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I-TASSER results for job id Rv3231c

[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
10.13 9 3htjA ET Rep, Mult 57,60,81,84,85,88,99,100,125,149,150
20.07 5 3g1mA RF3 Rep, Mult 64,81,82,85,126,132,133,136,146,149,150,153,166
30.04 3 5f04A 5TB Rep, Mult 64,81,85,101,109,122,126,132,133,146,149,150,153,154,166
40.04 3 4f8hA LMD Rep, Mult 56,59
50.03 2 2eh30 III Rep, Mult 101,109,112,113,118,122,125,140,143,144,146,147,148,150,151,154,155,156,161,164,165,168
60.03 2 1bjyB CTC Rep, Mult 162,166,169
70.03 2 1vi0B DCC Rep, Mult 147,150,151,154,155,158
80.01 1 2anuA ZN Rep, Mult 117,151
90.01 1 1mumA MG Rep, Mult 44,87
100.01 1 2dg80 III Rep, Mult 17,18,21,23,102,109,110,112,113,119,122,123,126,141,144,146,147,150,151,152,155,165,168,169
110.01 1 2np5C NDS Rep, Mult 31,33,37
120.01 1 3g7rA NA Rep, Mult 40,41,44,47
130.01 1 3q2jA CA Rep, Mult 139,141,143
140.01 1 4evdA CD Rep, Mult 46,47,50
150.01 1 2zyqB TAR Rep, Mult 34,43
160.01 1 4ej7A CA Rep, Mult 85,87,161

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
10.0602jkvA0.4574.730.0310.7511.1.1.44NA
20.0603djlA0.4665.140.1010.7811.3.99.-NA
30.0602x38A0.4834.480.0860.7402.7.1.153149
40.0601v4tA0.4204.580.0550.6752.7.1.2,2.7.1.1NA
50.0602zidA0.4424.310.0520.6803.2.1.70NA
60.0601h16A0.4464.510.0530.7102.3.1.54NA
70.0603b4xA0.4594.100.0830.6571.14.14.1123
80.0603c6gB0.4474.060.0510.6511.14.13.1548
90.0602a4zA0.5024.330.0900.7572.7.1.153125
100.0601izjA0.4414.940.0760.7343.2.1.135,3.2.1.1NA
110.0601a31A0.4424.330.0380.6455.99.1.2101
120.0601hbmA0.4684.980.0780.7632.8.4.1133
130.0601rr8C0.4794.000.0720.6805.99.1.2NA
140.0601e6yA0.4764.840.0590.7632.8.4.1NA
150.0601ea9C0.4424.980.0710.7573.2.1.54NA
160.0602x6fA0.4764.260.0850.7162.7.1.137,2.7.1.153,2.7.1.15461,64,123
170.0601xmeA0.4424.850.0750.7281.9.3.1NA
180.0601p6xA0.4425.160.0740.7282.7.1.21NA
190.0601jqkF0.4284.990.0680.7221.2.99.2123

