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I-TASSER results for job id Rv0724A

[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
10.06 3 3hiyB MG Rep, Mult 48,50
20.04 2 4ku8A GLY Rep, Mult 28,32
30.04 2 5i50A NUC Rep, Mult 40,43
40.04 2 1tkoB FE Rep, Mult 37,40
50.02 1 1kpgB CO3 Rep, Mult 20,21,22,104
60.02 1 1uvqA GLY Rep, Mult 22,79,104
70.02 1 2uyqA SAM Rep, Mult 64,67,72,73,74,75
80.02 1 1cvjA A Rep, Mult 20,106
90.02 1 2bfnA CA Rep, Mult 2,3
100.02 1 3pzqA MAL Rep, Mult 3,62,66
110.02 1 1d2hA SAH Rep, Mult 3,4,8,9,66,70
120.02 1 3thrB C2F Rep, Mult 74,76,104,106
130.02 1 3sm3A CA Rep, Mult 48,59
140.02 1 1tfyA MG Rep, Mult 17,50
150.02 1 4jhuA CU Rep, Mult 18,108
160.02 1 1lr5A BMA Rep, Mult 10,111
170.02 1 1l1eB CO3 Rep, Mult 17,72,73
180.02 1 1cruA HDN Rep, Mult 66,72
190.02 1 3n3uA ZN Rep, Mult 22,37
200.02 1 3ojcA CA Rep, Mult 73,87

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
10.0601nw7A0.4993.540.0760.7122.1.1.7216,71
20.0603cklB0.4723.930.0810.7482.8.2.-17
30.0603d35A0.5073.630.1050.7752.3.1.48NA
40.0603e05D0.4922.490.1320.6132.1.1.13267
50.0602ad1A0.4524.170.0950.7302.8.2.-NA
60.0603e05B0.4922.280.1340.6042.1.1.13210
70.0601kpiA0.5473.660.0740.8202.1.1.79NA
80.0601booA0.4883.510.0490.6942.1.1.113NA
90.0603c3yA0.4703.150.1140.6312.1.1.104NA
100.0601cjmA0.4454.030.0750.7032.8.2.1NA
110.0602p35A0.4843.170.0680.6852.1.1.144NA
120.0601wznA0.5293.410.1380.7392.1.1.-NA
130.0601kphC0.5573.600.0950.8292.1.1.79NA
140.0603nwoA0.4844.150.0840.7933.4.11.5NA
150.0602aovA0.4734.030.0230.7842.1.1.8NA
160.0601xxlA0.5413.360.0910.7752.1.1.-NA
170.0601o54A0.4772.970.1550.6402.1.1.-NA
180.0602h8kA0.4753.980.0590.7662.8.2.2NA
190.0603cf4A0.4704.320.0460.7391.2.99.2NA

(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
00.220.9151.360.280.992ckdA GO:0008168 GO:0016740 GO:0032259
10.210.8611.330.280.932uyoA GO:0008168 GO:0016740 GO:0032259
20.070.6173.000.090.843g5lA
30.070.6043.500.060.885je1A GO:0008168 GO:0016740 GO:0032259
40.070.6133.430.060.863bgvB GO:0003723 GO:0004482 GO:0005634 GO:0005654 GO:0005730 GO:0005845 GO:0006366 GO:0006370 GO:0006397 GO:0008168 GO:0016740 GO:0032259 GO:0036265 GO:0043235
50.070.6083.110.150.823d2lC GO:0008168 GO:0016740 GO:0032259
60.070.5793.060.130.803uj7A GO:0008168 GO:0016740 GO:0032259 GO:0046872 GO:0051536 GO:0051539
70.070.3674.230.010.594mwzB GO:0008168 GO:0016740 GO:0032259 GO:0046872 GO:0051536 GO:0051539
80.070.5663.470.110.844ineA GO:0000773 GO:0005737 GO:0006656 GO:0008152 GO:0008168 GO:0016740 GO:0032259 GO:0080101
90.070.5683.500.130.854krhA GO:0008152 GO:0008168 GO:0032259 GO:0046872 GO:0051536 GO:0051539
100.070.5993.020.110.803bkwA GO:0008152 GO:0008168 GO:0032259
110.070.5543.590.090.794gekG GO:0002098 GO:0008168 GO:0016300 GO:0016740 GO:0016743 GO:0030488 GO:0032259 GO:1904047
120.070.5333.220.080.733e7pA GO:0046872 GO:0051536 GO:0051539
130.070.3364.190.030.594iv8A GO:0000234 GO:0008152 GO:0008168 GO:0016740 GO:0032259 GO:0046872 GO:0051536 GO:0051539
140.070.5453.450.090.782gluA GO:0005737 GO:0008152 GO:0008168 GO:0008757 GO:0016740 GO:0032259
150.070.5413.280.100.761vl5A GO:0008152 GO:0008168 GO:0016740 GO:0032259
160.070.5443.940.090.822avnA GO:0008152 GO:0008168 GO:0016740 GO:0032259
170.070.5263.120.100.733f4kA GO:0005737 GO:0008168 GO:0008757 GO:0016740 GO:0032259 GO:0046872 GO:0051536 GO:0051539
180.070.5603.620.120.811kpgA GO:0005737 GO:0005886 GO:0006629 GO:0008168 GO:0008610 GO:0008825 GO:0016740 GO:0032259 GO:0046500 GO:0071768


Consensus prediction of GO terms
 
Molecular Function GO:0008168
GO-Score 0.47
Biological Processes GO:0032259
GO-Score 0.47
Cellular Component GO:0043235 GO:0005654 GO:0005845 GO:0005730
GO-Score 0.07 0.07 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.