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I-TASSER results for job id Rv0433

[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
10.66 42 1lgrA MN Rep, Mult 23,139,231,240,242
20.14 17 2d32A GLU Rep, Mult 25,135,136,137,139,185,242
30.05 8 2d32A ANP Rep, Mult 19,21,22,23,63,65,66,67,68,139,141,142,143,233,237,238,240
40.04 5 2gwcD BSC Rep, Mult 25,59,122,135,136,137,185,189,227,242
50.04 5 2d33B AF3 Rep, Mult 23,63,139,242
60.02 2 3o6xB MG Rep, Mult 25,56,57,63

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
10.1022d33A0.7823.350.1230.9256.3.2.225
20.0603b9jC0.3237.130.0330.5531.17.3.2,1.17.1.4NA
30.0601kyaA0.3786.590.0610.6121.10.3.2NA
40.0602gwdA0.8522.920.1800.9606.3.2.221,23,66
50.0602epoA0.3816.490.0500.6203.2.1.52NA
60.0603cuzA0.3757.030.0330.6362.3.3.9NA
70.0602hrgA0.3756.550.0450.6121.10.3.2NA
80.0602ow6A0.3776.870.0360.6383.2.1.114NA
90.0602h5uA0.3756.470.0840.6041.10.3.2NA
100.0601jqnA0.3826.660.0530.6254.1.1.31NA
110.0603ig5A0.8822.820.1100.9956.3.2.2289
120.0601lrwC0.3716.780.0330.6171.1.99.8NA
130.0603nztA0.7813.370.1180.9256.3.2.2NA
140.0601a65A0.3746.700.0560.6171.10.3.2NA
150.0601v10A0.3706.520.0690.6041.10.3.2NA
160.0601gycA0.3756.490.0720.6041.10.3.2NA
170.0603ebgA0.3776.480.0410.6013.4.11.-343
180.0602uu7A0.4603.700.1180.5456.3.1.2NA
190.0603fkyC0.4602.910.1360.5246.3.1.2NA
200.0601lrwA0.3726.800.0410.6171.1.99.8NA

