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I-TASSER results for job id Rv1433

[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
10.21 7 4jmxA IM2 Rep, Mult 195,210,212,224,228,232,243,244,245,246,248
20.06 2 1exvA 700 Rep, Mult 248,256,260
30.06 2 3cemA AVD Rep, Mult 227,228,253
40.06 2 2fkwD BCL Rep, Mult 264,267
50.04 1 4k73A CA Rep, Mult 48,49,262
60.03 1 3re0A CPT Rep, Mult 237,246
70.03 1 3bd7A CKB Rep, Mult 230,251,252
80.03 1 3cejA AVF Rep, Mult 215,217,218,227

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
10.0603flcX0.3856.550.0620.6942.7.1.30194,217
20.0602vsfA0.3895.950.0510.6493.6.4.1217
30.0602zf5Y0.3806.680.0390.6972.7.1.30227,230
40.0601aupA0.3686.480.0390.6421.4.1.2265
50.0601b26A0.3916.190.0570.6571.4.1.3122,265
60.0601e1yA0.3536.750.0440.6382.4.1.1NA
70.0601n63B0.3846.730.0460.7121.2.99.2NA
80.0602c4mC0.4006.330.0560.6792.4.1.1NA
90.0601rtkA0.3616.500.0720.6463.4.21.47230,254,256
100.0601fa9A0.3135.980.0490.5132.4.1.1NA
110.0603gpbA0.3155.830.0490.5132.4.1.1NA
120.0601w0iA0.3856.560.0480.6972.3.1.41NA
130.0601rs0A0.3606.370.0770.6353.4.21.47222
140.0601b3bE0.3916.150.0490.6461.4.1.3NA
150.0601ygpA0.3856.350.0480.6602.4.1.1176
160.0601ox0A0.3905.670.0660.6202.3.1.41NA
170.0602qllA0.3256.690.0480.6052.4.1.1NA
180.0602ix4A0.3916.050.0490.6492.3.1.413
190.0601bvuA0.3926.190.0570.6571.4.1.3122,265

(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
00.650.8010.920.990.824k73A GO:0008360 GO:0009252 GO:0016740 GO:0016746 GO:0071555
10.560.7341.840.540.794xvoA GO:0016740
20.510.7561.530.530.804jmnA GO:0005576 GO:0006508 GO:0008360 GO:0009252 GO:0016740 GO:0016746 GO:0018104 GO:0042597 GO:0071555 GO:0071972
30.290.6982.980.330.824qr7A GO:0005886 GO:0008360 GO:0009252 GO:0016020 GO:0016740 GO:0016746 GO:0046872 GO:0071555
40.190.6523.150.270.774z7aA GO:0016740
50.190.4274.180.140.554a52A GO:0008360 GO:0009252 GO:0016740 GO:0016757 GO:0016787 GO:0030435 GO:0031160 GO:0071555
60.130.4193.730.140.514xxtA GO:0004180 GO:0006508 GO:0016740 GO:0016787
70.130.4743.620.140.562hklA GO:0016020 GO:0016021 GO:0016740
80.120.4062.200.140.445bmqA GO:0016020 GO:0016021 GO:0016740
90.060.3186.540.040.561rf4A GO:0003824 GO:0003866 GO:0005737 GO:0008652 GO:0009073 GO:0009423 GO:0016740 GO:0016765
100.060.2546.320.020.453d2lC GO:0008168 GO:0016740 GO:0032259
110.060.2566.690.040.471bh3A GO:0006810 GO:0006811 GO:0009279 GO:0015288 GO:0016020 GO:0016021 GO:0046930 GO:0055085
120.060.3913.060.100.454lzhA GO:0016740
130.060.2446.630.040.443ga9L GO:0003840 GO:0006508 GO:0006749 GO:0008233 GO:0009405 GO:0016740 GO:0016787 GO:0045227
140.060.2016.190.090.344a3bG GO:0000291 GO:0000932 GO:0001172 GO:0003676 GO:0003697 GO:0003727 GO:0003899 GO:0003968 GO:0005634 GO:0005665 GO:0005737 GO:0006351 GO:0006366 GO:0006367 GO:0031369 GO:0045948 GO:0060213
150.060.1334.280.020.183ob9D GO:0003677 GO:0005634 GO:0005654 GO:0006338 GO:0006342 GO:0006351 GO:0006355 GO:0016568 GO:0016575 GO:0035064 GO:0035267 GO:0043968 GO:0043984 GO:0072487
160.060.1072.810.020.132n5jA GO:0000294 GO:0000932 GO:0001525 GO:0001933 GO:0002230 GO:0002376 GO:0003677 GO:0003682 GO:0003723 GO:0003729 GO:0003730 GO:0003824 GO:0004518 GO:0004519 GO:0004521 GO:0004532 GO:0004540 GO:0005634 GO:0005654 GO:0005737 GO:0005783 GO:0005791 GO:0005856 GO:0005886 GO:0006508 GO:0006915 GO:0006954 GO:0007275 GO:0007399 GO:0008152 GO:0008233 GO:0008234 GO:0010468 GO:0010508 GO:0010595 GO:0010628 GO:0010629 GO:0010656 GO:0010884 GO:0010942 GO:0016020 GO:0016579 GO:0016787 GO:0030154 GO:0030867 GO:0032088 GO:0032715 GO:0032720 GO:0034599 GO:0035198 GO:0035613 GO:0035925 GO:0036459 GO:0042149 GO:0042307 GO:0042347 GO:0042406 GO:0043022 GO:0043124 GO:0044828 GO:0045019 GO:0045600 GO:0045766 GO:0045944 GO:0046872 GO:0050713 GO:0051259 GO:0055118 GO:0061014 GO:0061158 GO:0071222 GO:0071347 GO:0071356 GO:0090501 GO:0090502 GO:0090503 GO:0098586 GO:1900016 GO:1900119 GO:1900165 GO:1900745 GO:1902714 GO:1903799 GO:1903936 GO:1904468 GO:1904628 GO:1904637 GO:1990869 GO:2000379 GO:2000627


Consensus prediction of GO terms
 
Molecular Function GO:0016746 GO:0043169 GO:0071972
GO-Score 0.88 0.57 0.51
Biological Processes GO:0071555 GO:0008360 GO:0018104 GO:0006508
GO-Score 0.88 0.88 0.51 0.51
Cellular Component GO:0071944 GO:0005576 GO:0042597
GO-Score 0.57 0.51 0.51

(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.