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I-TASSER results for job id Rv2235

[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
10.11 5 2h6bA 3C4 Rep, Mult 227,230
20.05 2 3serA CA Rep, Mult 34,36
30.05 2 4il6x CLA Rep, Mult 225,226
40.02 1 1g42A CP2 Rep, Mult 99,100
50.02 1 2r4jA IMD Rep, Mult 32,33,85,134
60.02 1 5a43B DMU Rep, Mult 25,33
70.02 1 3k7tB GP7 Rep, Mult 173,176,179
80.02 1 3rr5A MG Rep, Mult 162,246
90.02 1 3mq7E CA Rep, Mult 217,220
100.02 1 4q9iA ALA Rep, Mult 233,237
110.02 1 1mvyA GLC Rep, Mult 77,78,144,147,149
120.02 1 2o01H CLA Rep, Mult 114,118
130.02 1 3kziX CLA Rep, Mult 230,233
140.02 1 2yzjC MG Rep, Mult 91,108
150.02 1 2zpgB TB0 Rep, Mult 217,267
160.02 1 3aodA MIY Rep, Mult 45,78,80

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
10.0601z0hB0.2716.540.0380.4943.4.24.69159
20.0601a31A0.3275.860.0300.5285.99.1.2164
30.0602a4zA0.3035.800.0510.4872.7.1.153NA
40.0602vuaA0.2666.620.0250.4943.4.24.69164
50.0602je8B0.3736.260.0610.6243.2.1.25104
60.0602zuwC0.3516.030.0160.5832.4.1.211112
70.0603c5wA0.2296.330.0390.4023.1.3.16NA
80.0603btaA0.3596.960.0550.6793.4.24.69NA
90.0602gq3A0.3495.730.0350.5392.3.3.9NA
100.0601vncA0.2866.370.0240.5021.11.1.10206,208,210
110.0601n63B0.3446.680.0750.6311.2.99.2NA
120.0601y8bA0.2856.270.0470.4982.3.3.9NA
130.0601h16A0.3536.130.0360.5982.3.1.54NA
140.0601rr8C0.3315.780.0300.5245.99.1.2NA
150.0601jqoA0.3455.860.0510.5574.1.1.31NA
160.0601cjyA0.3675.700.0640.5833.1.1.4,3.1.1.5NA
170.0601iduA0.3525.970.0360.5831.11.1.10NA
180.0601s46A0.3326.510.0620.5832.4.1.4NA
190.0603b8cB0.3625.870.0470.5833.6.3.6NA

(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
00.100.6753.950.080.875gaoE GO:0000387 GO:0000398 GO:0000481 GO:0005634 GO:0005681 GO:0006397 GO:0008380 GO:0030529 GO:0045292 GO:0046540
10.060.3935.860.060.633syjA GO:0004175 GO:0004252 GO:0005576 GO:0006508 GO:0007155 GO:0008233 GO:0008236 GO:0009279 GO:0009986 GO:0016020 GO:0016021 GO:0016787 GO:0019867 GO:0042597 GO:0042802
20.060.4005.510.060.623ak5A GO:0004175 GO:0004252 GO:0005576 GO:0006508 GO:0008233 GO:0008236 GO:0009279 GO:0009405 GO:0009986 GO:0016020 GO:0016021 GO:0016787 GO:0019867 GO:0042597
30.060.3936.030.060.653h09B GO:0004175 GO:0004252 GO:0005576 GO:0006508 GO:0008233 GO:0008236 GO:0009279 GO:0009405 GO:0009986 GO:0016020 GO:0016021 GO:0016787 GO:0042597
40.060.2826.680.070.524g33A GO:0016165 GO:0016491 GO:0016702 GO:0042597 GO:0046872 GO:0051213 GO:0055114
50.060.3995.430.060.621wxrA GO:0004175 GO:0004252 GO:0005576 GO:0006508 GO:0008233 GO:0008236 GO:0009279 GO:0009405 GO:0009986 GO:0016020 GO:0016021 GO:0016787 GO:0019867 GO:0042597
60.060.2666.020.040.432d09A GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0042440 GO:0046872 GO:0055114
70.060.2046.780.040.384igdA GO:0001867 GO:0002376 GO:0004252 GO:0005509 GO:0005576 GO:0005615 GO:0006508 GO:0006898 GO:0006956 GO:0008233 GO:0008236 GO:0016787 GO:0042803 GO:0045087 GO:0045916 GO:0046872 GO:0048306
80.060.3446.230.040.584om9A GO:0004175 GO:0004252 GO:0005576 GO:0006508 GO:0008233 GO:0008236 GO:0009279 GO:0009405 GO:0009986 GO:0016020 GO:0016021 GO:0016787 GO:0019867 GO:0042597
90.060.2366.340.040.401azwA GO:0004177 GO:0005737 GO:0006508 GO:0008233 GO:0016787
100.060.3906.000.040.643szeA GO:0004175 GO:0004252 GO:0005576 GO:0006508 GO:0008233 GO:0008236 GO:0009279 GO:0009405 GO:0009986 GO:0016020 GO:0016021 GO:0016787 GO:0019867 GO:0042597
110.060.2556.480.040.452uuvC GO:0003824 GO:0005777 GO:0006629 GO:0008609 GO:0008610 GO:0008611 GO:0016491 GO:0016614 GO:0016740 GO:0043178 GO:0044351 GO:0050660 GO:0055114 GO:0071949
120.060.2876.580.050.521dabA GO:0005576 GO:0007155 GO:0009279 GO:0009405 GO:0009986 GO:0016020 GO:0016021 GO:0019867 GO:0042597
130.060.3986.440.040.725a9q1 GO:0000776 GO:0005487 GO:0005634 GO:0005635 GO:0005643 GO:0005829 GO:0006406 GO:0006409 GO:0006810 GO:0007062 GO:0007077 GO:0010827 GO:0015031 GO:0016032 GO:0016925 GO:0019083 GO:0031047 GO:0031080 GO:0051028 GO:0075733 GO:1900034
140.060.2635.950.040.432iouG GO:0007155 GO:0019867
150.060.2126.370.030.374exlB GO:0005886 GO:0006810 GO:0006817 GO:0015415 GO:0016020 GO:0016036 GO:0035435 GO:0042301
160.060.2256.270.040.393hsqA GO:0005737 GO:0006629 GO:0008610 GO:0008780 GO:0009245 GO:0016740 GO:0016746
170.060.2256.670.030.411gvfB GO:0003824 GO:0005829 GO:0005975 GO:0008270 GO:0009025 GO:0016829 GO:0016832 GO:0046872 GO:2001059
180.060.2276.670.040.413dahC GO:0000166 GO:0000287 GO:0004749 GO:0005524 GO:0005737 GO:0006015 GO:0009156 GO:0009165 GO:0016301 GO:0016310 GO:0016740 GO:0044249 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0004175 GO:0008236
GO-Score 0.36 0.36
Biological Processes GO:0019538
GO-Score 0.36
Cellular Component GO:0030313 GO:0044462 GO:0019867
GO-Score 0.36 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.