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I-TASSER results for job id Rv3691

[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 10 5hwsA NAP Rep, Mult 4,5,8,9,10,29,30,71,73,77,95,124,126,127,128,260
20.02 1 1u9iA MG Rep, Mult 206,241,244
30.02 1 1cq1B CA Rep, Mult 226,227
40.02 1 1u9iB MG Rep, Mult 206,241,297
50.02 1 1bg60 III Rep, Mult 182,184,187,206,213,285,289,292,295
60.02 1 1pgqA 2AM Rep, Mult 11,27,28,29,71,72,77,81
70.02 1 3v2d2 MG Rep, Mult 219,223
80.02 1 1n1gA BCP Rep, Mult 170,262,265,266
90.02 1 3d1lA MPR Rep, Mult 228,234
100.02 1 3nl5A TZE Rep, Mult 155,264
110.02 1 1xrmA III Rep, Mult 316,319
120.02 1 2gblC MG Rep, Mult 206,244
130.02 1 1g42A CP2 Rep, Mult 66,67
140.02 1 2jkvA NAP Rep, Mult 172,174,197
150.02 1 1w8qC CO Rep, Mult 17,21
160.02 1 3gg2A UGA Rep, Mult 81,82,107,108,110,111,114

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
10.3371bg6A0.8132.720.1230.9191.5.1.28261
20.2493c7aA0.6904.380.0770.8981.5.1.11261
30.0863egoA0.6233.760.0890.7721.1.1.169NA
40.0773ghyA0.6433.730.1030.7991.1.1.169NA
50.0673g17G0.6083.680.0660.7481.1.1.169NA
60.0673k96A0.5974.080.1040.7601.1.1.94NA
70.0671txgB0.5944.230.0800.7601.1.1.94199
80.0671txgA0.5884.290.0900.7571.1.1.94NA
90.0661x0xA0.5874.390.1010.7691.1.1.8NA
100.0603gg2A0.5014.640.0600.6701.1.1.22169
110.0603i83B0.6073.540.1060.7391.1.1.169NA
120.0601pgjA0.4995.210.0550.7121.1.1.44NA
130.0603hn2A0.6513.450.1250.7841.1.1.169NA
140.0601qmgA0.5245.420.0730.7601.1.1.86NA
150.0603fwnA0.4885.150.0480.6941.1.1.44NA
160.0601lj8A0.6374.280.0650.8351.1.1.6797
170.0602qytA0.5693.430.0990.6941.1.1.16917
180.0601yj8A0.5714.230.0660.7481.1.1.8NA
190.0603c7cB0.7114.210.0800.9071.5.1.1171,96,129
200.0603ckyC0.4844.640.0710.6521.1.1.29113,95,163
210.0602p4qA0.4824.960.0660.6791.1.1.44NA
220.0603hwrA0.6373.490.1250.7751.1.1.169NA
230.0603i83A0.6363.780.1140.7901.1.1.169NA
240.0601n1eA0.5834.260.1210.7631.1.1.8NA
250.0602plaA0.5884.460.0990.7721.1.1.8NA
260.0602jkvA0.5024.990.0590.7031.1.1.44NA
270.0601z82A0.5784.040.1010.7391.1.1.8NA
280.0602ofpB0.6113.820.1050.7571.1.1.169NA

(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
00.300.6513.450.120.783hn2A GO:0005737 GO:0008677 GO:0015940 GO:0016491 GO:0050661 GO:0055114
10.240.5834.260.120.761n1eA GO:0004367 GO:0005777 GO:0005975 GO:0006072 GO:0009331 GO:0016491 GO:0016616 GO:0020015 GO:0046168 GO:0051287 GO:0055114
20.170.8132.720.120.921bg6A GO:0008677 GO:0016491 GO:0047129 GO:0050662 GO:0055114
30.110.6904.380.080.903c7aA GO:0000166 GO:0016491 GO:0047830 GO:0050662 GO:0055114
40.100.6503.420.120.793hwrA GO:0000166 GO:0005737 GO:0008677 GO:0015940 GO:0016491 GO:0050661 GO:0055114
50.080.6433.730.100.803ghyA GO:0008677 GO:0016491 GO:0050661 GO:0055114
60.080.6073.540.110.743i83B GO:0005737 GO:0008677 GO:0015940 GO:0016491 GO:0050661 GO:0055114
70.080.6303.660.130.784ol9A GO:0005737 GO:0005829 GO:0008677 GO:0015940 GO:0016491 GO:0050661 GO:0055114
80.070.6273.860.120.785ayvB GO:0005737 GO:0008677 GO:0015940 GO:0016491 GO:0050661 GO:0055114
90.070.6363.780.110.793i83A GO:0005737 GO:0008677 GO:0015940 GO:0016491 GO:0050661 GO:0055114
100.070.6233.760.090.773egoA GO:0005737 GO:0008677 GO:0015940 GO:0016491 GO:0050661 GO:0055114
110.070.6113.820.100.762ofpB GO:0005737 GO:0008677 GO:0015940 GO:0016491 GO:0033317 GO:0050661 GO:0055114
120.070.5974.080.100.763k96A GO:0004367 GO:0005737 GO:0005975 GO:0006072 GO:0006629 GO:0006650 GO:0008654 GO:0009331 GO:0016491 GO:0016616 GO:0036439 GO:0046167 GO:0046168 GO:0047952 GO:0051287 GO:0055114
130.070.6083.680.070.753g17G GO:0005737 GO:0008677 GO:0015940 GO:0016491 GO:0050661 GO:0055114
140.070.5853.520.100.722qytA GO:0005737 GO:0008677 GO:0015940 GO:0016491 GO:0050661 GO:0055114
150.070.5913.430.080.713wfjF GO:0000166 GO:0005737 GO:0008677 GO:0015940 GO:0016491 GO:0050661 GO:0055114
160.070.5584.860.070.783wfiB GO:0000166 GO:0005737 GO:0008677 GO:0015940 GO:0016491 GO:0050661 GO:0055114
170.070.5904.010.100.751z82A GO:0004367 GO:0005737 GO:0005975 GO:0006072 GO:0006629 GO:0006650 GO:0008654 GO:0009331 GO:0016491 GO:0016616 GO:0036439 GO:0046167 GO:0046168 GO:0047952 GO:0051287 GO:0055114
180.070.5524.920.080.772ew2B GO:0005737 GO:0008677 GO:0015940 GO:0016491 GO:0050661 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0008677 GO:0050661 GO:0016646
GO-Score 0.47 0.36 0.34
Biological Processes GO:0055114 GO:0006072 GO:0046434 GO:1901136 GO:0044238 GO:0015940
GO-Score 0.65 0.48 0.48 0.48 0.42 0.36
Cellular Component GO:0005777 GO:1990204
GO-Score 0.48 0.48

(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.