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I-TASSER results for job id Rv0488

[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
10.09 5 4hfdE MBR Rep, Mult 65,66,106,109
20.07 4 4xk8L CLA Rep, Mult 40,72
30.06 3 3zuxA PTY Rep, Mult 34,37,41,59,66,105,109,115
40.04 2 1rsvA AZI Rep, Mult 72,175,178
50.04 2 1lghA BCL Rep, Mult 110,111,116
60.04 2 1uryA XE Rep, Mult 72,76,167,170,174
70.02 1 4ca5A FUC Rep, Mult 60,61,121
80.02 1 3nhjB FAD Rep, Mult 138,171
90.02 1 3fk7A 4DM Rep, Mult 166,170
100.02 1 1mx1F THA Rep, Mult 15,16,70,120,121,178
110.02 1 4o6mB MPG Rep, Mult 38,39
120.02 1 2wieA CVM Rep, Mult 40,44
130.02 1 1rsrB UUU Rep, Mult 32,69,73,102,105
140.02 1 1zoyC EPH Rep, Mult 44,47
150.02 1 2pnqA MG Rep, Mult 36,37

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
10.0601h16A0.3576.400.0370.7312.3.1.54NA
20.0602vuxB0.4805.230.0890.8011.17.4.1NA
30.0601z1lA0.3945.700.0200.6523.1.4.1746,56
40.0601mhyB0.4875.410.1130.8311.14.13.25NA
50.0602j2fA0.4914.770.0450.7511.14.19.2,1.14.99.6NA
60.0603b8eC0.4615.190.0610.7463.6.3.939,67
70.0603b8cA0.4665.500.0720.7863.6.3.6NA
80.0601fo4A0.4455.360.0380.7311.17.1.4NA
90.0601h0nA0.4905.280.0750.8261.17.4.1NA
100.0601sojL0.4455.470.0810.7413.1.4.17155
110.0603b9jI0.2724.720.0570.4281.17.1.4,1.17.3.262
120.0601fziA0.4785.420.0400.8211.14.13.25NA
130.0603b9jJ0.3765.190.0600.5971.17.1.4,1.17.3.2173
140.0603b8eA0.4645.270.0500.7563.6.3.9NA
150.0603b9jC0.4405.600.0750.7561.17.3.2,1.17.1.4NA
160.0602e1qA0.4495.490.0510.7461.17.3.2,1.17.1.4NA
170.0601qi9B0.4844.930.0620.7561.11.1.10NA
180.0602bq1I0.5105.220.0580.8211.17.4.1NA
190.0601smsA0.5195.210.0580.8411.17.4.1NA

(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
00.070.5824.670.090.874n7wA GO:0016020 GO:0016021
10.070.6034.400.070.894atvA GO:0005886 GO:0006810 GO:0006811 GO:0006814 GO:0006885 GO:0015081 GO:0015297 GO:0015491 GO:0015992 GO:0016020 GO:0016021 GO:0035725 GO:0055085 GO:0098655
20.070.5814.690.110.873zuxA GO:0016020 GO:0016021
30.070.5255.100.040.864mtjA GO:0003824 GO:0008152
40.060.3875.850.060.683owaC GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
50.060.5994.660.080.894cz8A GO:0006810 GO:0006812 GO:0015299 GO:0016020 GO:0016021 GO:0055085 GO:1902600
60.060.3875.770.040.685i2gA GO:0003824 GO:0008152
70.060.5974.530.110.864bwzA GO:0006810 GO:0006812 GO:0015299 GO:0016020 GO:0016021 GO:0046872 GO:0055085 GO:1902600
80.060.3025.870.030.553zq5A GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0005524 GO:0005622 GO:0006355 GO:0007165 GO:0009584 GO:0009585 GO:0009639 GO:0009881 GO:0009883 GO:0016301 GO:0016310 GO:0016740 GO:0018106 GO:0018298 GO:0023014 GO:0042802 GO:0046777 GO:0050896
90.060.4014.040.120.574czbB GO:0005886 GO:0006810 GO:0006811 GO:0006812 GO:0006814 GO:0015297 GO:0015299 GO:0016020 GO:0016021 GO:0042802 GO:0055085 GO:1902600
100.060.3546.050.040.701cm5A GO:0003824 GO:0005737 GO:0005829 GO:0005975 GO:0006006 GO:0006567 GO:0008152 GO:0008861 GO:0016020 GO:0016740 GO:0016746
110.060.5294.690.050.812f3oA GO:0003824 GO:0008152 GO:0016829
120.060.3515.310.040.583ug4C GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0046373 GO:0046556
130.060.5185.010.060.842yajC GO:0003824 GO:0008152 GO:0016829 GO:0043722
140.060.3515.260.050.571u0uA GO:0003824 GO:0005737 GO:0008152 GO:0009058 GO:0016740 GO:0016746 GO:0016747 GO:0050198
150.060.3885.950.050.695i2aB GO:0003824 GO:0008152
160.060.2835.700.050.502gauA GO:0003677 GO:0006351 GO:0006355
170.060.3194.790.060.512k60A GO:0002020 GO:0002115 GO:0005246 GO:0005509 GO:0005513 GO:0005737 GO:0005783 GO:0005789 GO:0005856 GO:0005874 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006816 GO:0006874 GO:0016020 GO:0016021 GO:0016529 GO:0030176 GO:0032237 GO:0032541 GO:0033017 GO:0042802 GO:0046872 GO:0051010 GO:0051924 GO:0070166 GO:1903779
180.060.3115.830.030.541pv9B GO:0005737 GO:0006508 GO:0008233 GO:0008237 GO:0016787 GO:0016805 GO:0046872 GO:0102009


Consensus prediction of GO terms
 
Molecular Function GO:0015491 GO:0015081 GO:0003995 GO:0050660
GO-Score 0.07 0.07 0.07 0.07
Biological Processes GO:0015992 GO:0035725 GO:0006885 GO:0055114
GO-Score 0.07 0.07 0.07 0.07
Cellular Component GO:0016021 GO:0005886
GO-Score 0.19 0.07

(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.