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I-TASSER results for job id Rv2295

[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
10.17 10 3qwvA ZN Rep, Mult 59,62,85,88
20.09 5 3oybA ZZX Rep, Mult 49,140,142,167,169,170,175
30.09 5 3oyiA MN Rep, Mult 49,50,175,178
40.04 2 3nf6A IMV Rep, Mult 112,116,119,149,152,153,156
50.03 2 3f2kA III Rep, Mult 93,95,100,102,125,208
60.03 2 3nf9A CD9 Rep, Mult 94,98,173,174,176,177,180,207
70.03 2 1asuA EPE Rep, Mult 88,90,91
80.02 1 3f2kA III Rep, Mult 95,97,98,100,128,209

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
10.0671vsdA0.5233.120.0440.6412.7.7.49103
20.0601v4tA0.3914.730.0820.5852.7.1.2,2.7.1.1177
30.0601qhaA0.4374.590.0540.6372.7.1.145
40.0603dlrA0.4813.260.0700.5942.7.7.7,2.7.7.49108,141
50.0602bmbA0.4224.150.0320.5992.5.1.15,2.7.6.3,4.1.2.25NA
60.0601ahpA0.4275.350.0490.6792.4.1.1NA
70.0601k6yA0.4912.890.0650.5902.7.7.49139
80.0601ekeB0.4273.760.0580.5803.1.26.4210
90.0602uv8G0.4265.140.0350.6602.3.1.86NA
100.0601zczB0.4194.630.0360.6373.5.4.10,2.1.2.3NA
110.0603f9mA0.4494.490.0650.6462.7.1.245
120.0603f9kI0.5243.560.0750.6652.7.7.49176,204
130.0603hm8A0.4424.680.0540.6562.7.1.155
140.0601u6zB0.4383.850.0530.5943.6.1.11NA
150.0601bl3C0.5153.330.0660.6372.7.7.49138
160.0602c4mC0.4315.250.0490.6842.4.1.1NA
170.0601ygpA0.4335.300.0670.6892.4.1.1NA
180.0602pffA0.4415.150.0590.7172.3.1.41,2.3.1.86NA
190.0601c0mA0.5433.210.0350.6742.7.7.4941
200.0602vkzG0.4265.150.0350.6602.3.1.38,3.1.2.14NA

