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I-TASSER results for job id Rv1359

[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
10.44 58 1wc5B APC Rep, Mult 45,46,47,48,49,50,87,88,89,119
20.17 29 1wc0A APC Rep, Mult 43,85,92,134,135,136,140,141,144,145,184
30.09 13 2gvzB FKP Rep, Mult 49,50,53,64,87,89,90
40.09 10 2bw7A ECS Rep, Mult 43,45,87,90,141,144,145,147,148
50.02 4 1wc6B MG Rep, Mult 45,87,89
60.01 2 2gvdB 128 Rep, Mult 43,136,137,138,141,144,184
70.00 1 1y10D CA Rep, Mult 20,141
80.00 1 1y10D CA Rep, Mult 19,128
90.00 1 1cul3 III Rep, Mult 53,61,62,64,65,66,68,69,72,73,82,83,85,86,87,128,136,138,141,145
100.00 1 2a6h3 III Rep, Mult 98,99,102,106,110
110.00 1 1azs0 III Rep, Mult 51,54,55

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
10.1381fx4A0.6202.340.2220.6964.6.1.1NA
20.1321cjkB0.5752.330.1230.6524.6.1.1NA
30.1161wc4A0.5722.700.1640.6604.6.1.1NA
40.0602c5sA0.4184.590.0580.5842.8.1.4118,231
50.0603gmaB0.4225.680.0610.6924.1.1.70NA
60.0602dqmA0.4145.640.0430.6643.4.11.2NA
70.0601ybtB0.5871.990.2280.6404.6.1.1NA
80.0603djlA0.4025.810.0580.6641.3.99.-NA
90.0602w01A0.6031.950.2140.6604.6.1.2NA
100.0603gf7A0.4045.710.0640.6604.1.1.70NA
110.0601vncA0.4105.870.0310.6641.11.1.10NA
120.0601w6jA0.4095.800.0410.6805.4.99.7NA
130.0602qv6D0.4514.490.0780.6043.5.4.2943,89
140.0602wz1A0.6052.100.1850.6684.6.1.2NA
150.0602x1cA0.4065.680.0780.6802.3.1.164120
160.0602ajqA0.4093.240.0540.4882.7.7.7101,119
170.0603mr2A0.4153.340.0830.4962.7.7.793,105,159
180.0601azsA0.5792.240.1560.6484.6.1.1NA
190.0601fx2A0.6182.340.2170.6964.6.1.1NA
200.0601dboA0.4055.580.0590.6524.2.2.19195
210.0601qssA0.4013.800.1230.5162.7.7.7113
220.0601bgxT0.4073.830.1150.5242.7.7.7NA

