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I-TASSER results for job id Rv1718

[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 1 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
10.53 29 3fa5B MG Rep, Mult 45,47,224
20.29 14 2y7gA AAE Rep, Mult 45,47,80,82,104,106,141,143,169,220,224
30.15 8 2y7fA KMH Rep, Mult 13,45,47,80,82,104,106,112,117,143,224
40.06 4 3lotB UNL Rep, Mult 12,47,82,224
50.06 9 1xbzA LX1 Rep, Mult 8,10,45,80,82,169,199,201,220,222,223
60.05 4 3e49B IMD Rep, Mult 171,172,176,177,178
70.02 2 3e49D IMD Rep, Mult 187,191,196,215,216
80.02 2 3lotA UNL Rep, Mult 143,220,224,225
90.01 2 1piiA PO4 Rep, Mult 9,200,201,221,222,223
100.01 1 3iizA UUU Rep, Mult 209,221,229,241,244,245,248
110.01 1 2y7fD MG Rep, Mult 60,64
120.01 1 3chvA ZN Rep, Mult 70
130.01 1 3e49D IMD Rep, Mult 203,228,230,231
140.01 1 3iivB MG Rep, Mult 45,104,220

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
10.1701tqxA0.6023.570.1380.7505.1.3.1NA
20.1701xi3A0.5972.990.1150.7062.5.1.3NA
30.1552v81A0.5913.350.1390.7244.1.2.21NA
40.1531vlwB0.5913.010.1250.7064.1.3.16NA
50.1451y0eA0.5893.300.1230.7025.1.3.9221
60.1401m5wF0.6454.020.1770.8162.6.99.247,222
70.1182yw3E0.5693.130.1440.6914.1.2.14NA
80.1171nsjA0.5813.510.0910.7215.3.1.24NA
90.0962h6rB0.5813.310.1160.7215.3.1.1141
100.0961xbzB0.6123.560.1140.7684.1.1.85NA
110.0951v5xA0.5713.560.1220.7065.3.1.24NA
120.0931xi3B0.5992.980.1150.7062.5.1.3205
130.0893f4wA0.6053.530.1020.7574.1.2.-48
140.0842yswA0.6033.360.1130.7394.2.1.1045
150.0832yswC0.6023.370.1230.7354.2.1.1084,199,202
160.0813inpA0.6003.650.1150.7545.1.3.1NA
170.0771h1yA0.5993.630.1240.7505.1.3.1NA
180.0771h1yB0.5983.560.1140.7465.1.3.1NA
190.0722fliC0.6013.410.1370.7355.1.3.1NA
200.0601cb7B0.6863.400.0850.8425.4.99.1139
210.0601b1yA0.6763.970.0560.8643.2.1.2NA
220.0601fa2A0.6734.060.0640.8713.2.1.2NA
230.0603gnrA0.6744.160.0650.9013.2.1.21NA
240.0601myrA0.6744.140.0650.8973.2.1.1475
250.0601gonA0.6884.190.1000.9123.2.1.21NA
260.0602e9lA0.6814.070.0690.9013.2.1.21NA
270.0602whjA0.6794.070.0870.8793.2.1.78139
280.0602uv8G0.6723.900.1000.8792.3.1.86NA
290.0601wkyA0.6804.140.0950.8793.2.1.78139
300.0602e3zA0.6824.200.0770.9123.2.1.21NA
310.0601dwaM0.6734.110.0690.8933.2.1.147NA
320.0602z1sA0.6824.250.0650.9123.2.1.21NA
330.0601nvmA0.6783.470.0630.8244.1.3.38NA
340.0601wdpA0.6784.000.0600.8753.2.1.2NA
350.0601e1eB0.6754.130.0940.8973.2.1.21NA
360.0602jf6B0.6704.230.0690.9013.2.1.105NA
370.0601np2A0.6824.190.0970.9013.2.1.21NA
380.0601tr1D0.6814.150.0830.9043.2.1.21101,197

(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
00.620.9661.080.360.992y7dD GO:0003824 GO:0016740 GO:0019475 GO:0046872
10.600.9561.320.351.003chvA GO:0003824 GO:0016740 GO:0019475
20.590.9541.440.341.003lotD GO:0003824 GO:0016740 GO:0019475 GO:0046872
30.590.9521.330.360.993fa5A GO:0003824 GO:0016740 GO:0019475 GO:0046872
40.570.9341.630.320.993c6cA GO:0003824 GO:0016740 GO:0019475
50.560.9501.520.341.003e49A GO:0003824 GO:0016740 GO:0019475 GO:0046872
60.550.9481.540.361.003e02A GO:0003824 GO:0016740 GO:0019475 GO:0046872
70.530.9331.600.340.983no5E GO:0003824 GO:0016740 GO:0019475 GO:0046872
80.420.8952.290.240.994nnaA GO:0003824 GO:0016740 GO:0019475 GO:0046872
90.340.9012.290.241.005ikyA GO:0003824 GO:0016740 GO:0019475
100.100.6124.440.080.843ij6A GO:0016787 GO:0046872
110.080.6144.210.050.792qq6B GO:0003824 GO:0008152 GO:0009063 GO:0046872
120.070.5823.810.110.751wv2A GO:0003824 GO:0005737 GO:0009228 GO:0009229 GO:0016740 GO:0016783
130.070.5974.240.060.811h7rA GO:0003824 GO:0004655 GO:0005829 GO:0006779 GO:0006782 GO:0006783 GO:0008270 GO:0016829 GO:0032791 GO:0033014 GO:0046872
140.070.5954.190.100.773e96B GO:0003824 GO:0008152 GO:0016829
150.070.5105.070.080.754u0pB GO:0003824 GO:0005737 GO:0009107 GO:0009249 GO:0016740 GO:0016783 GO:0016992 GO:0046872 GO:0051536 GO:0051539
160.070.5794.360.070.783es7A GO:0003824 GO:0008152 GO:0016829 GO:0046872
170.070.5913.600.080.742zadA GO:0003824 GO:0008152 GO:0016853 GO:0016855 GO:0016998 GO:0046872 GO:0071555
180.060.3755.620.060.601ji0A GO:0000166 GO:0005524 GO:0015658 GO:0015803 GO:0016887
190.060.3275.660.070.523ab1B GO:0004324 GO:0016491 GO:0050660 GO:0050661 GO:0055114
200.060.3076.100.050.511rwrA GO:0009986


Consensus prediction of GO terms
 
Molecular Function GO:0016740 GO:0046872
GO-Score 0.99 0.94
Biological Processes GO:0019475
GO-Score 0.99
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.