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I-TASSER results for job id Rv3732

[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 1l5gB UUU Rep, Mult 59,61,63,65,69
20.05 3 1rd4A L08 Rep, Mult 18,22,35,135,137,279,282,283,284,310,311,312,313,325,328
30.03 2 2xr9A ZN Rep, Mult 58,96,236,237
40.03 2 4q9lA PHE Rep, Mult 20,24
50.03 2 5li3B 9RB Rep, Mult 157,160
60.03 2 1dw2C NO Rep, Mult 160,161,164
70.03 2 2buqA CAQ Rep, Mult 178,179
80.03 2 4bzzA ACT Rep, Mult 21,25,330
90.02 1 3wmoP BCL Rep, Mult 26,27
100.02 1 3u7eB MG Rep, Mult 58,236
110.02 1 2vdoB III Rep, Mult 241,243,245
120.02 1 2vc2B 180 Rep, Mult 27,33,34,35,36,37,39
130.02 1 1u8cB UUU Rep, Mult 204,206,214,233,235
140.02 1 1e08A HEM Rep, Mult 35,59
150.02 1 1l5gB III Rep, Mult 91,92,94,99
160.02 1 1kj4B III Rep, Mult 84,89
170.02 1 1gz7A GOL Rep, Mult 76,220,221,224
180.02 1 2islB OXY Rep, Mult 142,201
190.02 1 2ww8A CA Rep, Mult 206,209,212,214,236
200.02 1 4iqdA PYR Rep, Mult 10,11

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
10.0601cleA0.4046.620.0520.6703.1.1.3NA
20.0601k4yA0.3976.000.0680.6053.1.1.1NA
30.0601f6wA0.3706.440.0270.5943.1.1.13,3.1.1.3NA
40.0602fj0A0.3896.710.0310.6483.1.1.1NA
50.0601e1eB0.4006.570.0570.6653.2.1.21NA
60.0601gz7C0.4016.550.0380.6653.1.1.3NA
70.0601ahpA0.3926.090.0850.6222.4.1.1NA
80.0602b4kA0.4046.040.0280.6193.1.1.43202
90.0601dwaM0.3946.920.0520.6793.2.1.147NA
100.0601ygpA0.3856.630.0480.6452.4.1.1NA
110.0601l7qA0.4056.060.0530.6223.1.1.1NA
120.0602hihA0.4085.980.0370.6223.1.1.3NA
130.0601lpsA0.4046.860.0510.6853.1.1.3NA
140.0602i6qA0.3944.710.0630.5343.4.21.43NA
150.0602jlgC0.3866.800.0480.6482.7.7.48NA
160.0601thgA0.3976.470.0420.6563.1.1.336,337
170.0601itwB0.3856.340.0380.6111.1.1.42NA
180.0601eveA0.3956.490.0560.6453.1.1.7NA
190.0601aknA0.4056.240.0340.6423.1.1.13,3.1.1.3237

(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
00.120.7274.050.070.923txaA GO:0016020 GO:0016021 GO:0046872
10.120.7094.210.070.902ww8A GO:0016020 GO:0016021
20.060.2916.960.060.513mjmA GO:0004151 GO:0006221 GO:0008270 GO:0016787 GO:0016812 GO:0019856 GO:0044205 GO:0046872
30.060.4414.960.080.613efoB GO:0000139 GO:0001701 GO:0002474 GO:0005737 GO:0005783 GO:0005789 GO:0005794 GO:0005829 GO:0006810 GO:0006886 GO:0006888 GO:0008270 GO:0012507 GO:0015031 GO:0016020 GO:0016192 GO:0019886 GO:0030127 GO:0048208 GO:0048471
40.060.2956.190.030.473pnuA GO:0004151 GO:0006221 GO:0016787 GO:0016812 GO:0019856 GO:0044205 GO:0046872
50.060.2957.270.040.521ytmA GO:0000166 GO:0004611 GO:0004612 GO:0005524 GO:0005737 GO:0006094 GO:0016829 GO:0016831 GO:0017076 GO:0046872
60.060.2647.340.040.492xidB GO:0016020 GO:0016021
70.060.2654.950.040.371j8dA GO:0005829 GO:0008781 GO:0009103 GO:0016311 GO:0016787 GO:0019143 GO:0046872
80.060.2785.390.060.413c3yA GO:0008168 GO:0008171 GO:0016740 GO:0032259 GO:0042409 GO:0046872
90.060.2556.150.040.402b69A GO:0005739 GO:0005794 GO:0016020 GO:0016021 GO:0016829 GO:0016831 GO:0032580 GO:0033320 GO:0042803 GO:0048040 GO:0051262 GO:0070062 GO:0070403
100.060.2466.370.030.393mydA GO:0005886 GO:0006810 GO:0009306 GO:0015031 GO:0016020 GO:0016021 GO:0044780 GO:0044781
110.060.2266.070.040.354lk3B GO:0005739 GO:0005794 GO:0016020 GO:0016021 GO:0016829 GO:0016831 GO:0032580 GO:0033320 GO:0042803 GO:0048040 GO:0051262 GO:0070062 GO:0070403
120.060.2316.810.030.394p0dA GO:0005576 GO:0005618
130.060.1946.220.030.313h7tA GO:0004252 GO:0006508 GO:0046872
140.060.2326.110.080.373p56D GO:0003676 GO:0003723 GO:0004518 GO:0004519 GO:0004523 GO:0004540 GO:0005634 GO:0005654 GO:0005737 GO:0006260 GO:0006298 GO:0006401 GO:0016070 GO:0016787 GO:0032299 GO:0043137 GO:0046872 GO:0090305 GO:0090501 GO:0090502
150.060.2777.030.060.481twaA GO:0001055 GO:0001172 GO:0003677 GO:0003899 GO:0003968 GO:0005634 GO:0005665 GO:0006351 GO:0006366 GO:0016740 GO:0016779 GO:0019985 GO:0043566 GO:0046872
160.060.1986.780.050.343kptB GO:0016020 GO:0016021
170.060.2256.310.060.364oq1A GO:0016020 GO:0016021
180.060.1906.390.040.314v96AA GO:0098025


Consensus prediction of GO terms
 
Molecular Function GO:0043169
GO-Score 0.46
Biological Processes GO:0044205 GO:0019856 GO:0002474 GO:0001701 GO:0019886 GO:0048208 GO:0006886
GO-Score 0.12 0.12 0.06 0.06 0.06 0.06 0.06
Cellular Component GO:0031224
GO-Score 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.