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I-TASSER results for job id Rv1515c

[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
10.36 28 1ve3A SAM Rep, Mult 40,44,47,77,78,79,98,99,100,103,124,125,126,141,142,143,146
20.09 6 5dm2A 5D9 Rep, Mult 27,39,40,44,47,142,143,145,146,171,172,194,195,201,205,284,289
30.03 2 1d2hA SAH Rep, Mult 98,99,100,103,124,125,126,143,146
40.01 1 4fs8A CA Rep, Mult 26,77
50.01 1 3jwgA MG Rep, Mult 77,141
60.01 1 3ou7D 2HE Rep, Mult 19,22,31,32,146,193,203

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
10.2033lccA0.5473.410.1200.6582.1.1.-77,85,122
20.1473e05D0.4992.710.0770.5742.1.1.132142
30.0832ex4A0.5773.660.0650.7112.1.1.-51
40.0753hnrA0.5133.260.1090.6142.1.1.-NA
50.0741wznA0.5963.180.1240.7012.1.1.-139,145
60.0671ri1A0.5834.030.0930.7382.1.1.5677
70.0671f38A0.4892.950.0940.5742.1.1.-NA
80.0672pxxA0.5123.230.1480.6013.4.24.71NA
90.0673e05B0.4962.810.0760.5742.1.1.132NA
100.0671xcjA0.5274.160.0870.6812.1.1.2NA
110.0672cl5A0.4863.350.1600.5842.1.1.6NA
120.0663grzB0.4672.700.1150.5302.1.1.-NA
130.0663bwmA0.4863.360.1600.5842.1.1.6NA
140.0663gdhA0.4843.250.1200.5772.1.1.-NA
150.0603i58A0.5423.890.0700.6782.1.1.-NA
160.0601uirB0.5334.400.0700.6882.5.1.16122,124
170.0601kpiA0.5364.520.0780.7082.1.1.79NA
180.0602ip2A0.5363.840.0830.6642.1.1.-58
190.0601tpyA0.5364.080.0890.6782.1.1.79NA
200.0602h11B0.5433.450.1540.6582.1.1.6739,84
210.0601kphC0.5444.310.0750.6952.1.1.7924,28,78
220.0601bhjA0.5873.620.1210.7222.1.1.20NA
230.0601fp2A0.5353.870.1000.6642.1.1.150NA
240.0603bgdA0.5473.590.1230.6682.1.1.67NA
250.0603eppB0.5953.840.1070.7522.1.1.5677,82,145
260.0601l1eA0.5203.730.0990.6412.1.1.79NA
270.0602e5wA0.5193.920.0830.6482.5.1.1677,154
280.0601ej6A0.5244.100.0770.6642.7.7.5075,77,80,106
290.0602o06A0.5404.460.0820.7012.5.1.1625,77,148
300.0601ri5A0.5814.000.0890.7352.1.1.5677,82,145
310.0603g5tA0.5764.410.0900.7452.1.1.14578
320.0602vdwG0.6034.280.0770.7822.7.7.50NA
330.0601kpgA0.5253.940.0930.6542.1.1.79NA

(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
00.340.7961.800.140.865dm2A GO:0008168 GO:0016740 GO:0032259
10.200.5433.810.140.663mggB GO:0008168 GO:0016740 GO:0032259
20.180.5452.650.170.623dh0B GO:0005737 GO:0008757 GO:0032259 GO:0046872 GO:0051536 GO:0051539
30.160.5233.660.080.643g5lA
40.160.5063.420.140.603sm3A GO:0008152 GO:0008168 GO:0016740 GO:0032259 GO:0046872
50.150.5173.220.110.614ymgB GO:0008171 GO:0032259 GO:0046872 GO:0051536 GO:0051539
60.150.5453.100.090.643dtnA GO:0046872
70.150.5374.270.130.684iv8A GO:0000234 GO:0008152 GO:0008168 GO:0016740 GO:0032259 GO:0046872 GO:0051536 GO:0051539
80.150.5273.020.110.613jwgA GO:0001510 GO:0008168 GO:0008171 GO:0008173 GO:0016740 GO:0032259
90.140.5583.350.130.664kifB GO:0008168 GO:0016740 GO:0017000 GO:0032259
100.140.5703.520.140.694oqdC GO:0008168 GO:0008757 GO:0016740 GO:0017000 GO:0032259 GO:0042803
110.130.5703.660.110.694necB GO:0008168 GO:0016740 GO:0032259
120.130.5463.530.100.663bxoA GO:0008168 GO:0008757 GO:0016740 GO:0017000 GO:0032259 GO:0042803
130.130.4763.360.110.573cggA GO:0008168 GO:0016740 GO:0032259
140.120.5192.910.110.593jwhA GO:0001510 GO:0008171 GO:0008173
150.120.5763.680.130.694pneB GO:0008152 GO:0008168 GO:0016740 GO:0032259
160.100.5203.730.100.641l1eA GO:0005737 GO:0006629 GO:0008168 GO:0008610 GO:0008825 GO:0009405 GO:0016740 GO:0032259 GO:0042783 GO:0046500 GO:0052167 GO:0071768
170.100.5133.440.130.613l8dA GO:0008152 GO:0008168 GO:0016740 GO:0032259
180.070.4592.910.080.543i9fB GO:0008152 GO:0008168 GO:0032259 GO:0046872
190.070.5754.330.130.734mwzB GO:0008168 GO:0016740 GO:0032259 GO:0046872 GO:0051536 GO:0051539
200.070.5733.640.100.703d2lC GO:0008168 GO:0016740 GO:0032259
210.070.5543.600.130.664kdcA GO:0005829 GO:0006744 GO:0008168 GO:0008425 GO:0008689 GO:0008757 GO:0016740 GO:0032259 GO:0043431 GO:0061542 GO:0102004


Consensus prediction of GO terms
 
Molecular Function GO:0008168 GO:0051540 GO:0046872
GO-Score 0.55 0.36 0.31
Biological Processes GO:0032259
GO-Score 0.63
Cellular Component GO:0044424
GO-Score 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.