(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
00.320.5942.630.150.684ni2A GO:0000166 GO:0004016 GO:0004383 GO:0004872 GO:0005525 GO:0005737 GO:0005886 GO:0006182 GO:0007263 GO:0008015 GO:0008074 GO:0008217 GO:0009190 GO:0009635 GO:0014070 GO:0016829 GO:0016849 GO:0020037 GO:0030828 GO:0035556 GO:0043167 GO:0043234 GO:0046982 GO:0052565 GO:0060087
10.300.6812.650.160.771y11A GO:0000166 GO:0004016 GO:0005524 GO:0005622 GO:0005886 GO:0006171 GO:0007165 GO:0008289 GO:0009190 GO:0009268 GO:0009405 GO:0016829 GO:0016849 GO:0030145 GO:0035556 GO:0046872
20.290.5722.700.160.661wc4A GO:0000155 GO:0000160 GO:0004016 GO:0005622 GO:0006171 GO:0007165 GO:0009190 GO:0016310 GO:0016772 GO:0016829 GO:0016849 GO:0018298 GO:0023014 GO:0035556 GO:0046872
30.280.5752.330.120.651cjkB GO:0000166 GO:0000287 GO:0004016 GO:0005524 GO:0005622 GO:0005737 GO:0005886 GO:0005887 GO:0006171 GO:0007188 GO:0007189 GO:0007193 GO:0008179 GO:0009190 GO:0016020 GO:0016021 GO:0016829 GO:0016849 GO:0019933 GO:0030145 GO:0030425 GO:0031683 GO:0035556 GO:0043234 GO:0045121 GO:0046872 GO:0046982 GO:1904322
40.270.6182.340.220.701fx2A GO:0000166 GO:0004016 GO:0005524 GO:0005622 GO:0006171 GO:0009190 GO:0016020 GO:0016021 GO:0016829 GO:0016849 GO:0035556 GO:0046872
50.250.5792.240.160.651azsA GO:0000166 GO:0004016 GO:0005524 GO:0005622 GO:0005886 GO:0005929 GO:0006171 GO:0007189 GO:0007193 GO:0007204 GO:0009190 GO:0016020 GO:0016021 GO:0016829 GO:0016849 GO:0019933 GO:0035556 GO:0042995 GO:0046872 GO:0061178 GO:0072372 GO:1904322
60.250.5971.990.220.651ybtB GO:0004016 GO:0004383 GO:0004601 GO:0005622 GO:0006171 GO:0006182 GO:0009190 GO:0016787 GO:0016849 GO:0030145 GO:0035556 GO:0042803 GO:0046872 GO:0098869
70.250.6202.340.220.701fx4A GO:0000166 GO:0004016 GO:0005524 GO:0005622 GO:0006171 GO:0009190 GO:0016020 GO:0016021 GO:0016829 GO:0016849 GO:0035556 GO:0046872
80.230.5702.510.230.653mr7A GO:0005622 GO:0009190 GO:0016787 GO:0016849 GO:0035556
90.220.7093.500.120.864yutA GO:0005622 GO:0009190 GO:0009785 GO:0009882 GO:0016849 GO:0035556 GO:0071949
100.210.5982.150.190.663r5gB GO:0004016 GO:0005622 GO:0005886 GO:0006171 GO:0007165 GO:0009190 GO:0009405 GO:0016020 GO:0016021 GO:0016849 GO:0035556
110.200.6032.100.190.674ni2B GO:0000166 GO:0004016 GO:0004383 GO:0004872 GO:0005525 GO:0005737 GO:0005886 GO:0006182 GO:0007263 GO:0008015 GO:0008074 GO:0009190 GO:0016829 GO:0016849 GO:0020037 GO:0035556 GO:0038060 GO:0043231 GO:0046872 GO:0071732
120.200.5922.030.150.653et6A GO:0000166 GO:0004016 GO:0004383 GO:0005886 GO:0006182 GO:0007165 GO:0008074 GO:0009190 GO:0016829 GO:0016849 GO:0020037 GO:0035556
130.190.6031.950.210.662w01A GO:0004016 GO:0005622 GO:0005886 GO:0006171 GO:0007165 GO:0009190 GO:0016020 GO:0016021 GO:0016849 GO:0035556
140.180.5652.700.220.644wp3C GO:0004016 GO:0005622 GO:0006171 GO:0009190 GO:0016829 GO:0016849 GO:0035556
150.160.5692.570.130.644p2fA GO:0000166 GO:0000287 GO:0004016 GO:0005524 GO:0005622 GO:0005886 GO:0006171 GO:0007165 GO:0009190 GO:0016020 GO:0016021 GO:0016829 GO:0016849 GO:0030145 GO:0035556 GO:0046872
160.070.6273.470.160.764oyzA GO:0000166 GO:0000287 GO:0003351 GO:0004016 GO:0005524 GO:0005634 GO:0005737 GO:0005739 GO:0005829 GO:0005856 GO:0005886 GO:0005929 GO:0006171 GO:0007283 GO:0009190 GO:0015630 GO:0016020 GO:0016829 GO:0016849 GO:0030145 GO:0030424 GO:0030425 GO:0030426 GO:0031514 GO:0035556 GO:0042995 GO:0043025 GO:0043065 GO:0045177 GO:0045178 GO:0046872 GO:0048471 GO:0051117 GO:0071241 GO:0071890
170.060.3176.620.050.593bjeA GO:0003824 GO:0004731 GO:0004850 GO:0009116 GO:0016740 GO:0016757 GO:0046872
180.060.2886.360.040.522ajrA GO:0000166 GO:0005524 GO:0005975 GO:0008662 GO:0009024 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0046835 GO:0046872
190.060.3084.580.020.444hh0A GO:0000166 GO:0009785 GO:0009882 GO:0071949
200.060.2946.470.040.533dwlA GO:0000147 GO:0000166 GO:0003779 GO:0005524 GO:0005737 GO:0005829 GO:0005856 GO:0005885 GO:0006897 GO:0030041 GO:0030479 GO:0032153 GO:0034314 GO:0044396 GO:0051285 GO:0051666 GO:1903475


Consensus prediction of GO terms
 
Molecular Function GO:0004016 GO:0005524 GO:0038023 GO:0004673 GO:0032403 GO:0019899 GO:0046982 GO:0030145 GO:0020037 GO:0005525 GO:0004383 GO:0008289
GO-Score 0.82 0.63 0.58 0.58 0.57 0.57 0.51 0.50 0.32 0.32 0.32 0.30
Biological Processes GO:0006171 GO:0006468 GO:0019935 GO:0071407 GO:0007187 GO:1904321 GO:1901655 GO:0071396 GO:0030828 GO:0008217 GO:0009635 GO:0060087 GO:0052565 GO:0007263 GO:0009405 GO:0009268
GO-Score 0.74 0.58 0.57 0.57 0.57 0.57 0.57 0.57 0.32 0.32 0.32 0.32 0.32 0.32 0.30 0.30
Cellular Component GO:0043005 GO:0031226 GO:0036477 GO:0098857 GO:0016021 GO:0008074
GO-Score 0.57 0.57 0.57 0.57 0.48 0.32

(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.