GO:0031966
GO-Score 0.10 0.10

(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.