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I-TASSER results for job id Rv1339

[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
10.56 76 2ohiH FE Rep, Mult 78,80,81,180,236
20.49 64 3x2zA NI Rep, Mult 76,78,158,180
30.02 3 1ww1A ZN Rep, Mult 27,180,236
40.01 3 3iemB SSU Rep, Mult 19,21,42,48,59,60,61,68,264
50.00 1 2cbn0 III Rep, Mult 29,30,31,32,35,55,56,58,59,62,63,77,78,83,84,86,87,90,91,113,114,120,121,122,160
60.00 1 3md7A NA Rep, Mult 209,210,214,219
70.00 1 1zkp0 III Rep, Mult 28,29,30,32,55,59,62,78,79,80,84,86,87,90,91,239,240
80.00 1 2fk6A NUC Rep, Mult 44,46,67,69,94,95

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
10.3411y44A0.8641.260.2200.8973.1.26.1123,86,88
20.3062fk6A0.8771.270.2130.9123.1.26.1186
30.0603hnnA0.4894.640.0820.6701.-.-.-NA
40.0601b1yA0.4595.420.0530.7033.2.1.2NA
50.0601jjeB0.4784.080.0780.6233.5.2.6NA
60.0601q0lA0.4655.460.0430.7141.1.1.267209
70.0603dhaA0.5024.590.1170.6853.1.1.-NA
80.0601itxA0.4625.360.0800.6963.2.1.14NA
90.0601znbB0.4764.530.0980.6413.5.2.6160,236
100.0602gcuA0.4823.600.1040.6043.1.2.680
110.0602ohhA0.4974.980.1120.6921.-.-.-80
120.0601a8tA0.4813.900.0870.6153.5.2.6180
130.0602gmnA0.4784.320.1030.6263.5.2.680
140.0601l9yA0.4744.170.1170.6193.5.2.680
150.0601qh5A0.5074.170.1410.6373.1.2.6NA
160.0601alkA0.4635.980.0540.7693.1.3.1NA
170.0602cbnA0.8651.370.2790.9053.1.26.1129,78,80,86,88
180.0601ajbA0.4646.020.0500.7733.1.3.1NA
190.0601gimA0.4656.040.0720.7846.3.4.4NA
200.0601adeA0.4575.500.1090.7296.3.4.4NA
210.0602dkfA0.6753.430.2130.8173.1.-.-NA

(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
00.590.8781.260.220.911y44A GO:0004518 GO:0004519 GO:0008033 GO:0008270 GO:0016787 GO:0016891 GO:0034414 GO:0042779 GO:0042781 GO:0046872 GO:0090502
10.570.8022.580.260.901zkpA GO:0046872
20.510.7003.040.190.823g1pB GO:0008081 GO:0016787 GO:0019700 GO:0030145 GO:0046872
30.490.7382.390.220.822e7yA GO:0016787 GO:0034414 GO:0042781 GO:0046872
40.450.7482.380.210.841ww1A GO:0016787 GO:0034414 GO:0042781 GO:0046872
50.440.7213.460.170.882i7vA GO:0000398 GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0005634 GO:0005654 GO:0005847 GO:0006369 GO:0006378 GO:0006379 GO:0006397 GO:0006398 GO:0006406 GO:0008409 GO:0016787 GO:0030529 GO:0031124 GO:0046872 GO:0090305 GO:0090502
60.420.8651.370.280.902cbnA GO:0004518 GO:0004519 GO:0004527 GO:0004532 GO:0008033 GO:0008270 GO:0016787 GO:0016891 GO:0034414 GO:0042779 GO:0042781 GO:0046872 GO:0090502 GO:0090503
70.390.7473.540.140.912xr1B GO:0003676 GO:0003723 GO:0046872
80.380.6803.450.210.823a4yA GO:0003723 GO:0004518 GO:0004519 GO:0005737 GO:0006364 GO:0016787 GO:0046872 GO:0090305
90.340.4874.240.100.643adrA GO:0008270 GO:0046872
100.310.8031.620.210.853zwfA GO:0004518 GO:0004519 GO:0005634 GO:0005737 GO:0005829 GO:0008033 GO:0016787 GO:0016891 GO:0034414 GO:0042779 GO:0042781 GO:0046872 GO:0090502
110.240.6503.720.130.822p4zB GO:0016787 GO:0046872
120.210.8771.270.210.912fk6A GO:0004518 GO:0004519 GO:0008033 GO:0008270 GO:0016787 GO:0016891 GO:0034414 GO:0042779 GO:0042781 GO:0046872 GO:0090502
130.130.7203.410.170.872i7tA GO:0000398 GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0005634 GO:0005654 GO:0005847 GO:0006369 GO:0006378 GO:0006379 GO:0006397 GO:0006398 GO:0006406 GO:0008409 GO:0016787 GO:0030529 GO:0031124 GO:0046872 GO:0090305 GO:0090502
140.120.7193.160.140.863zq4A GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0004527 GO:0004534 GO:0005737 GO:0006364 GO:0006396 GO:0006397 GO:0008270 GO:0016787 GO:0046872 GO:0090501 GO:0090502 GO:0090503
150.070.7213.290.140.875a0tA GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0004527 GO:0004534 GO:0005737 GO:0006364 GO:0006396 GO:0008270 GO:0016787 GO:0046872 GO:0090501 GO:0090502 GO:0090503
160.070.5414.490.130.733aj3A GO:0016787 GO:0042820 GO:0046872 GO:0047585
170.070.4854.310.140.641ztcA
180.070.5315.100.140.761p9eA GO:0016787 GO:0046872
190.070.5295.000.140.754xukA GO:0016787
200.070.7473.540.140.912ycbB GO:0003676 GO:0003723 GO:0046872
210.070.5004.820.100.681e5dA GO:0009055 GO:0010181 GO:0016491 GO:0022904 GO:0046872 GO:0055114
220.070.5024.680.120.682qedA GO:0004416 GO:0016787 GO:0019243 GO:0046872
230.070.4854.870.190.674le6A GO:0004063 GO:0016311 GO:0016787 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0042781 GO:0008270 GO:0030145 GO:0008081
GO-Score 0.88 0.59 0.51 0.51
Biological Processes GO:0034414 GO:0019700
GO-Score 0.88 0.51
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.