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I-TASSER results for job id Rv1514c

[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
10.41 31 4d11B UDP Rep, Mult 12,13,14,43,68,70,71,91,92,93,200,205
20.30 24 2z86B UGA Rep, Mult 12,13,14,43,68,70,71,74,91,92,93,174,175,176,177,200,205
30.03 3 4fiyA MN Rep, Mult 16,91,93,200
40.02 2 2z86C MN Rep, Mult 93,94,203
50.01 1 1h7qA MG Rep, Mult 112,114
60.01 1 1yp2A PMB Rep, Mult 11,13,40,41,42,63,64

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
10.1491vgwB0.5433.340.0920.6602.7.7.6071,95,99,153
20.0672px7A0.5123.480.1560.6262.7.7.6023,71,96,202
30.0661i52A0.5463.490.1010.6762.7.7.60,2.7.7.-31
40.0661vpaA0.5353.240.0630.6492.7.7.6031
50.0662vsiB0.5353.700.0800.6722.7.7.6095
60.0663lw6A0.5433.320.0920.6642.4.1.133177
70.0661h7eA0.5483.970.0710.7022.7.7.3831
80.0662agdA0.5613.730.1020.6952.4.1.9095
90.0663k8dA0.5444.000.0760.7142.7.7.3831
100.0662pa4B0.5753.880.0650.7412.7.7.931
110.0661wvcA0.5353.600.0950.6792.7.7.33NA
120.0663f1cB0.5333.870.0680.6792.7.7.6095,202
130.0661vicA0.5293.910.0880.6792.7.7.3831
140.0602vs4A0.5503.690.0700.6992.4.1.8757
150.0601on8A0.6193.950.0790.8012.4.1.223159
160.0601hm8A0.5723.710.0440.7252.7.7.2331
170.0602ux8G0.5504.150.0760.7292.7.7.9226
180.0603hl3A0.5703.520.1300.7142.7.7.2422
190.0601kwsA0.5853.400.0720.7102.4.1.13597,197
200.0603fwwA0.5643.790.0810.7212.3.1.157,2.7.7.2331
210.0602d0jA0.5843.480.1120.7142.4.1.135NA
220.0602cu2A0.5614.160.0990.7482.7.7.13NA
230.0601foaA0.6204.410.0530.8172.4.1.101NA
240.0601fggA0.5843.420.0720.7102.4.1.135NA
250.0602d0jC0.5833.570.1120.7182.4.1.13597
260.0601h7tA0.5493.960.0710.7022.7.7.38NA
270.0601fxoB0.5493.830.0820.7142.7.7.24NA
280.0603dk5A0.5813.300.0710.7022.3.1.15731
290.0602yqjA0.5664.070.0390.7412.7.7.2344,76
300.0602e3dC0.5693.730.0590.7212.7.7.9NA
310.0602oi6B0.5773.800.0890.7292.3.1.157,2.7.7.23NA
320.0601v82A0.5833.500.0830.7142.4.1.135NA

