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I-TASSER results for job id Rv3594

[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
10.33 17 1ohtA ZN Rep, Mult 45,158,170
20.23 11 3d2yA III Rep, Mult 46,47,48,67,88,89,90,91,104,111,158,166,168,170
30.04 3 3cxaA TRE Rep, Mult 46,47,48,69,158,166,168,170
40.04 3 4bxdA MAG Rep, Mult 47,49,111,168
50.04 3 3rt4D LP5 Rep, Mult 89,90,91,103,104,156,160,161,162
60.02 2 3rt4C LP5 Rep, Mult 65,88,89,90,91,104,105,162
70.01 1 2cb3A MLD Rep, Mult 138,139,142,146
80.01 1 1aro1 III Rep, Mult 51,56,64,86

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
10.2743d2yA0.7322.470.1480.8183.5.1.2888,91,111
20.0601bgaA0.3855.610.0540.6153.2.1.21246
30.0602cerA0.4065.920.0390.6803.2.1.23NA
40.0601hn0A0.4146.160.0650.6954.2.2.20NA
50.0601kblA0.3975.290.0350.6002.7.9.1NA
60.0601e1eB0.4045.530.0680.6443.2.1.21NA
70.0601v03A0.4016.110.0390.6693.2.1.21NA
80.0601aroL0.4052.950.1790.4733.5.1.28168
90.0601vcoA0.4045.580.0580.6336.3.4.277
100.0601wcgA0.4005.680.0260.6443.2.1.147NA
110.0603cmjA0.3995.620.0650.6403.2.1.21NA
120.0601ohtA0.3983.190.1100.4763.5.1.2846,56,73,89,104,158
130.0603latA0.4023.480.1130.4803.2.1.96,3.5.1.2891,111
140.0601gnxA0.4005.560.0600.6363.2.1.21NA
150.0601vcmA0.4035.580.0530.6336.3.4.2NA
160.0601s1mB0.4045.610.0400.6336.3.4.2NA
170.0602p0mB0.3406.860.0210.6251.13.11.33170
180.0601hp4A0.3996.020.0810.6763.2.1.52111
190.0601dwaM0.4035.600.0520.6443.2.1.147NA
200.0601yb0B0.4022.780.1400.4663.5.1.28168

(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
00.340.7322.470.150.823d2yA GO:0008270 GO:0008745 GO:0009253 GO:0009254 GO:0009279 GO:0009392 GO:0016020 GO:0016787 GO:0019867 GO:0046872 GO:0071555
10.340.7331.910.170.794bj4A GO:0008745 GO:0009253 GO:0009254 GO:0019867 GO:0046872
20.340.7282.320.160.804bxdA GO:0008745 GO:0009253 GO:0009254 GO:0019867 GO:0046872
30.140.4013.820.150.501j3gA GO:0005737 GO:0008745 GO:0009253 GO:0016787 GO:0046872 GO:0071555
40.140.4052.950.180.471aroL GO:0003824 GO:0008152 GO:0008270 GO:0008745 GO:0009253 GO:0016787 GO:0019076 GO:0019835 GO:0030430 GO:0042742 GO:0046872
50.060.3942.650.160.453hmbB GO:0005576 GO:0008745 GO:0009253 GO:0016787 GO:0030420 GO:0030435 GO:0071555
60.060.3705.620.050.574qlbD GO:0004373 GO:0005978 GO:0016740 GO:0016757
70.060.3475.770.040.554hvlA GO:0004252 GO:0006508 GO:0016020 GO:0016021 GO:0046872
80.060.3186.050.050.521cvrA GO:0004197 GO:0004198 GO:0005509 GO:0005576 GO:0006508 GO:0008233 GO:0008234 GO:0009405 GO:0016787
90.060.3015.960.060.494rkcA GO:0003824 GO:0006520 GO:0008483 GO:0008793 GO:0009058 GO:0016740 GO:0030170 GO:0080130
100.060.3035.500.040.463h9uC GO:0000166 GO:0004013 GO:0005829 GO:0006730 GO:0016787 GO:0033353
110.060.3045.040.060.451so8A GO:0001540 GO:0003857 GO:0004303 GO:0005496 GO:0005737 GO:0005739 GO:0005759 GO:0005886 GO:0006629 GO:0007569 GO:0008033 GO:0008709 GO:0009083 GO:0016491 GO:0018454 GO:0030283 GO:0030331 GO:0033327 GO:0042802 GO:0044822 GO:0047015 GO:0051287 GO:0051289 GO:0055114 GO:0070901 GO:0090646
120.060.3836.350.060.664zhjB GO:0009058 GO:0015995 GO:0016851
130.060.2996.890.020.574r0mA GO:0003824 GO:0008152 GO:0016740 GO:0031177
140.060.2846.410.040.504yjdA GO:0003884 GO:0005102 GO:0005741 GO:0005777 GO:0005778 GO:0005829 GO:0006562 GO:0016491 GO:0036088 GO:0042416 GO:0046416 GO:0046983 GO:0048037 GO:0055114 GO:0055130 GO:0070178 GO:0071949
150.060.2365.950.030.401zjrA GO:0000049 GO:0002938 GO:0003723 GO:0006396 GO:0008033 GO:0008168 GO:0008173 GO:0009020 GO:0016740 GO:0032259
160.060.2536.270.040.443bh2A GO:0016829 GO:0016831 GO:0047602
170.060.4416.030.060.724zhjA GO:0009058 GO:0015995 GO:0016851
180.060.2505.650.020.391byeA GO:0004364 GO:0016740


Consensus prediction of GO terms
 
Molecular Function GO:0008745 GO:0008270 GO:0009392
GO-Score 0.79 0.43 0.34
Biological Processes GO:0009253 GO:0009254 GO:0071555
GO-Score 0.79 0.71 0.43
Cellular Component GO:0009279
GO-Score 0.34

(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.