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I-TASSER results for job id Rv1255c

[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 19 5aqcB 5JB Rep, Mult 24,101,102,127,130,157,160
20.09 15 5fmpA NUC Rep, Mult 35,36,37,38,48,52,57,58
30.08 15 5f08A 5TG Rep, Mult 77,90,91,95,98,131,134,137,153,156,160,182
40.06 11 3zqlB QNA Rep, Mult 47,49,50,53,54
50.06 13 3btjA DEQ Rep, Mult 66,69,70,72,73,101,102,105,112,126
60.04 8 3angB DCC Rep, Mult 112,121,122,125,148,151,154,158,160,161
70.03 7 3angD DCC Rep, Mult 158,162,165,166,168,169
80.02 5 5cw8A 55X Rep, Mult 24,69,72,73,98,101,102,105,107,134,154,157,160,164
90.02 4 3btjB DEQ Rep, Mult 109,112,165,166
100.02 3 3lsrA QNA Rep, Mult 8,36,37,38,42,48,49,52
110.01 3 1vi0A DCC Rep, Mult 66,69,70,98,101,112,117,124,128,131,132,135,150,151,153,154,157
120.01 2 3angA DCC Rep, Mult 166,169
130.01 3 3b6cA SDN Rep, Mult 157,160,161,164
140.01 2 2np5A NDS Rep, Mult 168,169,170,171,172
150.00 1 3angB DCC Rep, Mult 162,166,169,177,181
160.00 1 3angA DCC Rep, Mult 18,22,23,62
170.00 1 1bjyB CTC Rep, Mult 153,157,160
180.00 1 2id3B CA Rep, Mult 39,43
190.00 1 3lsjB COA Rep, Mult 180,183,184
200.00 1 2xptA K Rep, Mult 112,115,116,117

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
10.0601z0hB0.3375.370.0230.5453.4.24.6965
20.0603hi7A0.4505.300.0370.7521.4.3.22NA
30.0603fwnA0.3506.240.0430.6731.1.1.44NA
40.0602z1qB0.4505.430.0560.7521.3.99.3NA
50.0601qbaA0.4425.390.0700.7573.2.1.5221,23,39
60.0602e9bA0.4435.110.0710.7183.2.1.41109,161
70.0607reqB0.4434.590.0980.6635.4.99.2NA
80.0601e5dA0.4484.900.0340.6981.-.-.-NA
90.0601syyA0.4594.680.0570.6781.17.4.1NA
100.0601ea9C0.4425.000.0580.7083.2.1.5421
110.0602vuxB0.4284.510.0570.6291.17.4.1NA
120.0601d8cA0.4554.390.0640.6582.3.3.940
130.0602aaaA0.4424.510.0610.6583.2.1.118,21
140.0602w90B0.4535.270.0240.7481.1.1.44NA
150.0601jqoA0.4455.090.0380.7184.1.1.3171,154
160.0602taaA0.4484.650.0540.6833.2.1.118,56
170.0601h0nA0.4414.550.0620.6531.17.4.1NA
180.0602z8yD0.4425.790.0790.7971.2.7.4,1.2.99.270,102
190.0602np0A0.4604.960.0320.7183.4.24.69175

