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I-TASSER results for job id Rv1434

[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
10.20 35 1z7lA TBR Rep, Mult 18,21,22,25
20.13 24 1ea4J NUC Rep, Mult 25,26,29
30.06 10 4oxnA 2NV Rep, Mult 27,30,31
40.04 7 4rqiC III Rep, Mult 18,21
50.03 6 2qfnA OXY Rep, Mult 13,19,23
60.02 4 2z8yD SF4 Rep, Mult 8,10,11,15,17
70.02 3 3pciA IHB Rep, Mult 9,11,12,13
80.01 3 3slbA CYT Rep, Mult 6,7,14,15,16,18,43
90.01 2 1ss4B GSH Rep, Mult 2,3,4
100.01 2 1o94C AMP Rep, Mult 20,24,34,35,37,38,44,45
110.01 1 3r5aD P0A Rep, Mult 2,25
120.01 1 4yiyA MG Rep, Mult 16,17
130.01 2 1t8yB PO4 Rep, Mult 40,43,44
140.00 1 1o95E AMP Rep, Mult 20,34,35,37,38,43,44,45
150.00 1 3f1h1 MG Rep, Mult 44,45
160.00 1 4fzxD NUC Rep, Mult 26,29,33,34
170.00 1 3wvdB TAN Rep, Mult 7,21

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
10.0601yaaB0.5023.080.0240.9332.6.1.1NA
20.0603l4dB0.4773.110.0710.9111.14.13.7030
30.0603kb9A0.5083.330.0680.9784.2.3.37NA
40.0602je8B0.4673.170.1140.9113.2.1.2525
50.0601q5nA0.5762.820.0670.9335.5.1.2NA
60.0601q8zB0.5092.550.0240.9112.7.11.110
70.0602wafA0.5152.940.1400.8893.4.-.-NA
80.0602dd5H0.5102.500.0440.7783.5.5.8NA
90.0602f7kA0.5072.750.0240.9332.7.1.35NA
100.0603h09B0.5032.520.0790.8223.4.21.7210,20
110.0602z8yD0.5482.640.0230.9331.2.7.4,1.2.99.2NA
120.0601wjdA0.2773.070.0280.6443.1.26.413,27
130.0602fenD0.5522.910.0440.9335.5.1.226
140.0601dofA0.5742.800.0670.9334.3.2.2NA
150.0601yisA0.5622.900.0220.9334.3.2.213
160.0601tj7A0.5042.760.0230.9114.3.2.1NA
170.0602dd4H0.5092.500.0440.7783.5.5.8NA
180.0601k62B0.5142.870.0440.9114.3.2.1NA
190.0601m7xB0.5073.110.0440.9332.4.1.18NA

(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
00.070.4003.000.070.691yisA GO:0003824 GO:0004018 GO:0006163 GO:0006164 GO:0006189 GO:0016829 GO:0044208 GO:0051262 GO:0070626
10.070.5172.890.040.911i0aA GO:0003824 GO:0005212 GO:0042450
20.070.5742.800.070.931dofA GO:0003824 GO:0004018 GO:0006163 GO:0009152 GO:0016829 GO:0051262 GO:0070626
30.070.4733.030.110.911yfmA GO:0003824 GO:0004333 GO:0005737 GO:0005739 GO:0005759 GO:0005829 GO:0006099 GO:0006106 GO:0006108 GO:0016829 GO:0045239 GO:0051262
40.070.4793.070.090.913tv2A GO:0003824 GO:0004333 GO:0005737 GO:0006099 GO:0006106 GO:0016829 GO:0045239
50.070.4952.920.070.913rrpA GO:0003824 GO:0004333 GO:0005737 GO:0006099 GO:0006106 GO:0016829 GO:0045239
60.070.4812.880.020.912e9fB GO:0003824 GO:0004056 GO:0005737 GO:0006526 GO:0008652 GO:0016829 GO:0042450
70.070.4332.610.000.714efcA GO:0000166 GO:0003824 GO:0004018 GO:0006163 GO:0006164 GO:0006188 GO:0006189 GO:0009152 GO:0016829 GO:0044208 GO:0046872 GO:0051262 GO:0070626
80.070.4802.940.110.911vdkA GO:0003824 GO:0004333 GO:0005737 GO:0006099 GO:0006106 GO:0016829 GO:0045239
90.070.5702.570.040.911f1oA GO:0003824 GO:0004018 GO:0006164 GO:0006167 GO:0006189 GO:0009152 GO:0016829 GO:0044208 GO:0051262 GO:0070626
100.070.4962.990.090.911yfeA GO:0003824 GO:0004333 GO:0005737 GO:0005829 GO:0006099 GO:0006106 GO:0006108 GO:0006979 GO:0008152 GO:0016829 GO:0045239 GO:0051262
110.070.4923.440.040.933e04D GO:0003824 GO:0004333 GO:0005737 GO:0005739 GO:0005759 GO:0005829 GO:0006099 GO:0006106 GO:0006108 GO:0016829 GO:0045239 GO:0048873 GO:0051262 GO:0070062
120.070.3772.530.050.711c3cA GO:0003824 GO:0004018 GO:0006163 GO:0006164 GO:0006189 GO:0009152 GO:0016829 GO:0044208 GO:0051262 GO:0070626
130.070.3632.810.100.712qgaC GO:0000166 GO:0003824 GO:0004018 GO:0006164 GO:0006188 GO:0006189 GO:0009152 GO:0016829 GO:0044208 GO:0070626
140.070.4723.120.020.931jswB GO:0003824 GO:0005829 GO:0006099 GO:0006106 GO:0006108 GO:0006531 GO:0008652 GO:0008797 GO:0016020 GO:0016829 GO:0051262
150.070.4862.970.090.913rd8A GO:0003824 GO:0004333 GO:0005737 GO:0006099 GO:0006106 GO:0016829 GO:0045239
160.070.5342.860.040.911k7wD GO:0003824 GO:0004056 GO:0005212 GO:0006526 GO:0008652 GO:0016829 GO:0042450
170.070.4903.000.070.914apbD GO:0003824 GO:0004333 GO:0005576 GO:0005618 GO:0005737 GO:0005829 GO:0005886 GO:0006099 GO:0006106 GO:0006108 GO:0016829 GO:0040007 GO:0045239 GO:0051262
180.070.5492.690.090.911re5D GO:0003824 GO:0016853 GO:0019619 GO:0047472


Consensus prediction of GO terms
 
Molecular Function GO:0004018 GO:0070626 GO:0004333 GO:0005212
GO-Score 0.13 0.13 0.13 0.07
Biological Processes GO:0051259
GO-Score 0.37
Cellular Component GO:0045239 GO:0005759 GO:0005829
GO-Score 0.13 0.07 0.07

(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.