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I-TASSER results for job id Rv1507A

[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 3 4ub8d CLA Rep, Mult 47,50,53,54
20.06 3 3wmmE CRT Rep, Mult 46,47,50,51
30.04 2 1vltA ASP Rep, Mult 62,69
40.04 2 5curA BM0 Rep, Mult 9,10,167
50.04 2 3cejB AVF Rep, Mult 8,9,28
60.04 2 3cuxA MG Rep, Mult 27,110,134
70.04 2 3iabA NUC Rep, Mult 5,32,43,44,45,48,49,50,84,85,88,91,92,95,137,138
80.04 2 1c8lA CFF Rep, Mult 23,63,65
90.02 1 3sfwA ZN Rep, Mult 57,84,115
100.02 1 4e5tA MG Rep, Mult 26,130,166
110.02 1 1ldbA SO4 Rep, Mult 96,115,141,144
120.02 1 4tnhH CLA Rep, Mult 51,55
130.02 1 3nl3A MG Rep, Mult 63,64,78
140.02 1 1eccA MN Rep, Mult 123,153,154
150.02 1 3nl5A TZE Rep, Mult 32,69
160.02 1 2gm9A 3TH Rep, Mult 7,11,14,109,165

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
10.0601aldA0.5804.250.0260.8624.1.2.13NA
20.0603gpbA0.5724.070.0410.8562.4.1.119
30.0602o7vA0.5964.130.0740.8923.4.23.164,39,82
40.0601jjiA0.5873.930.1030.8683.1.1.1NA
50.0601b41A0.5674.830.0750.9463.1.1.7NA
60.0601fbaC0.5814.290.0390.8684.1.2.13107,130
70.0601j33A0.5733.910.0560.8442.4.2.2171
80.0603mmtA0.5874.160.0330.8624.1.2.1343
90.0601maaD0.5694.890.0820.9463.1.1.7NA
100.0601f6wA0.5794.780.0380.9403.1.1.13,3.1.1.3NA
110.0601cleA0.5684.800.0630.9463.1.1.3NA
120.0601fdjA0.5824.290.0260.8684.1.2.13NA
130.0601lpsA0.5674.820.0570.9463.1.1.3129,165
140.0601adoA0.5794.270.0260.8684.1.2.13NA
150.0601vbgA0.5724.440.0590.8742.7.9.1NA
160.0601aknA0.5784.780.0320.9463.1.1.13,3.1.1.3NA
170.0602pc4C0.5764.320.0330.8684.1.2.13NA
180.0602qdgA0.5814.230.0530.8684.1.2.13NA
190.0603kx6A0.5824.240.0330.8684.1.2.13NA

(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
00.070.5754.340.070.884kryE GO:0005737 GO:0008126 GO:0008152 GO:0009056 GO:0016787 GO:0034338 GO:0043433 GO:0051346 GO:0052689
10.070.6003.980.100.893eblA GO:0005634 GO:0005737 GO:0008152 GO:0009056 GO:0009739 GO:0009740 GO:0009939 GO:0010325 GO:0010331 GO:0016787 GO:0048444
20.070.5994.090.070.892o7rA GO:0008152 GO:0016787 GO:0052689
30.070.5933.960.090.892zsiA GO:0005634 GO:0005737 GO:0008152 GO:0009739 GO:0009740 GO:0009939 GO:0010331 GO:0010476 GO:0016787 GO:0048444
40.070.5884.020.080.874v2iA GO:0008152 GO:0016787 GO:0052689
50.070.5654.390.050.884n5hX GO:0008152 GO:0016787
60.070.5843.940.110.873zwqA GO:0008152 GO:0016787
70.070.5854.160.070.881lzkA GO:0008152 GO:0016787
80.070.5794.780.040.941f6wA GO:0003824 GO:0004771 GO:0004806 GO:0004872 GO:0005576 GO:0005615 GO:0005737 GO:0005887 GO:0006629 GO:0006641 GO:0006707 GO:0007158 GO:0007416 GO:0008201 GO:0009062 GO:0009986 GO:0016042 GO:0016787 GO:0018350 GO:0030157 GO:0030299 GO:0042043 GO:0044241 GO:0044258 GO:0045202 GO:0047372 GO:0050804 GO:0052689 GO:0070062
90.070.5883.900.100.863qh4A GO:0008152 GO:0016787
100.070.5724.230.120.884j7aA GO:0008152 GO:0016787
110.070.5564.040.070.833h04A GO:0008152 GO:0016787
120.070.5873.910.050.864ou5A GO:0008152 GO:0016787
130.070.5944.040.100.881qz3A GO:0008152 GO:0016787
140.070.5684.120.160.864c87A GO:0008152 GO:0016787
150.070.5873.930.100.871jjiA GO:0008152 GO:0016787
160.070.5853.840.130.864p9nA GO:0008152 GO:0016787
170.070.5494.880.040.931thgA GO:0004806 GO:0005576 GO:0006629 GO:0016042 GO:0016787
180.070.5873.860.110.873aikA GO:0008152 GO:0016787 GO:0042802 GO:0052689


Consensus prediction of GO terms
 
Molecular Function GO:0016788
GO-Score 0.37
Biological Processes GO:0009939 GO:0009056 GO:0048444 GO:0043433 GO:0010325 GO:0051346
GO-Score 0.13 0.13 0.13 0.07 0.07 0.07
Cellular Component GO:0044424
GO-Score 0.38

(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.