(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
00.300.7153.120.110.934ichA GO:0003677 GO:0006351 GO:0006355
10.290.7283.200.140.953g7rB GO:0003677 GO:0003700 GO:0006351 GO:0006355
20.290.7692.630.120.943htaA GO:0003677 GO:0006351 GO:0006355
30.290.6723.250.130.913f1bA GO:0003677 GO:0006351 GO:0006355
40.270.7013.270.110.913on2B GO:0003677 GO:0006351 GO:0006355
50.260.7162.920.110.922id6A GO:0003677 GO:0006351 GO:0006355
60.260.6973.180.120.915d18A GO:0003677 GO:0006351 GO:0006355
70.250.7292.880.070.922uxhA GO:0003677 GO:0006351 GO:0006355
80.240.7183.150.140.943kkdC GO:0003677 GO:0006351 GO:0006355
90.240.6843.240.060.922f07A GO:0003677 GO:0006351 GO:0006355
100.220.7642.870.140.952dg8B GO:0003677 GO:0006351 GO:0006355
110.220.6343.350.120.893dewA GO:0003677 GO:0006351 GO:0006355 GO:0016020 GO:0016021
120.220.7093.490.100.953bcgA GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0008144 GO:0042493 GO:0043565 GO:0045892
130.220.6123.510.100.863egqA GO:0003677 GO:0006351 GO:0006355
140.210.7462.910.110.933e7qB GO:0003677 GO:0003700 GO:0006351 GO:0006355
150.200.6913.360.180.923t6nA GO:0003677 GO:0003700 GO:0006351 GO:0006355
160.200.6893.750.100.953bruA GO:0003677 GO:0006351 GO:0006355
170.190.6153.540.130.853bqyA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677
180.190.7133.240.080.933p9tA GO:0003677 GO:0006351 GO:0006355
190.190.6323.640.060.893nnrA GO:0003677 GO:0006351 GO:0006355
200.180.7333.010.110.933whcA GO:0003677 GO:0005737 GO:0006351 GO:0006355 GO:0006629 GO:0006631 GO:0016042
210.160.6543.620.080.912zcnD GO:0003677 GO:0006351 GO:0006355
220.160.6683.550.070.923kz9B GO:0003677 GO:0006351 GO:0006355
230.160.6363.680.110.892rasB GO:0003677 GO:0006351 GO:0006355
240.150.6583.550.070.883vvxA GO:0003677 GO:0006351 GO:0006355
250.140.6393.600.100.882y31A GO:0003677 GO:0006351 GO:0006355 GO:0045892
260.140.7123.140.140.923ppbA GO:0003677 GO:0006351 GO:0006355
270.130.7093.380.090.943vibC GO:0003677 GO:0006351 GO:0006355
280.130.7213.300.150.952g3bA GO:0003677 GO:0006351 GO:0006355
290.130.7063.480.130.952hyjA GO:0003677 GO:0003700 GO:0006351 GO:0006355
300.120.6893.470.130.942nx4A GO:0003677 GO:0006351 GO:0006355
310.120.6823.020.110.892eh3A GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0046872
320.120.7103.390.110.943lhqA GO:0003677 GO:0003700 GO:0006351 GO:0006355
330.110.6833.490.080.932pbxA
340.110.6353.850.080.923geuA GO:0003677 GO:0006351 GO:0006355
350.100.6823.740.120.954l62A GO:0000976 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355
360.090.6553.250.120.853bniA GO:0003677 GO:0006351 GO:0006355
370.090.6493.280.060.862qkoB GO:0003677 GO:0006351 GO:0006355
380.090.6663.540.070.923on4A GO:0003677 GO:0006351 GO:0006355
390.080.7043.230.090.933lwjA GO:0003677 GO:0006351 GO:0006355
400.080.6693.170.120.913mvpA GO:0003677 GO:0006351 GO:0006355
410.070.6493.510.100.883cjdA GO:0003677 GO:0006351 GO:0006355
420.070.6543.760.110.893vuqC GO:0003677 GO:0006351 GO:0006355
430.070.6583.680.110.923s5rA GO:0003677 GO:0006351 GO:0006355
440.070.6493.570.140.913knwA GO:0003677 GO:0006351 GO:0006355
450.070.6333.950.110.904pxiB GO:0003677 GO:0006351 GO:0006355
460.070.6773.560.110.951t33A GO:0003677 GO:0003700 GO:0006351 GO:0006355
470.070.6223.670.070.863rh2A GO:0003677 GO:0006351 GO:0006355
480.070.6353.960.070.932fbqA GO:0000976 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0044212 GO:0045893 GO:0050714
490.070.6243.740.070.873cdlB GO:0003677 GO:0006351 GO:0006355
500.070.5553.600.080.783ljlA GO:0003677
510.070.6143.470.070.854auxA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0003677 GO:0001071
GO-Score 0.81 0.58
Biological Processes GO:0006355
GO-Score 0.81
Cellular Component
GO-Score

(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.