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I-TASSER results for job id Rv1025

[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
10.14 9 1s5lD FE Rep, Mult 85,115
20.08 5 1rpwB DID Rep, Mult 59,63,66,111,115,136,139
30.06 4 3frqA ERY Rep, Mult 3,7,63,66,81,84,86,93,96,110,111,135,138,139
40.05 3 2uxiA G50 Rep, Mult 67,70,71,78,81,113
50.03 2 3arcd CLA Rep, Mult 60,64
60.03 2 1vi0B DCC Rep, Mult 115,118,119,122,123
70.03 2 1jt0C QNA Rep, Mult 43,49,51,52,53,54,57,58
80.03 2 5jreH ADE Rep, Mult 64,65,116
90.02 1 3i59A N6S Rep, Mult 68,71
100.02 1 2a68P MG Rep, Mult 59,62
110.02 1 3i54D CMP Rep, Mult 64,68

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
10.0601mhyD0.4955.140.0520.8651.14.13.25NA
20.0602ztgA0.4774.820.0850.7746.1.1.717
30.0602infA0.4814.230.0450.7234.1.1.37NA
40.0603cuzA0.4964.760.0760.8392.3.3.9109
50.0603cyvA0.4864.310.0660.7424.1.1.37NA
60.0601bwlA0.4784.490.0330.7611.6.99.1NA
70.0601yuyA0.4714.840.0840.8002.7.7.48NA
80.0601wdpA0.4824.610.0650.7683.2.1.2109
90.0601fa2A0.4784.780.0680.7683.2.1.2NA
100.0601fziA0.4985.070.0710.8581.14.13.25NA
110.0603cuxA0.4874.830.0670.8322.3.3.9NA
120.0602pulA0.4794.370.0500.7482.7.1.100NA
130.0603btaA0.4804.630.0580.7553.4.24.69NA
140.0603crlB0.4914.810.0850.7932.7.11.248,90,95
150.0602np0A0.4544.970.0430.7743.4.24.69NA
160.0601y8pA0.4854.890.0680.8062.7.11.2NA
170.0601z0hB0.3375.470.0550.6133.4.24.6959
180.0601i1iP0.5033.980.0580.7163.4.24.1686
190.0602fhcA0.4825.130.0960.8653.2.1.41109

(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
00.210.6233.790.070.893bhqA GO:0003677 GO:0006351 GO:0006355
10.160.6373.460.100.893geuA GO:0003677 GO:0006351 GO:0006355
20.120.6963.090.130.912q24B GO:0003677 GO:0006351 GO:0006355
30.110.6353.540.100.862rekB GO:0003677 GO:0006351 GO:0006355
40.110.6573.230.090.892oerB GO:0003677 GO:0006351 GO:0006355
50.100.5973.200.100.783vuqC GO:0003677 GO:0006351 GO:0006355
60.100.6273.840.040.903rh2A GO:0003677 GO:0006351 GO:0006355
70.090.6004.020.090.893g7rB GO:0003677 GO:0003700 GO:0006351 GO:0006355
80.090.5943.940.080.892g3bA GO:0003677 GO:0006351 GO:0006355
90.080.5843.830.120.842qwtA GO:0003677 GO:0006351 GO:0006355
100.070.6243.710.050.882o7tA GO:0003677 GO:0006351 GO:0006355
110.070.6153.640.070.892zcnD GO:0003677 GO:0006351 GO:0006355
120.070.6044.170.060.903nnrA GO:0003677 GO:0006351 GO:0006355
130.070.5834.070.060.865f1jA GO:0003677 GO:0006351 GO:0006355
140.070.6173.460.130.854gctC GO:0000976 GO:0003677 GO:0003700 GO:0005737 GO:0005829 GO:0006355 GO:0007049 GO:0009295 GO:0010974 GO:0043565 GO:0043590 GO:0051301 GO:0051302
150.070.6044.030.070.891sgmA GO:0003677 GO:0006351 GO:0006355
160.070.5284.570.140.854cgrA GO:0003677 GO:0006351 GO:0006355
170.070.5864.040.070.884pxiB GO:0003677 GO:0006351 GO:0006355
180.070.5843.810.100.833cwrA GO:0003677 GO:0006351 GO:0006355


Consensus prediction of GO terms
 
Molecular Function GO:0003677
GO-Score 0.53
Biological Processes GO:0006355
GO-Score 0.53
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.