(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
00.410.8911.280.230.945d1wD GO:0003677 GO:0006351 GO:0006355
10.330.6243.620.160.842g3bA GO:0003677 GO:0006351 GO:0006355
20.320.6572.780.170.813bniA GO:0003677 GO:0006351 GO:0006355
30.300.6993.280.140.892f07A GO:0003677 GO:0006351 GO:0006355
40.280.5594.280.140.834l62A GO:0000976 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355
50.260.6643.400.130.882hytA GO:0003677 GO:0006351 GO:0006355
60.240.5284.610.100.773vprA GO:0003677 GO:0006351 GO:0006355 GO:0042802
70.240.6783.380.190.873bjbB GO:0003677 GO:0006351 GO:0006355
80.230.5754.140.140.813ppbA GO:0003677 GO:0006351 GO:0006355
90.210.5244.350.180.752qwtA GO:0003677 GO:0006351 GO:0006355
100.210.5294.770.110.803f1bA GO:0003677 GO:0006351 GO:0006355
110.210.6033.690.160.813vuqC GO:0003677 GO:0006351 GO:0006355
120.210.6273.990.170.865d18A GO:0003677 GO:0006351 GO:0006355
130.200.5903.940.130.824auxA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677 GO:0046872
140.200.6753.620.180.904cgrA GO:0003677 GO:0006351 GO:0006355
150.190.5614.280.170.814nn1A GO:0003677 GO:0003700 GO:0006351 GO:0006355
160.190.5014.470.150.773egqA GO:0003677 GO:0006351 GO:0006355
170.190.6273.950.140.872qibA GO:0003677 GO:0003700 GO:0006351 GO:0006355
180.190.5414.540.090.803mvpA GO:0003677 GO:0006351 GO:0006355
190.190.5704.560.100.863lhqA GO:0003677 GO:0003700 GO:0006351 GO:0006355
200.170.6084.190.130.883hggA GO:0003677 GO:0006351 GO:0006355
210.170.5114.370.170.762q24B GO:0003677 GO:0006351 GO:0006355
220.170.6043.480.130.814hkuA GO:0003677 GO:0006351 GO:0006355
230.170.5754.360.160.823he0C GO:0003677 GO:0006351 GO:0006355
240.170.6083.660.110.814mk6A GO:0003677 GO:0006351 GO:0006355
250.160.5424.720.170.863c2bA GO:0003677 GO:0006351 GO:0006355
260.160.5684.520.110.863qbmA GO:0003677 GO:0003700 GO:0006351 GO:0006355
270.150.5704.650.110.863bcgA GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0008144 GO:0042493 GO:0043565 GO:0045892
280.150.5464.580.070.822id6A GO:0003677 GO:0006351 GO:0006355
290.150.6283.950.140.883bhqA GO:0003677 GO:0006351 GO:0006355
300.150.5604.760.210.843pasB GO:0003677 GO:0006351 GO:0006355
310.150.5574.590.070.862rasB GO:0003677 GO:0006351 GO:0006355
320.140.5504.500.130.833npiA GO:0003677 GO:0006351 GO:0006355
330.140.5794.190.180.855f1jA GO:0003677 GO:0006351 GO:0006355
340.140.5604.720.070.852uxhA GO:0003677 GO:0006351 GO:0006355
350.140.5423.950.140.742o7tA GO:0003677 GO:0006351 GO:0006355
360.130.6423.760.170.883c07A GO:0003677 GO:0006351 GO:0006355
370.120.5084.730.070.773ccyA GO:0003677 GO:0006351 GO:0006355
380.100.4674.790.090.702iaiA GO:0003677 GO:0006351 GO:0006355
390.100.6653.280.160.852zb9A GO:0003677 GO:0006351 GO:0006355
400.080.5354.320.110.783cdlB GO:0003677 GO:0006351 GO:0006355
410.080.6134.010.180.863cwrA GO:0003677 GO:0006351 GO:0006355
420.080.6204.080.180.862zcxA GO:0003677 GO:0006351 GO:0006355
430.070.5854.120.150.844jl3C GO:0003677 GO:0006351 GO:0006355
440.070.5893.870.120.832iu5A GO:0003677 GO:0006351 GO:0006355
450.070.5763.940.140.822fq4A GO:0003677 GO:0006351 GO:0006355
460.070.5853.950.120.822raeA GO:0003677 GO:0006351 GO:0006355
470.070.5054.400.180.752rekB GO:0003677 GO:0006351 GO:0006355
480.070.5484.610.100.853dpjA GO:0003677 GO:0006351 GO:0006355
490.070.5044.540.130.752guhA GO:0003677 GO:0006351 GO:0006355


Consensus prediction of GO terms
 
Molecular Function GO:0044212 GO:1990837 GO:0001071
GO-Score 0.55 0.55 0.55
Biological Processes GO:0006355
GO-Score 0.86
Cellular Component GO:0044444
GO-Score 0.55

(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.