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I-TASSER results for job id Rv2250c

[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 4 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
10.12 34 3br5A RHQ Rep, Mult 62,65,66,69,72,93,94,97,101,120,124,161
20.10 30 4dw6A 0MN Rep, Mult 73,82,83,86,87,90,94,117,121,127,128,131,154,157,158,161,162,184
30.10 28 3btcA MGR Rep, Mult 69,94,97,108,121,124,125,154,155,158
40.05 12 1jt0C QNA Rep, Mult 11,42,43,44,45,46,49,50
50.04 11 3angD DCC Rep, Mult 68,90,104,114,115,118,121,145,148,151,154,155,158
60.04 8 1jt0A QNA Rep, Mult 32,33,44,48,53,54
70.04 11 3q3sA O8B Rep, Mult 73,83,86,87,90,94,101,105,117,121,124,127,128,154,157,158,161,162,165,184
80.02 7 1vi0B DCC Rep, Mult 159,162,163,166,167,170,171
90.02 7 3whcA ST9 Rep, Mult 61,62,65,66,69,90,93,97,100,101,105,114,117,118,121,122,125,147,150,154
100.02 6 2dg80 III Rep, Mult 23,24,27,29,98,99,102,103,105,106,108,109,110,114,117,118,121,149,152,154,155,158,159,160,163,165,166,168,179,182,183,186
110.01 2 3lsjA COA Rep, Mult 79,82,137,188,189
120.01 2 3lsrA QNA Rep, Mult 32,33,34,38,44,45,48
130.01 3 2dtz0 III Rep, Mult 101,102,105,106,108,121,145,152,155,156,158,159,162,163,164,176,179,180,183,184,186,187
140.01 3 2i10B NPO Rep, Mult 121,122,151
150.01 3 3p9tA TCL Rep, Mult 66,69,87,105,120,121,124,128,153,154,157
160.01 2 3lsjA COA Rep, Mult 83,86,184,185,188
170.00 1 2eh3A MG Rep, Mult 85,88
180.00 1 3angB DCC Rep, Mult 163,167,171,172,175,179
190.00 1 3locA URA Rep, Mult 163
200.00 1 1bjyA CTC Rep, Mult 180,184

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
10.0602b4kA0.4576.200.0610.9103.1.1.43NA
20.0601mpxA0.4486.290.0380.8893.2.1.43NA
30.0602e8yA0.4595.080.0770.7623.2.1.4114,53
40.0601uokA0.4524.660.0600.7043.2.1.10NA
50.0601s6yA0.4465.140.0490.7253.2.1.86NA
60.0603jvpD0.4525.320.0510.7722.7.1.16NA
70.0602zf5Y0.4505.610.0570.7992.7.1.3018
80.0601bxnE0.4564.600.0630.6724.1.1.3917
90.0603c46B0.4056.150.0480.7572.7.7.6NA
100.0601gowA0.4535.260.0370.7723.2.1.23NA
110.0602ze0A0.4484.670.0740.7093.2.1.20NA
120.0601rblA0.4604.370.0790.6614.1.1.39NA
130.0601gk8A0.4604.430.0470.6614.1.1.39NA
140.0602wanA0.4465.180.0410.7573.2.1.4132
150.0602cerA0.4464.990.0440.7463.2.1.2354
160.0602d0tB0.4745.220.0470.8041.13.11.5234
170.0602fhcA0.4075.450.0560.7143.2.1.4120
180.0602z8yD0.4125.570.0800.7201.2.7.4,1.2.99.222,59,63,103
190.0602a4zA0.4474.650.0760.7092.7.1.15329

