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I-TASSER results for job id Rv2179c

[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
10.52 82 1j53A MN Rep, Mult 6,7,8,145
20.16 33 3g10A MN Rep, Mult 6,90,95
30.16 30 2iocB D5M Rep, Mult 6,7,8,9,11,44,46,47,50,51,94,145
40.02 3 4okkA MG Rep, Mult 5,6,89,90,145,149
50.01 3 5dk5A MES Rep, Mult 8,50,51,141,145
60.00 1 3ngyD III Rep, Mult 65,67,68,71,75
70.00 1 4okeB MG Rep, Mult 37,65,66,67

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
10.5272gbzA0.7552.920.1450.9463.1.-.-8,140
20.4282is3B0.6632.720.1260.7923.1.13.-8,140
30.1681w0hA0.7373.220.1210.9343.1.11.-95,143
40.0931fxxA0.7533.130.0870.9583.1.11.18,140
50.0672p51A0.7453.580.1460.9763.1.13.46,143,147
60.0602guiA0.7093.000.1350.8812.7.7.78,140
70.0601hjrC0.4694.350.0650.7023.1.22.46,99,148
80.0602o4iA0.7333.180.1330.9233.1.11.26,8,94,99,145
90.0601q8iA0.6243.740.1330.8392.7.7.776,146
100.0602jguA0.6363.650.1030.8512.7.7.770,74
110.0602ajqA0.5983.070.1090.7622.7.7.770,101
120.0601s5jA0.6483.360.1230.8452.7.7.7NA
130.0602oa8B0.7323.120.1330.9233.1.11.26,8,94,145
140.0602p1jB0.5843.660.1290.7562.7.7.7NA
150.0601tgoA0.6393.370.0970.8452.7.7.7113
160.0601cjyA0.4674.880.0510.7443.1.1.4,3.1.1.5NA
170.0601whvA0.2224.740.0960.3633.1.13.4101
180.0602zf5Y0.4714.890.0410.7982.7.1.30NA
190.0603flcX0.4334.730.0860.7142.7.1.3098
200.0601wljA0.6863.120.1010.8813.1.13.18,140
210.0602gv9B0.6343.530.1350.8512.7.7.729,135,145
220.0602a1rB0.7473.270.0810.9463.1.13.49,10
230.0603hz6A0.4774.860.0480.7862.7.1.1749

