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I-TASSER results for job id Rv3351c

[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
10.10 5 4oalA 245 Rep, Mult 56,58,89,115,119,150,154
20.08 4 1zr6A FAD Rep, Mult 150,152,153
30.04 2 2y3rA TIR Rep, Mult 49,50,51,54,56,89,119,121,153
40.04 2 3rjaA ABL Rep, Mult 44,89,117,119,121,153
50.04 2 4rku4 CLA Rep, Mult 132,135
60.04 2 2qlaA ZN Rep, Mult 140,144
70.02 1 1g291 MG Rep, Mult 178,179
80.02 1 5awvB 3MY Rep, Mult 170,173
90.02 1 1nqeA C8E Rep, Mult 88,118
100.02 1 2wdxA BMA Rep, Mult 39,43,44
110.02 1 4rku4 CLA Rep, Mult 131,132
120.02 1 4il6R HEM Rep, Mult 138,142
130.02 1 2dyo1 III Rep, Mult 125,129,131,132,133,135,136,139,140,141,142,143,145,146,147,161,162,163
140.02 1 3rj8A FAD Rep, Mult 49,150,152,153

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
10.0601pn0C0.3976.310.0590.6971.14.13.7NA
20.0602ckpB0.3255.600.0400.5042.7.1.32NA
30.0602pywA0.3916.210.0630.6782.7.1.100137
40.0603dq0A0.5603.510.0920.7011.5.99.12NA
50.0601kv9A0.4006.270.0550.6971.1.99.-NA
60.0603f2sA0.4006.040.0650.6592.7.1.32NA
70.0601lrwC0.4026.430.0360.7161.1.99.8154
80.0602exrA0.5363.640.1050.6861.5.99.12NA
90.0602c4mC0.3976.530.0660.7052.4.1.1NA
100.0602zuwC0.3946.120.0470.6702.4.1.211153
110.0602pffD0.4206.140.0560.7202.3.1.8672
120.0602d0vA0.4006.440.0410.7121.1.99.8NA
130.0601ahuA0.4914.430.0820.6891.1.3.38,1.1.3.13NA
140.0603l4uA0.4105.970.0540.7053.2.1.20,3.2.1.3NA
150.0602pffA0.4166.160.0480.7242.3.1.41,2.3.1.86NA
160.0602o1xC0.3776.560.0580.6932.2.1.7NA
170.0601zy9A0.4006.490.0560.7083.2.1.22135,137
180.0602uxwA0.4056.110.0160.6701.3.99.-77
190.0602ppqA0.4035.600.0380.6252.7.1.39NA

(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
00.090.6751.550.200.723w8wB GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0050660 GO:0055114
10.070.6222.780.140.723popA GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0050660 GO:0055114
20.070.6262.840.120.732y08B GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0050660 GO:0055114
30.070.6182.660.140.722ipiA GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0017000 GO:0050660 GO:0055114
40.070.6052.710.150.712bvfA GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0018530 GO:0050660 GO:0055114
50.070.6052.940.150.714ud8A GO:0000166 GO:0003824 GO:0005618 GO:0009506 GO:0009793 GO:0010197 GO:0016491 GO:0016614 GO:0045551 GO:0050660 GO:0055114
60.070.6023.130.140.714pveA GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0050660 GO:0055114
70.070.6072.890.140.715d79A GO:0003824 GO:0016491 GO:0016614 GO:0050660 GO:0055114
80.070.6033.180.150.723vteA GO:0003824 GO:0005576 GO:0016491 GO:0016614 GO:0048046 GO:0050660 GO:0055114
90.070.6172.900.140.723d2jA GO:0003824 GO:0009820 GO:0016023 GO:0016491 GO:0016614 GO:0031410 GO:0050468 GO:0050660 GO:0055114
100.070.5983.090.170.714dnsA GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0050660 GO:0055114
110.070.5943.040.170.705awvA GO:0003824 GO:0004497 GO:0016491 GO:0016614 GO:0016746 GO:0016757 GO:0050660 GO:0055114
120.070.5603.570.110.714o95A GO:0000166 GO:0003824 GO:0009690 GO:0016491 GO:0016614 GO:0019139 GO:0050660 GO:0055114
130.070.5603.510.090.703s1eA GO:0003824 GO:0005576 GO:0005615 GO:0009690 GO:0016491 GO:0016614 GO:0019139 GO:0050660 GO:0055114
140.070.5503.290.100.684oalA GO:0000166 GO:0003824 GO:0009690 GO:0016491 GO:0016614 GO:0019139 GO:0050660 GO:0055114
150.070.5493.610.100.702exrA GO:0003824 GO:0009690 GO:0009823 GO:0016491 GO:0016614 GO:0019139 GO:0050660 GO:0055114
160.070.5613.580.120.714ml8A GO:0000166 GO:0003824 GO:0009690 GO:0016491 GO:0016614 GO:0019139 GO:0050660 GO:0055114
170.070.5593.580.120.714mlaB GO:0000166 GO:0003824 GO:0009690 GO:0016491 GO:0016614 GO:0019139 GO:0050660 GO:0055114
180.070.4784.390.140.664p8lA GO:0003824 GO:0003885 GO:0016020 GO:0016491 GO:0016614 GO:0045227 GO:0050660 GO:0055114 GO:0071555


Consensus prediction of GO terms
 
Molecular Function GO:0050660 GO:0016614
GO-Score 0.32 0.32
Biological Processes GO:0055114
GO-Score 0.32
Cellular Component
GO-Score

(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.