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I-TASSER results for job id Rv0798c

[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 2 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
10.49 3 3dktA III Rep, Mult 1,6,20,24,34,42,229,230,231
20.17 3 2whxA ADP Rep, Mult 23,24,25,26,27,28
30.06 1 3enhA TBR Rep, Mult 154,157,161,167
40.06 1 3en9B TBR Rep, Mult 167,216,218,221
50.06 1 2jlsA ADP Rep, Mult 115,116,117,249

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
10.0602dkiA0.3776.320.0490.6411.14.13.23NA
20.0601l7qA0.3776.100.0870.6413.1.1.1NA
30.0603hmjA0.3726.000.0590.6452.3.1.86NA
40.0602vwbA0.3686.010.0420.6263.4.24.5726
50.0603e90D0.1786.020.0170.3023.4.21.91261
60.0601nfgA0.4075.310.0660.6193.5.2.2186,187
70.0601qf6A0.3765.550.0450.5896.1.1.3NA
80.0601gkrA0.3985.380.0630.6043.5.2.2NA
90.0603d64B0.3725.920.0270.6153.3.1.1145,215
100.0601uaaA0.3775.740.0420.6083.6.4.12NA
110.0601ie7C0.3976.220.0500.6723.5.1.5NA
120.0602bhrA0.3286.160.0390.5513.4.21.91NA
130.0602is4B0.3756.040.0420.6153.6.1.-NA
140.0602icsA0.3694.920.0800.5363.5.4.2210
150.0602ftwA0.3945.650.0830.6343.5.2.2NA
160.0602vr2A0.3795.950.0860.6343.5.2.2228,229
170.0603e74B0.3895.800.0880.6193.5.2.545
180.0602qeqB0.2976.210.0520.5023.4.21.91176
190.0601kogH0.3096.020.0850.5366.1.1.3116,117,119

(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
00.620.9770.830.350.993dktA GO:0005576 GO:0006508 GO:0008233 GO:0016787 GO:0019835 GO:0042742
10.400.7742.950.200.914pt2A GO:0006508 GO:0008233 GO:0042742
20.170.6333.760.100.803ddxA GO:0019012 GO:0019028 GO:0019076 GO:0039620
30.110.7012.980.180.832e0zA GO:0006508 GO:0008233 GO:0016491 GO:0042742 GO:0046872 GO:0055114
40.080.6523.850.080.833bjqE GO:0019028
50.080.6384.520.050.893bqwA GO:0019028
60.070.6244.290.100.851yueA GO:0019012 GO:0019028 GO:0039621
70.060.4142.750.120.483j1aG GO:0019012 GO:0019028 GO:0019076 GO:0039620
80.060.3306.730.100.622x41A GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0102483
90.060.3055.380.050.463btnA GO:0003824 GO:0005634 GO:0005737 GO:0006595 GO:0006596 GO:0033387 GO:0042177 GO:0042978 GO:0043085 GO:1902269
100.060.2825.220.030.412qjjA GO:0000287 GO:0003824 GO:0005975 GO:0008152 GO:0008927 GO:0009063 GO:0016052 GO:0016829 GO:0046872 GO:0047929
110.060.3125.660.030.484n48B GO:0003676 GO:0004483 GO:0005634 GO:0005654 GO:0005737 GO:0006370 GO:0006397 GO:0008168 GO:0016740 GO:0032259 GO:0080009 GO:0097309
120.060.3115.980.040.523c0yA GO:0000118 GO:0000122 GO:0001570 GO:0003682 GO:0003714 GO:0004407 GO:0005080 GO:0005634 GO:0005654 GO:0005737 GO:0006351 GO:0006355 GO:0007043 GO:0016568 GO:0016575 GO:0016787 GO:0016925 GO:0019789 GO:0019901 GO:0030182 GO:0032041 GO:0032703 GO:0033613 GO:0045668 GO:0045892 GO:0046872 GO:0051402 GO:0070491 GO:0070932 GO:0071260 GO:0071889 GO:0090050 GO:1901215 GO:1901223
130.060.2715.900.060.464gxpA GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483
140.060.2466.050.060.425iw7D GO:0000461 GO:0000462 GO:0003924 GO:0005525 GO:0005634 GO:0005730 GO:0005737 GO:0030688 GO:0034511 GO:0042254 GO:0043021
150.060.3086.260.050.533c0zC GO:0000118 GO:0000122 GO:0001570 GO:0003682 GO:0003714 GO:0004407 GO:0005080 GO:0005634 GO:0005654 GO:0005737 GO:0006351 GO:0006355 GO:0007043 GO:0016568 GO:0016575 GO:0016787 GO:0016925 GO:0019789 GO:0019901 GO:0030182 GO:0032041 GO:0032703 GO:0033613 GO:0045668 GO:0045892 GO:0046872 GO:0051402 GO:0070491 GO:0070932 GO:0071260 GO:0071889 GO:0090050 GO:1901215 GO:1901223
160.060.2756.390.070.465iw7B GO:0000461 GO:0000462 GO:0003924 GO:0005525 GO:0005634 GO:0005730 GO:0005737 GO:0030688 GO:0034511 GO:0042254 GO:0043021
170.060.2486.520.030.454m7xA GO:0000166 GO:0004594 GO:0005524 GO:0005737 GO:0015937 GO:0016301 GO:0016310 GO:0016740
180.060.2786.160.050.485iw7A GO:0000461 GO:0000462 GO:0003924 GO:0005525 GO:0005634 GO:0005730 GO:0005737 GO:0030688 GO:0034511 GO:0042254 GO:0043021


Consensus prediction of GO terms
 
Molecular Function GO:0008233
GO-Score 0.80
Biological Processes GO:0042742 GO:0006508 GO:0019835 GO:0019058
GO-Score 0.80 0.80 0.62 0.34
Cellular Component GO:0005576 GO:0019030
GO-Score 0.62 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.