(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
00.440.7282.860.180.922np5A GO:0003677 GO:0006351 GO:0006355
10.440.9531.180.171.002f07A GO:0003677 GO:0006351 GO:0006355
20.400.7863.040.170.991rktA GO:0003677 GO:0006351 GO:0006355
30.390.7382.670.200.903vuqC GO:0003677 GO:0006351 GO:0006355
40.380.6863.370.110.923ppbA GO:0003677 GO:0006351 GO:0006355
50.360.7742.740.170.943whcA GO:0003677 GO:0005737 GO:0006351 GO:0006355 GO:0006629 GO:0006631 GO:0016042
60.350.7882.600.170.943on2B GO:0003677 GO:0006351 GO:0006355
70.330.6613.560.110.883f1bA GO:0003677 GO:0006351 GO:0006355
80.320.6753.470.110.913pasB GO:0003677 GO:0006351 GO:0006355
90.320.7173.300.170.954l62A GO:0000976 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355
100.310.7143.180.160.933dcfA GO:0003677 GO:0006351 GO:0006355
110.310.7203.150.150.953vibC GO:0003677 GO:0006351 GO:0006355
120.300.6273.260.200.832qwtA GO:0003677 GO:0006351 GO:0006355
130.300.7193.150.110.931jt0A GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0045892
140.290.7243.130.170.952genA GO:0003677 GO:0003700 GO:0006351 GO:0006355
150.290.7333.170.190.965f1jA GO:0003677 GO:0006351 GO:0006355
160.280.7033.340.160.932fq4A GO:0003677 GO:0006351 GO:0006355
170.270.6503.770.180.902oerB GO:0003677 GO:0006351 GO:0006355
180.270.6883.710.200.934cgrA GO:0003677 GO:0006351 GO:0006355
190.270.7582.960.180.974ichA GO:0003677 GO:0006351 GO:0006355
200.270.6363.580.130.853ccyA GO:0003677 GO:0006351 GO:0006355
210.270.6973.430.160.935d1wD GO:0003677 GO:0006351 GO:0006355
220.270.7183.120.120.943he0C GO:0003677 GO:0006351 GO:0006355
230.260.7053.380.130.942rasB GO:0003677 GO:0006351 GO:0006355
240.260.6353.890.120.943nnrA GO:0003677 GO:0006351 GO:0006355
250.260.7552.660.120.923lwjA GO:0003677 GO:0006351 GO:0006355
260.250.6443.830.110.903s5rA GO:0003677 GO:0006351 GO:0006355
270.250.7583.080.150.963angC GO:0003677 GO:0006351 GO:0006355
280.250.7622.920.130.963e7qB GO:0003677 GO:0003700 GO:0006351 GO:0006355
290.240.7442.220.150.872dg8B GO:0003677 GO:0006351 GO:0006355
300.240.7503.230.120.963hggA GO:0003677 GO:0006351 GO:0006355
310.240.7203.030.120.903cjdA GO:0003677 GO:0006351 GO:0006355
320.240.6094.020.140.843vvxA GO:0003677 GO:0006351 GO:0006355
330.240.7383.200.140.953f0cA GO:0003677 GO:0006351 GO:0006355
340.230.6923.050.190.904jl3C GO:0003677 GO:0006351 GO:0006355
350.230.7412.900.150.944yzeA GO:0000976 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0045892
360.230.7183.000.140.902y31A GO:0003677 GO:0006351 GO:0006355 GO:0045892
370.230.6094.020.200.882q24B GO:0003677 GO:0006351 GO:0006355
380.220.6663.170.080.854w97A GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0010468 GO:0019217
390.220.6813.660.150.943bjbB GO:0003677 GO:0006351 GO:0006355
400.220.6493.770.110.903on4A GO:0003677 GO:0006351 GO:0006355
410.220.6693.080.130.864auxA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677 GO:0046872
420.220.6343.500.110.832ibdA GO:0003677 GO:0006351 GO:0006355
430.220.7822.960.150.983bhqA GO:0003677 GO:0006351 GO:0006355
440.220.7143.430.170.953cwrA GO:0003677 GO:0006351 GO:0006355
