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I-TASSER results for job id Rv1073

[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
10.14 9 3tv5C RCP Rep, Mult 115,120,121,124
20.11 7 1stxA MN Rep, Mult 178,215,226,227
30.11 7 2jfrA MG Rep, Mult 228,229
40.02 1 5esrA CO Rep, Mult 182,199
50.02 1 4y8aB ZN Rep, Mult 226,256
60.02 1 3pgqB GY3 Rep, Mult 119,120,123,136,139
70.02 1 3fozB CA Rep, Mult 280,283
80.02 1 2x24B X24 Rep, Mult 185,188,189
90.02 1 4e45D ZN Rep, Mult 238,242
100.02 1 3ff6C RCP Rep, Mult 67,68,70,71
110.02 1 3h0qB B37 Rep, Mult 62,63,65,68
120.02 1 1brrB ARC Rep, Mult 227,279
130.02 1 5cg6A MG Rep, Mult 274,277

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
10.0601s9rA0.4085.490.0450.6293.5.3.6NA
20.0603kx2B0.4086.060.0580.6783.6.4.13NA
30.0603ff6A0.4346.220.0750.7286.4.1.2,6.3.4.1448
40.0601clcA0.4086.160.0570.6823.2.1.4NA
50.0601kb0A0.4056.200.0690.6851.1.99.-NA
60.0601ua4A0.4046.690.0900.7282.7.1.147NA
70.0601xc6A0.3376.900.0440.6293.2.1.23NA
80.0601m7jA0.4135.990.0210.6853.5.1.81NA
90.0601sllA0.4126.380.0230.7144.2.2.15257
100.0601h54B0.4066.780.0570.7462.4.1.8NA
110.0601ie7C0.4186.390.0560.7143.5.1.5NA
120.0601sliA0.4126.000.0420.6824.2.2.15,3.2.1.18NA
130.0601vrgA0.4026.240.0480.6856.4.1.2139
140.0601a5kC0.4276.110.0560.7033.5.1.5271
150.0601on3E0.4106.270.0360.6932.1.3.1NA
160.0601yniB0.3786.770.0550.6893.5.3.23186
170.0601uyvA0.4296.120.0390.7146.3.4.14,6.4.1.2NA
180.0601gkpA0.4076.280.0400.6933.5.2.2NA
190.0601r7aA0.3836.520.0760.6752.4.1.7226,262

(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
00.070.4125.980.040.672a7sA GO:0000166 GO:0003989 GO:0004658 GO:0005524 GO:0005618 GO:0005886 GO:0009317 GO:0015977 GO:0016874 GO:0043234
10.070.4276.000.050.714wyoB GO:0000166 GO:0003824 GO:0003989 GO:0004075 GO:0005524 GO:0005737 GO:0005783 GO:0005789 GO:0006606 GO:0006629 GO:0006631 GO:0006633 GO:0006998 GO:0008152 GO:0016020 GO:0016874 GO:0042759 GO:0046872 GO:2001295
20.060.4296.120.040.711uyvA GO:0000166 GO:0003824 GO:0003989 GO:0004075 GO:0005524 GO:0005737 GO:0005783 GO:0005789 GO:0006606 GO:0006629 GO:0006631 GO:0006633 GO:0006998 GO:0008152 GO:0016020 GO:0016874 GO:0042759 GO:0046872 GO:2001295
30.060.4236.490.040.741uyrA GO:0000166 GO:0003824 GO:0003989 GO:0004075 GO:0005524 GO:0005737 GO:0005783 GO:0005789 GO:0006606 GO:0006629 GO:0006631 GO:0006633 GO:0006998 GO:0008152 GO:0016020 GO:0016874 GO:0042759 GO:0046872 GO:2001295
40.060.4346.470.060.764asiC GO:0000166 GO:0001894 GO:0003824 GO:0003989 GO:0004075 GO:0005524 GO:0005730 GO:0005737 GO:0005739 GO:0005829 GO:0006084 GO:0006629 GO:0006631 GO:0006633 GO:0006768 GO:0006853 GO:0008152 GO:0015629 GO:0016874 GO:0031325 GO:0035338 GO:0044268 GO:0046872 GO:0051289 GO:0055088 GO:0070062 GO:0071380 GO:2001295
50.060.4106.270.040.691on3E GO:0003989 GO:0006633 GO:0009317 GO:0016740 GO:0016874 GO:0047154
60.060.3346.700.040.602bzrA GO:0000166 GO:0003989 GO:0004658 GO:0005524 GO:0005618 GO:0005886 GO:0009317 GO:0015977 GO:0016874 GO:0043234
70.060.4105.700.050.644g2rB GO:0000166 GO:0003989 GO:0004658 GO:0005524 GO:0005618 GO:0009317 GO:0016874 GO:0019367 GO:0040007
80.060.4145.950.070.673iavA GO:0003989 GO:0006633 GO:0009317 GO:0016874
90.060.4056.070.030.671x0uA GO:0003989 GO:0004658 GO:0006633 GO:0009317 GO:0016874
100.060.3586.820.060.661acoA GO:0003994 GO:0005506 GO:0005634 GO:0005739 GO:0006099 GO:0006101 GO:0008152 GO:0016829 GO:0043209 GO:0046872 GO:0051536 GO:0051539
110.060.4135.850.050.664rcnB GO:0003824 GO:0004075 GO:0005524 GO:0016874 GO:0046872
120.060.4276.100.080.712x24B
130.060.3575.670.070.564rcnA GO:0003824 GO:0004075 GO:0005524 GO:0016874 GO:0046872
140.060.4346.220.070.733ff6A GO:0000166 GO:0003824 GO:0003989 GO:0004075 GO:0005524 GO:0005634 GO:0005739 GO:0005741 GO:0005829 GO:0006084 GO:0006629 GO:0006631 GO:0006633 GO:0006768 GO:0006853 GO:0008152 GO:0010629 GO:0010884 GO:0010906 GO:0012505 GO:0016020 GO:0016874 GO:0031325 GO:0031667 GO:0031999 GO:0043086 GO:0046322 GO:0046872 GO:0050995 GO:0051289 GO:0060421 GO:0097009 GO:2001295
150.060.3956.890.060.733ueqA GO:0003824 GO:0005576 GO:0005975 GO:0016740 GO:0016757 GO:0047669
160.060.3166.340.060.545cs4B GO:0000166 GO:0003824 GO:0003989 GO:0004075 GO:0005524 GO:0005737 GO:0005783 GO:0005789 GO:0006606 GO:0006629 GO:0006631 GO:0006633 GO:0006998 GO:0008152 GO:0016020 GO:0016874 GO:0042759 GO:0046872 GO:2001295
170.060.4015.950.030.651vrgA GO:0003989 GO:0004658 GO:0016740 GO:0016874
180.060.3396.650.020.613n6rB GO:0004658 GO:0016874


Consensus prediction of GO terms
 
Molecular Function GO:0016421 GO:0032559 GO:0035639 GO:0032550 GO:0016879 GO:0043169
GO-Score 0.57 0.57 0.57 0.57 0.47 0.47
Biological Processes GO:0008610 GO:0071616 GO:2001293 GO:0072330 GO:0044744 GO:0001676 GO:0010256 GO:0017038 GO:0006997 GO:1902593 GO:0044802
GO-Score 0.47 0.47 0.47 0.47 0.36 0.36 0.36 0.36 0.36 0.36 0.36
Cellular Component GO:0042175 GO:0044432
GO-Score 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.