(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
00.670.9211.110.980.964hecB GO:0000287 GO:0003676 GO:0004518 GO:0004527 GO:0004532 GO:0008408 GO:0016787 GO:0040007 GO:0046872 GO:0090305 GO:0090503
10.520.7423.160.110.952igiA GO:0000175 GO:0003676 GO:0004518 GO:0004527 GO:0005737 GO:0005829 GO:0006259 GO:0006401 GO:0008310 GO:0016787 GO:0016788 GO:0016896 GO:0034611 GO:0046872 GO:0090305 GO:0090501 GO:0090503
20.380.7512.870.140.933tr8A GO:0000175 GO:0003676 GO:0004518 GO:0004527 GO:0005737 GO:0016787 GO:0016788 GO:0016896 GO:0090305 GO:0090503
30.350.7552.920.140.952gbzA GO:0000175 GO:0003676 GO:0004518 GO:0004527 GO:0005737 GO:0016787 GO:0016788 GO:0016896 GO:0090305 GO:0090503
40.330.7773.190.130.982f96A GO:0000287 GO:0003676 GO:0004518 GO:0004527 GO:0004540 GO:0006396 GO:0008033 GO:0016787 GO:0016896 GO:0046872 GO:0090305 GO:0090501 GO:0090503
50.310.7032.960.140.863ngyC GO:0000287 GO:0003676 GO:0004518 GO:0004527 GO:0004540 GO:0005829 GO:0006396 GO:0008033 GO:0016787 GO:0016896 GO:0046872 GO:0090305 GO:0090501 GO:0090503
60.290.7453.190.130.951j9aA GO:0000175 GO:0003676 GO:0004518 GO:0004527 GO:0005737 GO:0016787 GO:0016788 GO:0016896 GO:0090305 GO:0090503
70.280.7492.980.130.945cy4C GO:0003676 GO:0004518 GO:0004527 GO:0005737 GO:0016787 GO:0016788 GO:0016896 GO:0090305 GO:0090503
80.260.7103.260.110.915fkvD GO:0003676 GO:0003677 GO:0003887 GO:0004518 GO:0004527 GO:0006260 GO:0016740 GO:0016779 GO:0016787 GO:0044776 GO:0045004 GO:0046872 GO:0071897 GO:0090305
90.230.7493.230.090.954rg8A GO:0003676 GO:0004518 GO:0004527 GO:0004529 GO:0006281 GO:0006974 GO:0008852 GO:0016787 GO:0046872 GO:0090305
100.220.5843.660.130.762p1jB GO:0003676 GO:0003677 GO:0003824 GO:0003887 GO:0004518 GO:0004527 GO:0005737 GO:0006260 GO:0006261 GO:0008408 GO:0016740 GO:0016779 GO:0016787 GO:0071897 GO:0090305
110.150.7883.170.130.983v9xB GO:0000287 GO:0003676 GO:0004518 GO:0004527 GO:0004540 GO:0005829 GO:0006396 GO:0008033 GO:0016787 GO:0016896 GO:0046872 GO:0090305 GO:0090501 GO:0090503
120.140.7513.330.080.952a1sC GO:0000166 GO:0000184 GO:0000289 GO:0003676 GO:0003723 GO:0003730 GO:0004518 GO:0004527 GO:0004535 GO:0005634 GO:0005730 GO:0005737 GO:0005829 GO:0006402 GO:0007292 GO:0009451 GO:0016787 GO:0019901 GO:0043488 GO:0044822 GO:0046872 GO:0090305 GO:0090503
130.140.7513.480.120.984gmjB GO:0000175 GO:0000289 GO:0000290 GO:0000932 GO:0003676 GO:0003700 GO:0003723 GO:0004518 GO:0004527 GO:0004532 GO:0004535 GO:0004871 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0005975 GO:0006351 GO:0006355 GO:0006417 GO:0006977 GO:0007165 GO:0008284 GO:0008285 GO:0010629 GO:0016020 GO:0016787 GO:0030014 GO:0031047 GO:0033962 GO:0035195 GO:0043928 GO:0045944 GO:0046872 GO:0060213 GO:0061014 GO:0090305 GO:0090503 GO:1900153
140.130.7523.200.080.964js4A GO:0000175 GO:0000287 GO:0000738 GO:0003676 GO:0003677 GO:0003697 GO:0004518 GO:0004527 GO:0004529 GO:0006281 GO:0006308 GO:0006974 GO:0008310 GO:0008852 GO:0016787 GO:0046872 GO:0051575 GO:0090503
150.130.7453.580.150.982p51A GO:0000289 GO:0003676 GO:0003723 GO:0003729 GO:0004518 GO:0004527 GO:0004535 GO:0005634 GO:0005737 GO:0005829 GO:0006351 GO:0006355 GO:0016787 GO:0030014 GO:0030015 GO:0046872 GO:0090305 GO:0090503
160.120.7413.380.150.974b8cA GO:0000175 GO:0000289 GO:0000932 GO:0003676 GO:0003723 GO:0004518 GO:0004527 GO:0005634 GO:0005737 GO:0006351 GO:0006355 GO:0006357 GO:0006368 GO:0016787 GO:0030015 GO:0032968 GO:0046872 GO:0090305 GO:0090503
170.120.7253.340.070.943c95A GO:0000175 GO:0000287 GO:0000738 GO:0003676 GO:0003677 GO:0003697 GO:0004518 GO:0004527 GO:0004529 GO:0006281 GO:0006308 GO:0006974 GO:0008310 GO:0008852 GO:0016787 GO:0046872 GO:0051575 GO:0090503
180.110.7273.300.090.923d45B GO:0000166 GO:0000184 GO:0000289 GO:0003676 GO:0003723 GO:0004518 GO:0004527 GO:0004535 GO:0005634 GO:0005730 GO:0005737 GO:0006402 GO:0016787 GO:0019901 GO:0044822 GO:0046872 GO:0090305 GO:0090503


Consensus prediction of GO terms
 
Molecular Function GO:0003676 GO:0000175 GO:0000287 GO:0034611 GO:0008310
GO-Score 0.96 0.81 0.78 0.52 0.52
Biological Processes GO:0090503 GO:0040007 GO:0006401 GO:0006259 GO:0008033
GO-Score 0.96 0.67 0.52 0.52 0.33
Cellular Component GO:0005829
GO-Score 0.52

(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.