450.220.6223.540.120.843colA GO:0003677 GO:0006351 GO:0006355
460.210.7003.800.120.942pbxA
470.210.6553.760.140.904mxmA GO:0003677 GO:0006351 GO:0006355
480.210.6693.710.120.932id6A GO:0003677 GO:0006351 GO:0006355
490.210.6683.390.170.893cdlB GO:0003677 GO:0006351 GO:0006355
500.210.6653.530.130.902zcnD GO:0003677 GO:0006351 GO:0006355
510.210.7272.670.150.883htaA GO:0003677 GO:0006351 GO:0006355
520.210.6823.490.120.923qkxA GO:0003677 GO:0006351 GO:0006355
530.200.6673.760.100.913mvpA GO:0003677 GO:0006351 GO:0006355
540.190.6683.120.180.872pz9A GO:0003677 GO:0003700 GO:0006351 GO:0006355
550.190.6603.450.140.893zqgA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677 GO:0046872
560.190.6813.510.140.893b81A GO:0003677 GO:0006351 GO:0006355
570.180.6733.300.180.883bqyA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677
580.180.6723.890.100.923kz9B GO:0003677 GO:0006351 GO:0006355
590.180.6943.320.080.883vp5A GO:0003677 GO:0006351 GO:0006355 GO:0046872
600.180.6323.560.090.844me9A GO:0003677 GO:0006351 GO:0006355
610.180.6214.170.170.953rh2A GO:0003677 GO:0006351 GO:0006355
620.180.5914.120.100.852g7lA GO:0003677 GO:0006351 GO:0006355 GO:0045892
630.170.6573.230.160.853zqfA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677 GO:0046872
640.170.6973.230.150.913aqtB GO:0003677 GO:0006351 GO:0006355
650.170.6663.100.110.872eh3A GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0046872
660.160.6313.970.100.902qtqA GO:0003677 GO:0006351 GO:0006355
670.140.7313.320.170.982nx4A GO:0003677 GO:0006351 GO:0006355
680.140.6494.350.070.923nrgA GO:0003677 GO:0003700 GO:0006351 GO:0006355
690.140.6503.690.130.913geuA GO:0003677 GO:0006351 GO:0006355
700.140.7033.330.100.943g7rB GO:0003677 GO:0003700 GO:0006351 GO:0006355
710.130.6413.750.080.914mk6A GO:0003677 GO:0006351 GO:0006355
720.120.6843.370.160.923knwA GO:0003677 GO:0006351 GO:0006355
730.120.7003.390.120.901sgmA GO:0003677 GO:0006351 GO:0006355
740.120.6773.760.140.942g7sA GO:0003677 GO:0006351 GO:0006355
750.110.6673.210.080.882qkoB GO:0003677 GO:0006351 GO:0006355
760.110.6993.360.140.932zcxA GO:0003677 GO:0006351 GO:0006355
770.110.6963.490.130.943bruA GO:0003677 GO:0006351 GO:0006355
780.100.6623.670.080.912iu5A GO:0003677 GO:0006351 GO:0006355
790.100.5614.730.110.893gziA GO:0003677 GO:0006351 GO:0006355
800.100.7523.240.150.953c07A GO:0003677 GO:0006351 GO:0006355
810.090.6703.070.150.862vprA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677 GO:0046872
820.090.6123.870.110.862fd5A GO:0003677 GO:0003700 GO:0006351 GO:0006355
830.080.6303.850.130.872raeA GO:0003677 GO:0006351 GO:0006355
840.070.5834.440.100.892dg7A GO:0003677 GO:0006351 GO:0006355
850.070.5873.900.120.853kkcA GO:0003677 GO:0006351 GO:0006355
860.070.5994.100.050.892fbqA GO:0000976 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0044212 GO:0045893 GO:0050714


Consensus prediction of GO terms
 
Molecular Function GO:0003677
GO-Score 0.93
Biological Processes GO:0006355
GO-Score 0.93
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.