(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
00.590.8991.390.260.931tt4A GO:0000166 GO:0004357 GO:0005524 GO:0016874 GO:0016879 GO:0042398
10.470.9231.110.260.941r8gB GO:0000166 GO:0004357 GO:0005524 GO:0016874 GO:0016879 GO:0042398
20.380.7823.360.120.932d32A GO:0000166 GO:0004357 GO:0005524 GO:0005829 GO:0006750 GO:0006972 GO:0016874 GO:0046872 GO:0071243 GO:0071288
30.320.7583.430.110.903ln7A GO:0000166 GO:0000287 GO:0003824 GO:0004357 GO:0004363 GO:0005524 GO:0006750 GO:0008152 GO:0016874 GO:0030145 GO:0046872
40.300.8832.800.110.993ig8A GO:0000166 GO:0004357 GO:0005524 GO:0005622 GO:0005737 GO:0006750 GO:0016874 GO:0017109 GO:0042542 GO:0046686
50.300.8263.050.180.942gwcF GO:0000166 GO:0004357 GO:0005524 GO:0006750 GO:0009507 GO:0009536 GO:0016874 GO:0042398
60.240.7813.370.120.933nztA GO:0000166 GO:0004357 GO:0005524 GO:0006750 GO:0016874
70.190.5594.120.120.694hppA GO:0003824 GO:0004356 GO:0006542 GO:0006807 GO:0046872
80.130.7493.600.140.903ln6A GO:0000166 GO:0000287 GO:0003824 GO:0004357 GO:0004363 GO:0005524 GO:0006750 GO:0008152 GO:0016874 GO:0030145 GO:0046872
90.060.3246.720.060.533pukA GO:0005737 GO:0005829 GO:0005886 GO:0006810 GO:0006887 GO:0006904 GO:0007420 GO:0015031 GO:0015758 GO:0016020 GO:0016192 GO:0016323 GO:0016324 GO:0017075 GO:0019905 GO:0022615 GO:0030073 GO:0031091 GO:0032868 GO:0042581 GO:0043312 GO:0045955 GO:0051291 GO:0061024 GO:0070062 GO:0070527 GO:0070820
100.060.2817.110.050.483lmmD GO:0005524
110.060.2446.740.050.414recA GO:0000287 GO:0000724 GO:0003677 GO:0004518 GO:0004519 GO:0004527 GO:0004528 GO:0005634 GO:0005654 GO:0005737 GO:0006281 GO:0006289 GO:0006974 GO:0008409 GO:0016787 GO:0016788 GO:0017108 GO:0033683 GO:0036297 GO:0043130 GO:0045171 GO:0046872 GO:0070336
120.060.2767.410.030.493uowB GO:0003921 GO:0003922 GO:0005524 GO:0005829 GO:0006164 GO:0006177 GO:0016462 GO:0016874
130.060.3076.640.050.504xviA GO:0000724 GO:0003676 GO:0003677 GO:0003887 GO:0005634 GO:0005654 GO:0005730 GO:0005737 GO:0006260 GO:0006261 GO:0006281 GO:0006974 GO:0008409 GO:0016740 GO:0016779 GO:0019985 GO:0030332 GO:0036297 GO:0090305
140.060.2646.700.060.434p7aA GO:0000289 GO:0000712 GO:0000793 GO:0000794 GO:0000795 GO:0001673 GO:0002204 GO:0003682 GO:0003697 GO:0005524 GO:0005634 GO:0005654 GO:0005694 GO:0005712 GO:0006281 GO:0006298 GO:0006303 GO:0006974 GO:0007049 GO:0007060 GO:0007126 GO:0007129 GO:0007131 GO:0007140 GO:0007283 GO:0008630 GO:0016020 GO:0016321 GO:0016446 GO:0016447 GO:0016887 GO:0030983 GO:0032137 GO:0032389 GO:0032407 GO:0043060 GO:0045132 GO:0045141 GO:0045143 GO:0045190 GO:0045950 GO:0048477 GO:0051257
150.060.2826.980.030.484uoxC GO:0003824 GO:0003992 GO:0005829 GO:0006526 GO:0008483 GO:0009447 GO:0016740 GO:0030170 GO:0033094 GO:0042802
160.060.2677.040.040.464rebA GO:0000287 GO:0000724 GO:0003677 GO:0004518 GO:0004519 GO:0004527 GO:0004528 GO:0005634 GO:0005654 GO:0005737 GO:0006281 GO:0006289 GO:0006974 GO:0008409 GO:0016787 GO:0016788 GO:0017108 GO:0033683 GO:0036297 GO:0043130 GO:0045171 GO:0046872 GO:0070336
170.060.2605.460.050.383iccA GO:0000166 GO:0016491 GO:0055114
180.060.2737.310.070.484ribB GO:0000287 GO:0000724 GO:0003677 GO:0004518 GO:0004519 GO:0004527 GO:0004528 GO:0005634 GO:0005654 GO:0005737 GO:0006281 GO:0006289 GO:0006974 GO:0008409 GO:0016787 GO:0016788 GO:0017108 GO:0033683 GO:0036297 GO:0043130 GO:0045171 GO:0046872 GO:0070336
190.060.2355.320.050.343g7rB GO:0003677 GO:0003700 GO:0006351 GO:0006355


Consensus prediction of GO terms
 
Molecular Function GO:0005524 GO:0004357 GO:0030145 GO:0000287 GO:0004363
GO-Score 0.94 0.94 0.32 0.32 0.32
Biological Processes GO:0006750 GO:0071288 GO:0071243 GO:0006972 GO:0046686 GO:0042542
GO-Score 0.70 0.38 0.38 0.38 0.30 0.30
Cellular Component GO:0005829 GO:0017109
GO-Score 0.38 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.