(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
00.310.8112.860.150.932z86C GO:0016740 GO:0016757 GO:0047238 GO:0050510
10.260.7732.190.160.841h7qA GO:0016740 GO:0016757
20.190.5933.650.100.735ekeC GO:0005886 GO:0016020 GO:0016021 GO:0016740 GO:0016757
30.190.5922.410.200.663bcvA GO:0016740
40.190.7394.000.120.942d7iA GO:0000139 GO:0004653 GO:0005794 GO:0006486 GO:0006493 GO:0016020 GO:0016021 GO:0016266 GO:0016740 GO:0016757 GO:0030246 GO:0046872
50.140.7523.850.120.954hg6A GO:0000166 GO:0006011 GO:0016020 GO:0016021 GO:0016740 GO:0016757 GO:0016759 GO:0016760 GO:0030244 GO:0035438
60.090.5613.730.100.692agdA GO:0000138 GO:0000139 GO:0002064 GO:0002526 GO:0003831 GO:0003945 GO:0004461 GO:0005576 GO:0005615 GO:0005794 GO:0005886 GO:0005975 GO:0005989 GO:0006012 GO:0006486 GO:0006487 GO:0007155 GO:0007339 GO:0007341 GO:0008092 GO:0008285 GO:0008378 GO:0009101 GO:0009312 GO:0009611 GO:0009897 GO:0009986 GO:0016020 GO:0016021 GO:0016323 GO:0016740 GO:0016757 GO:0018146 GO:0019901 GO:0030057 GO:0030112 GO:0030145 GO:0030175 GO:0030198 GO:0030879 GO:0031526 GO:0032580 GO:0035250 GO:0042060 GO:0042127 GO:0042803 GO:0042995 GO:0043014 GO:0043065 GO:0045136 GO:0046872 GO:0048487 GO:0048754 GO:0050900 GO:0051270 GO:0060046 GO:0060054 GO:0060055 GO:0060058 GO:0070062
70.090.5453.540.100.671fgxB GO:0000138 GO:0002064 GO:0002526 GO:0003831 GO:0003945 GO:0004461 GO:0005576 GO:0005615 GO:0005794 GO:0005886 GO:0005975 GO:0005989 GO:0006012 GO:0006486 GO:0006487 GO:0007155 GO:0007339 GO:0007341 GO:0008092 GO:0008285 GO:0008378 GO:0009101 GO:0009312 GO:0009897 GO:0009986 GO:0016020 GO:0016021 GO:0016323 GO:0016740 GO:0016757 GO:0030057 GO:0030112 GO:0030145 GO:0030175 GO:0030198 GO:0030879 GO:0031526 GO:0032580 GO:0035250 GO:0042060 GO:0042127 GO:0042803 GO:0042995 GO:0043014 GO:0043065 GO:0045136 GO:0046872 GO:0048487 GO:0048754 GO:0050900 GO:0051270 GO:0060046 GO:0060054 GO:0060055 GO:0060058 GO:0070062
80.070.7313.780.140.921xhbA GO:0004653 GO:0005576 GO:0005794 GO:0006486 GO:0006493 GO:0016020 GO:0016021 GO:0016740 GO:0016757 GO:0018242 GO:0018243 GO:0030145 GO:0030246 GO:0032580 GO:0046872 GO:0048471
90.070.5363.010.110.632we9B GO:0046872
100.070.5082.670.140.583d5nA
110.070.5352.880.120.632wawA
120.070.7173.720.130.904d11C GO:0000139 GO:0002378 GO:0004653 GO:0005576 GO:0005789 GO:0005794 GO:0005795 GO:0006486 GO:0006493 GO:0016020 GO:0016021 GO:0016266 GO:0016740 GO:0016757 GO:0018242 GO:0018243 GO:0030145 GO:0030173 GO:0030246 GO:0032580 GO:0046872 GO:0048471 GO:0070062
130.070.4843.320.070.602e8bA GO:0000166 GO:0003824 GO:0005525 GO:0005737 GO:0006777 GO:0016740 GO:0019720 GO:0046872 GO:0061603 GO:0070568
140.070.7313.900.130.934d0tA GO:0000139 GO:0002378 GO:0004653 GO:0005576 GO:0005789 GO:0005794 GO:0005795 GO:0006486 GO:0006493 GO:0016020 GO:0016021 GO:0016266 GO:0016740 GO:0016757 GO:0018242 GO:0018243 GO:0030145 GO:0030173 GO:0030246 GO:0032580 GO:0046872 GO:0048471 GO:0070062
150.060.3455.560.060.571vknA GO:0003942 GO:0005737 GO:0006526 GO:0008652 GO:0016491 GO:0016620 GO:0046983 GO:0051287 GO:0055114
160.060.3275.060.030.491cydA GO:0004090 GO:0005739 GO:0005759 GO:0006116 GO:0016491 GO:0043621 GO:0051262 GO:0055114
170.060.3024.750.080.443eozB GO:0004614 GO:0004619 GO:0006096 GO:0016020 GO:0016021 GO:0016853
180.060.2975.700.030.472hpsA GO:0005509 GO:0046872
190.060.2896.460.040.511yxaA GO:0004867 GO:0005576 GO:0005615 GO:0006953 GO:0010466 GO:0010951 GO:0030414 GO:0034097 GO:0043434 GO:0070062 GO:0072562
200.060.2835.290.040.423hs3A GO:0003677 GO:0003700 GO:0006351 GO:0006355
210.060.2535.260.040.395a52A GO:0005096 GO:0005543 GO:0005634 GO:0005886 GO:0008289 GO:0009738 GO:0009789 GO:0016020 GO:0043547 GO:0046872
220.060.2485.530.050.392xt2A GO:0016746
230.060.2566.210.050.464u9wB GO:0006629 GO:0008080 GO:0016740 GO:0016746
240.060.2356.290.040.424prhD GO:0005886 GO:0016020 GO:0016021 GO:0031295 GO:0050776 GO:0050852
250.060.2225.300.040.353fouA GO:0016020 GO:0016021 GO:0016491 GO:0016679 GO:0046872 GO:0051536 GO:0051537 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0043169 GO:0050510 GO:0047238
GO-Score 0.38 0.31 0.31
Biological Processes GO:0006493
GO-Score 0.38
Cellular Component GO:0071944 GO:0098588 GO:0044431 GO:0016021
GO-Score 0.39 0.38 0.38 0.35

(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.