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I-TASSER results for job id Rv2668

[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
10.05 3 2vuoA NAG Rep, Mult 55,89,142
20.05 3 4lm8A CA Rep, Mult 53,54,171
30.05 3 1swiC BNZ Rep, Mult 5,9
40.05 3 1p7hM QNA Rep, Mult 148,150,151,156
50.04 2 3mxgA XLS Rep, Mult 171,172
60.04 2 2o93M QNA Rep, Mult 34,38,39,40,43
70.04 2 3ictA FAD Rep, Mult 117,119
80.02 1 2o93O QNA Rep, Mult 33,41,170
90.02 1 1smyF MG Rep, Mult 7,8,101
100.02 1 1o75B PDX Rep, Mult 132,140,142
110.02 1 2f2hA XTG Rep, Mult 41,44
120.02 1 2qkiD III Rep, Mult 87,88,89,90,99,120,145
130.02 1 1uwwA CA Rep, Mult 87,144
140.02 1 3m9gA ZN Rep, Mult 115,165
150.02 1 1j9sA NO2 Rep, Mult 129,167,169
160.02 1 3q79A 3CX Rep, Mult 20,164
170.02 1 3pczA BAM Rep, Mult 44,80,82,98,99

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
10.0603hhsA0.4524.610.0430.6991.14.18.1NA
20.0602qhfA0.4304.920.1050.6994.2.3.5154
30.0601lnsA0.4304.870.0630.6763.4.14.11NA
40.0601g0dA0.4274.230.0800.6302.3.2.13NA
50.0601umfC0.4294.910.0590.6884.2.3.571
60.0601qbaA0.4434.250.1130.6593.2.1.52108,110
70.0603im1A0.4504.730.0560.6943.6.4.13NA
80.0601rm6A0.4345.350.0640.7751.3.99.20NA
90.0602x42A0.4864.180.0950.7053.2.1.2146
100.0601gc5A0.4485.150.0370.7512.7.1.147154
110.0601qaxA0.4325.030.0760.7231.1.1.88NA
120.0603hhsB0.4494.460.0570.6821.14.18.1NA
130.0601yq2A0.4514.430.0910.6823.2.1.23NA
140.0602e1qA0.3445.520.0610.6131.17.3.2,1.17.1.4NA
150.0601dgjA0.4355.680.0550.8031.2.-.-NA
160.0601gp6A0.4374.750.0390.6821.14.11.19NA
170.0601jrpB0.4364.980.0560.7401.17.1.4132,138
180.0601ua4A0.4544.990.0570.7572.7.1.147NA
190.0601q1lA0.4304.680.0620.6764.2.3.5145

(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
00.360.6931.280.200.731lmiA GO:0005576 GO:0005615 GO:0005618
10.210.5423.170.140.683cfuA GO:0005886 GO:0016020
20.070.5114.260.070.754d0jA GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483
30.070.5143.230.150.664r4gA GO:0005886 GO:0016020
40.070.4864.020.100.692x41A GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0102483
50.060.3825.940.070.714i8dB GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0102483
60.060.3665.420.070.664iibA GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483
70.060.3585.110.030.583ut0A GO:0004553 GO:0005975 GO:0008152 GO:0016798 GO:0046872
80.060.5054.260.090.745fjiA GO:0000272 GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483
90.060.3535.880.040.673wlqA GO:0004553 GO:0005975 GO:0016787
100.060.4734.200.080.694zo6A GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
110.060.3425.960.030.654gnvB GO:0004553 GO:0004563 GO:0005737 GO:0005975 GO:0007049 GO:0008152 GO:0008360 GO:0009252 GO:0009254 GO:0016787 GO:0016798 GO:0051301 GO:0071555
120.060.3545.390.050.633abzB GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483
130.060.3535.340.060.623abzA GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483
140.060.5084.270.090.755fjjA GO:0000272 GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0008422 GO:0016052 GO:0016787 GO:0016798 GO:0030245 GO:0102483
150.060.3425.340.040.603sqlA GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
160.060.3305.200.040.574gyjA GO:0004553 GO:0004563 GO:0005576 GO:0005618 GO:0005886 GO:0005975 GO:0008152 GO:0008360 GO:0009252 GO:0009254 GO:0016020 GO:0016787 GO:0016798 GO:0071555
170.060.4964.050.110.714i3gB GO:0004553 GO:0005975
180.060.3225.430.050.592oxnA GO:0004553 GO:0004563 GO:0005737 GO:0005975 GO:0007049 GO:0008152 GO:0008360 GO:0009252 GO:0009254 GO:0009273 GO:0016787 GO:0016798 GO:0046677 GO:0051301 GO:0071555


Consensus prediction of GO terms
 
Molecular Function GO:0102483 GO:0008422
GO-Score 0.13 0.13
Biological Processes GO:0030245
GO-Score 0.07
Cellular Component GO:0016020 GO:0005618 GO:0005615
GO-Score 0.39 0.36 0.36

(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.