[Home] [Server] [About] [Statistics] [Annotation]

I-TASSER results for job id Rv1395

[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
10.08 4 1d5yB NUC Rep, Mult 292,324,327,331
20.08 4 1bl0A NUC Rep, Mult 261,262,274,277,278,281,286,288,289,322,323,326,327,330,336,337,338,339
30.08 4 2d4qB POP Rep, Mult 274,278
40.04 2 1jyxB NA Rep, Mult 263,264,265,268,271
50.04 2 1s5lI CLA Rep, Mult 319,325
60.04 2 3w6vA NUC Rep, Mult 272,274,275,278,279,289,292,319,328,331
70.02 1 4tt0B IOD Rep, Mult 148,149,152
80.02 1 3gbgA PAM Rep, Mult 123,131,133,304,333,335,343
90.02 1 1hn1B NA Rep, Mult 90,94,103,104,106
100.02 1 1n38A CH1 Rep, Mult 302,303,312,315,316,317
110.02 1 4rku4 CLA Rep, Mult 151,154
120.02 1 4qvpK MG Rep, Mult 276,280
130.02 1 1n35A CH1 Rep, Mult 294,295,297,332

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
10.0603khuB0.3796.310.0430.6081.1.1.22NA
20.0601cb8A0.3826.850.0390.6664.2.2.5NA
30.0602cjqA0.3717.020.0680.6572.7.7.48,3.4.21.113NA
40.0602cqsA0.3916.590.0390.6602.4.1.20NA
50.0602zuwC0.3826.310.0530.6022.4.1.211107,221,232
60.0601ayxA0.3866.480.0570.6313.2.1.3239
70.0602nq5A0.3886.680.0900.6392.1.1.14239
80.0602ze9A0.4116.230.0680.6633.1.4.4289,291
90.0602hcsA0.3276.760.0480.5642.7.7.48,3.4.21.91NA
100.0603i9v10.3786.580.0640.6311.6.99.588,93
110.0602wyhA0.3786.810.0740.6453.2.1.24NA
120.0602ow6A0.3916.550.0580.6453.2.1.114220
130.0602dqmA0.3836.050.0410.6053.4.11.2NA
140.0602azdB0.3806.440.0390.6162.4.1.1NA
150.0601ojnA0.4066.420.0450.6744.2.2.1329
160.0602pziA0.3896.140.0850.6162.7.11.1102
170.0601ofdA0.3826.560.0420.6251.4.7.1NA
180.0601s4fA0.3787.140.0540.6802.7.7.48254
190.0602eabA0.4056.700.0550.6803.2.1.63NA

(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
00.430.8731.410.220.915chhA GO:0000987 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0019172 GO:0019243 GO:0043565
10.070.4146.580.080.693wirA GO:0003824 GO:0005975 GO:0016740 GO:0016757 GO:0030246 GO:0033831
20.060.4316.460.060.711h54B GO:0003824 GO:0005975 GO:0030246
30.060.4246.770.040.722yk0A GO:0004872 GO:0009405 GO:0016020 GO:0016021 GO:0046872
40.060.3816.700.030.664p1tA GO:0004872 GO:0009405 GO:0016021
50.060.3556.000.050.561zroA GO:0004872 GO:0009405 GO:0016021
60.060.3535.840.030.552wauA GO:0004872 GO:0009405 GO:0016021 GO:0016337 GO:0020002 GO:0020013 GO:0020030 GO:0020033 GO:0020035 GO:0046789 GO:0050839
70.060.3495.780.040.534nuuB GO:0004872 GO:0009405 GO:0016020 GO:0016021
80.060.3375.620.040.512y8dA GO:0004872 GO:0009405 GO:0016021
90.060.3535.780.030.543cpzA GO:0004872 GO:0009405 GO:0016021
100.060.3385.890.050.533vuvA GO:0004872 GO:0009405 GO:0009986 GO:0016020 GO:0016021 GO:0042493 GO:0046812 GO:0046872
110.060.3626.010.050.564gf2A GO:0004872 GO:0009405 GO:0016020 GO:0016021
120.060.3325.630.030.494k2uA GO:0004872 GO:0008201 GO:0009405 GO:0016020 GO:0016021 GO:0020009 GO:0030260 GO:0046789
130.060.3035.740.040.465f3jA GO:0004872 GO:0009405 GO:0016020 GO:0016021
140.060.2852.100.310.313mklB GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0043565
150.060.2836.680.030.484ur3A GO:0046872 GO:0051536 GO:0051539
160.060.2724.900.050.374ur3E GO:0046872 GO:0051536 GO:0051539
170.060.2842.720.140.321xs9A GO:0000987 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0019172 GO:0019243 GO:0043565 GO:0045892 GO:0045893 GO:0046677
180.060.2761.930.170.303oouA GO:0000160 GO:0003677 GO:0003700 GO:0005622 GO:0006351 GO:0006355 GO:0043565


Consensus prediction of GO terms
 
Molecular Function GO:0019172 GO:0003700 GO:0000987
GO-Score 0.43 0.43 0.43
Biological Processes GO:0006355 GO:0019243
GO-Score 0.43 0.43
Cellular Component GO:0005829
GO-Score 0.43

(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.