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I-TASSER results for job id Rv0784

[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
10.26 4 2cc0A ACT Rep, Mult 5,65,69,109,110,111,112,134,186
20.13 2 2nt0D GOL Rep, Mult 18,22,25,26,56,59,60
30.06 1 3rxzA ZN Rep, Mult 65,69
40.06 1 2v3eA NND Rep, Mult 89,91,122

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
10.2032iw0A0.7252.840.1080.8423.5.1.4167,189
20.1582w3zA0.7062.890.1380.8293.5.1.41112
30.1101c92A0.6164.130.1010.8513.2.1.96107
40.0671v5xA0.5413.470.0670.6895.3.1.24NA
50.0672cz5A0.5443.860.0680.7374.1.1.23NA
60.0662czfA0.5273.920.0570.7284.1.1.2331,58,65
70.0662v81A0.5114.290.0600.7284.1.2.21NA
80.0661c3fA0.6204.040.1010.8513.2.1.96NA
90.0661nsjA0.5343.580.0430.6935.3.1.24133
100.0661xi3A0.5273.660.0540.6972.5.1.3NA
110.0661w0mA0.5444.040.0680.7465.3.1.1NA
120.0661xbzB0.5344.260.0400.7544.1.1.85123
130.0661u83A0.5503.810.0690.7374.4.1.19NA
140.0661xi3B0.5273.670.0540.6972.5.1.366
150.0661vqtA0.4923.950.0580.6754.1.1.23NA
160.0601ll6A0.6584.030.0990.9033.2.1.1419
170.0602epoB0.6534.070.0760.9033.2.1.52NA
180.0602fhcA0.6344.740.0780.9433.2.1.4133,89,133
190.0601fa2A0.6574.170.0670.9083.2.1.2NA
200.0602gjxA0.6364.240.0580.9033.2.1.52NA
210.0602wyhA0.6723.990.1130.9253.2.1.2438
220.0601v03A0.6194.640.0520.9123.2.1.21NA
230.0601w9pA0.6604.050.1080.9033.2.1.14NA
240.0603gh4A0.6514.170.0580.9173.2.1.52NA
250.0601gonA0.6354.110.0580.8863.2.1.2198
260.0602ow6A0.7103.830.0740.9433.2.1.114NA
270.0601d2kA0.6554.050.0940.9033.2.1.14NA
280.0601b1yA0.6644.030.0530.9033.2.1.213
290.0601xc6A0.6554.340.0450.9303.2.1.2392
300.0601wdpA0.6554.070.0630.8953.2.1.245
310.0602e9bA0.6394.660.1000.9393.2.1.4182,105,127,129
320.0602epoA0.6624.050.0620.9083.2.1.52NA
330.0602fhbA0.6334.730.0690.9433.2.1.41NA
340.0601hp4A0.6454.180.0310.9123.2.1.5260

(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
00.310.7912.490.140.921z7aA GO:0003824 GO:0005975 GO:0016810
10.290.8022.450.120.924ly4A GO:0000272 GO:0003824 GO:0005975 GO:0016787 GO:0016810 GO:0045493 GO:0046555 GO:0046872 GO:0071555
20.250.7132.380.110.822vyoA GO:0003824 GO:0005975 GO:0016810
30.250.7252.840.110.842iw0A GO:0003824 GO:0004099 GO:0005975 GO:0016787 GO:0016810 GO:0046872
40.240.4755.040.050.745jp6A GO:0003824 GO:0005975 GO:0016787 GO:0016810
50.210.6902.660.110.802cc0A GO:0003824 GO:0004553 GO:0005975 GO:0016810 GO:0030246 GO:0030247 GO:0046872
60.200.7142.220.120.804m1bA GO:0003824 GO:0005975 GO:0016810
70.170.8232.250.140.933rxzC GO:0003824 GO:0005975 GO:0016810 GO:0046872
80.160.7122.250.090.794l1gA GO:0003824 GO:0005975 GO:0016787 GO:0016810
90.160.7882.540.150.923cl6A GO:0003824 GO:0005975 GO:0016810
100.150.7922.500.130.923s6oC GO:0003824 GO:0005975 GO:0016810
110.150.7372.990.120.883wx7A GO:0003824 GO:0004553 GO:0005576 GO:0005975 GO:0016810 GO:0030246 GO:0046872
120.120.7062.890.140.832w3zA GO:0003824 GO:0005975 GO:0016810 GO:0046872
130.110.7042.580.100.812c71A GO:0000272 GO:0003824 GO:0004553 GO:0005975 GO:0016810 GO:0030246 GO:0045493
140.110.7042.540.100.822y8uB GO:0003824 GO:0004099 GO:0005975 GO:0016810
150.100.7022.350.100.791ny1A GO:0003824 GO:0005975 GO:0016787 GO:0016810 GO:0030435 GO:0046872 GO:0071555
160.100.7032.400.120.802c1gA GO:0003824 GO:0005886 GO:0005975 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0016810 GO:0046872
170.080.6582.200.110.742j13A GO:0003824 GO:0005975 GO:0016810 GO:0019213
180.070.6174.290.070.883hqpA GO:0000166 GO:0000287 GO:0003824 GO:0004743 GO:0005524 GO:0006096 GO:0016301 GO:0016310 GO:0016740 GO:0030955 GO:0046872
190.070.7363.020.110.884nyuA GO:0003824 GO:0004099 GO:0004553 GO:0005576 GO:0005975 GO:0016787 GO:0016810 GO:0030246
200.060.3545.270.070.571n1zA GO:0000287 GO:0008152 GO:0009507 GO:0009536 GO:0010333 GO:0016829 GO:0016853 GO:0046211 GO:0046872 GO:0047926
210.060.3915.310.050.632gjtA GO:0000902 GO:0002548 GO:0003093 GO:0003105 GO:0004721 GO:0004725 GO:0005001 GO:0005886 GO:0005887 GO:0006470 GO:0007411 GO:0010812 GO:0010977 GO:0016020 GO:0016021 GO:0016311 GO:0016324 GO:0016328 GO:0016787 GO:0016791 GO:0017147 GO:0030027 GO:0030032 GO:0030424 GO:0030426 GO:0032835 GO:0035335 GO:0036060 GO:0042803 GO:0043005 GO:0043197 GO:0070062 GO:0072112 GO:0090090 GO:0090260


Consensus prediction of GO terms
 
Molecular Function GO:0052689 GO:0016811 GO:0019213 GO:0046872
GO-Score 0.58 0.49 0.49 0.46
Biological Processes GO:0000272 GO:0045229 GO:0045491
GO-Score 0.58 0.58 0.58
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.