(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
00.140.7392.800.040.884u7bA GO:0003677 GO:0004518 GO:0004519 GO:0005634 GO:0006310 GO:0015074 GO:0016787 GO:0046872 GO:0090305
10.120.7092.620.060.833k9kA GO:0000014 GO:0000729 GO:0000737 GO:0000793 GO:0003677 GO:0003690 GO:0003697 GO:0003824 GO:0004518 GO:0004519 GO:0005634 GO:0005694 GO:0006281 GO:0006303 GO:0006974 GO:0008152 GO:0008168 GO:0008270 GO:0008283 GO:0010452 GO:0015074 GO:0016568 GO:0016740 GO:0016787 GO:0018024 GO:0031297 GO:0032259 GO:0034968 GO:0035861 GO:0042800 GO:0042803 GO:0043566 GO:0044547 GO:0044774 GO:0046872 GO:0046975 GO:0051568 GO:0071157 GO:0090305 GO:0097676 GO:2000373 GO:2001034 GO:2001251
20.090.6972.410.050.812f7tA GO:0003677 GO:0004518 GO:0004519 GO:0005634 GO:0006310 GO:0015074 GO:0016787 GO:0046872 GO:0090305
30.070.5303.660.040.683jcaA GO:0003676 GO:0003677 GO:0003824 GO:0003887 GO:0003964 GO:0004518 GO:0004519 GO:0004523 GO:0006278 GO:0006310 GO:0008152 GO:0008270 GO:0015074 GO:0016740 GO:0016779 GO:0016787 GO:0046718 GO:0046872 GO:0075713 GO:0090305 GO:0090502
40.070.5223.360.040.663hpgB GO:0003676 GO:0003677 GO:0003824 GO:0003964 GO:0004170 GO:0004190 GO:0004518 GO:0004519 GO:0004523 GO:0004533 GO:0006278 GO:0006310 GO:0006508 GO:0008152 GO:0008233 GO:0008270 GO:0009117 GO:0015074 GO:0016740 GO:0016779 GO:0016787 GO:0046080 GO:0046718 GO:0046872 GO:0075713 GO:0090305 GO:0090502 GO:0090503
50.070.5513.360.040.684bacA GO:0003676 GO:0003723 GO:0003824 GO:0003887 GO:0003964 GO:0004190 GO:0004518 GO:0004519 GO:0004523 GO:0006278 GO:0006310 GO:0006508 GO:0008152 GO:0008233 GO:0015074 GO:0016740 GO:0016779 GO:0016787 GO:0019012 GO:0030430 GO:0042025 GO:0046718 GO:0046872 GO:0071897 GO:0075713 GO:0075732 GO:0090305 GO:0090502
60.070.5403.590.030.695ejkA GO:0003676 GO:0003677 GO:0003723 GO:0003824 GO:0003887 GO:0003964 GO:0004190 GO:0004518 GO:0004519 GO:0004523 GO:0005198 GO:0006278 GO:0006310 GO:0006508 GO:0008152 GO:0008233 GO:0008270 GO:0015074 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0019012 GO:0019013 GO:0019028 GO:0046718 GO:0046872 GO:0075713 GO:0090305 GO:0090502
70.070.5243.550.070.673f9kA GO:0003676 GO:0003677 GO:0003723 GO:0003824 GO:0003887 GO:0003964 GO:0004190 GO:0004518 GO:0004519 GO:0004523 GO:0004533 GO:0005198 GO:0006278 GO:0006310 GO:0006508 GO:0008152 GO:0008233 GO:0008270 GO:0008289 GO:0015074 GO:0016020 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0019012 GO:0019013 GO:0019028 GO:0019076 GO:0020002 GO:0030430 GO:0033644 GO:0039657 GO:0042025 GO:0044174 GO:0046718 GO:0046872 GO:0055036 GO:0072494 GO:0075713 GO:0075732 GO:0090305 GO:0090502 GO:0090503
80.070.5143.360.070.641bi4C GO:0003676 GO:0003677 GO:0003723 GO:0003824 GO:0003887 GO:0003964 GO:0004190 GO:0004518 GO:0004519 GO:0004523 GO:0004533 GO:0005198 GO:0005546 GO:0006278 GO:0006310 GO:0006508 GO:0008152 GO:0008233 GO:0008270 GO:0008289 GO:0015074 GO:0016020 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0019012 GO:0019013 GO:0019028 GO:0019076 GO:0020002 GO:0030430 GO:0033644 GO:0039526 GO:0039651 GO:0039657 GO:0042025 GO:0042802 GO:0044174 GO:0046718 GO:0046872 GO:0055036 GO:0072494 GO:0075713 GO:0075732 GO:0090305 GO:0090502 GO:0090503
90.070.5162.750.070.614pa1A GO:0003676 GO:0003677 GO:0003824 GO:0003964 GO:0004170 GO:0004190 GO:0004518 GO:0004519 GO:0004523 GO:0004533 GO:0006278 GO:0006310 GO:0006508 GO:0008152 GO:0008233 GO:0008270 GO:0009117 GO:0015074 GO:0016740 GO:0016779 GO:0016787 GO:0046080 GO:0046718 GO:0046872 GO:0075713 GO:0090305 GO:0090502 GO:0090503
100.070.4933.040.060.613kkrA GO:0003676 GO:0003677 GO:0003723 GO:0003824 GO:0003887 GO:0003964 GO:0004190 GO:0004518 GO:0004519 GO:0004523 GO:0004533 GO:0006278 GO:0006310 GO:0006508 GO:0008152 GO:0008233 GO:0008270 GO:0015074 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0019012 GO:0019013 GO:0019028 GO:0019076 GO:0039660 GO:0046718 GO:0046872 GO:0075521 GO:0075606 GO:0075713 GO:0090305 GO:0090502 GO:0090503
110.070.4912.860.070.581k6yB GO:0003676 GO:0003677 GO:0003723 GO:0003824 GO:0003887 GO:0003964 GO:0004190 GO:0004518 GO:0004519 GO:0004523 GO:0004533 GO:0005198 GO:0005546 GO:0006278 GO:0006310 GO:0006508 GO:0008152 GO:0008233 GO:0008270 GO:0008289 GO:0015074 GO:0016020 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0019012 GO:0019013 GO:0019028 GO:0019076 GO:0020002 GO:0030430 GO:0033644 GO:0039526 GO:0039651 GO:0039657 GO:0042025 GO:0042802 GO:0044174 GO:0046718 GO:0046872 GO:0055036 GO:0072494 GO:0075713 GO:0075732 GO:0090305 GO:0090502 GO:0090503
120.070.5023.030.090.611ex4A GO:0003676 GO:0003677 GO:0003723 GO:0003824 GO:0003887 GO:0003964 GO:0004190 GO:0004518 GO:0004519 GO:0004523 GO:0004533 GO:0005198 GO:0005576 GO:0005654 GO:0005829 GO:0005886 GO:0006278 GO:0006310 GO:0006508 GO:0008152 GO:0008233 GO:0008270 GO:0008289 GO:0008907 GO:0015074 GO:0016020 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0019012 GO:0019013 GO:0019028 GO:0019058 GO:0019061 GO:0019064 GO:0019068 GO:0019072 GO:0019076 GO:0020002 GO:0030260 GO:0030430 GO:0033644 GO:0039526 GO:0039651 GO:0039657 GO:0042025 GO:0042802 GO:0044174 GO:0046718 GO:0046872 GO:0051169 GO:0055036 GO:0072494 GO:0075713 GO:0075732 GO:0090305 GO:0090502 GO:0090503
130.060.4095.300.050.661rblA GO:0000287 GO:0004497 GO:0009853 GO:0015977 GO:0015979 GO:0016491 GO:0016829 GO:0016984 GO:0019253 GO:0046872 GO:0055114
140.060.2825.700.040.484di3E GO:0006810 GO:0030288
150.060.2926.450.040.574etpA GO:0000166 GO:0000741 GO:0000742 GO:0000743 GO:0003777 GO:0005524 GO:0005634 GO:0005737 GO:0005816 GO:0005856 GO:0005874 GO:0005881 GO:0007018 GO:0007049 GO:0007064 GO:0007067 GO:0007126 GO:0008017 GO:0008569 GO:0046982 GO:0051301 GO:0060236
160.060.2715.310.050.452bv6A GO:0003677 GO:0003700 GO:0005737 GO:0006351 GO:0006355 GO:0009405
170.060.2675.930.090.504ri0A GO:0001558 GO:0004175 GO:0004252 GO:0005520 GO:0005576 GO:0006508 GO:0008233 GO:0008236 GO:0016787 GO:0030512 GO:0030514
180.060.2804.620.020.421tiqA GO:0004145 GO:0004596 GO:0006474 GO:0008080 GO:0016740 GO:0016746 GO:0030435 GO:0031248 GO:0043939


Consensus prediction of GO terms
 
Molecular Function GO:0046914 GO:0003677 GO:0004519
GO-Score 0.46 0.39 0.39
Biological Processes GO:0015074 GO:0090305 GO:0006310
GO-Score 0.39 0.39 0.32
Cellular Component GO:0005634
GO-Score 0.30

(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.