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I-TASSER results for job id Rv0577

[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 3 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
10.20 2 3oxhA PMB Rep, Mult 40,49,107,110,132
20.09 1 3oxhA XYL Rep, Mult 139,145,146,190
30.06 1 1f9z0 III Rep, Mult 7,15,16,17,18,61,205,206,207,208,209,210,212,250,253,255,257
40.06 1 2quvA PO4 Rep, Mult 83,84,85,112
50.06 1 2quvB PO4 Rep, Mult 119,120,121,157
60.06 1 1lkdA BP6 Rep, Mult 207,250,251,253
70.06 1 1zalB PO4 Rep, Mult 120,121,152,153,154,156

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
10.0751kmyA0.6504.210.1340.9001.13.11.39NA
20.0601didA0.3916.320.0680.6785.3.1.5NA
30.0601gnxA0.4185.760.0710.6703.2.1.21NA
40.0601e5jA0.3965.730.0660.6403.2.1.4161
50.0601fbaC0.4056.000.0590.6674.1.2.13NA
60.0601lpsA0.3766.290.0540.6673.1.1.3NA
70.0601px8A0.4215.900.0440.6903.2.1.37NA
80.0601oc5A0.3825.710.0490.6253.2.1.91NA
90.0601bwkA0.3925.990.0730.6471.6.99.1NA
100.0601htiA0.3755.990.0330.6325.3.1.1NA
110.0602madH0.3816.830.0640.7281.4.99.3119
120.0601qw6A0.3965.850.0630.6591.14.13.39NA
130.0601xc6A0.4136.550.0510.7553.2.1.23NA
140.0601f9zA0.4062.490.1800.4604.4.1.5NA
150.0601d0cA0.3975.930.0860.6591.14.13.39NA
160.0601xfbA0.4195.770.0450.6704.1.2.13NA
170.0601g5aA0.3776.260.0540.6592.4.1.4148
180.0601fdjA0.3756.250.0790.6514.1.2.13NA
190.0601s46A0.3656.370.0510.6592.4.1.485
200.0603bllA0.3866.330.0690.6702.4.2.29NA

(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
00.330.6564.180.110.902ehzA GO:0003824 GO:0006725 GO:0008198 GO:0016491 GO:0016702 GO:0019439 GO:0046872 GO:0051213 GO:0055114 GO:1901170
10.190.6504.210.130.901kmyA GO:0003824 GO:0005506 GO:0006725 GO:0008198 GO:0016491 GO:0018583 GO:0019439 GO:0042178 GO:0046872 GO:0051213 GO:0055114
20.170.6764.220.120.923hpvA GO:0003824 GO:0006725 GO:0008198 GO:0016491 GO:0018577 GO:0019439 GO:0046872 GO:0051213 GO:0055114
30.150.6514.240.120.901eilA GO:0003824 GO:0005506 GO:0006725 GO:0008198 GO:0016491 GO:0018583 GO:0019439 GO:0042178 GO:0046872 GO:0051213 GO:0055114
40.150.6704.030.160.913b59A GO:0046872 GO:0051213 GO:0055114
50.140.6544.290.100.912wl9A GO:0003824 GO:0005506 GO:0006725 GO:0008198 GO:0016491 GO:0019439 GO:0042178 GO:0046872 GO:0051213 GO:0055114
60.130.6414.350.120.902zi8A GO:0003824 GO:0005506 GO:0006629 GO:0006707 GO:0006725 GO:0008198 GO:0008202 GO:0008203 GO:0009405 GO:0016042 GO:0016491 GO:0019439 GO:0046872 GO:0047071 GO:0051213 GO:0055114 GO:0070723
70.120.6764.070.100.913lm4D GO:0016491 GO:0018577 GO:0046872 GO:0051213 GO:0055114
80.100.6534.250.120.923vb0A GO:0003824 GO:0006725 GO:0008198 GO:0016491 GO:0019439 GO:0046872 GO:0051213 GO:0055114
90.100.6753.980.140.901f1uA GO:0046872 GO:0051213 GO:0055114
100.100.6763.900.120.904ghcC GO:0046872 GO:0051213 GO:0055114
110.100.3873.350.170.474hc5D GO:0051213 GO:0055114
120.060.3692.820.170.441lqkA GO:0004364 GO:0005737 GO:0016740 GO:0046677 GO:0046872
130.060.3643.560.110.463hnqA GO:0009405
140.060.3833.250.160.463rmuA GO:0004493 GO:0005739 GO:0005759 GO:0016853 GO:0019626 GO:0046491 GO:0046872
150.060.3673.410.150.461npbA GO:0004364 GO:0005737 GO:0016740 GO:0046677 GO:0046872
160.060.3537.180.030.711gjqA GO:0009055 GO:0016491 GO:0020037 GO:0042597 GO:0046872 GO:0050418 GO:0050421 GO:0055114
170.060.3506.540.070.644wghA GO:0016491 GO:0055114
180.060.3547.210.070.711aomB GO:0009055 GO:0016491 GO:0020037 GO:0042597 GO:0046872 GO:0050418 GO:0050421 GO:0055114
190.060.2936.450.090.522rb9D


Consensus prediction of GO terms
 
Molecular Function GO:0008198 GO:0019114 GO:0018583
GO-Score 0.62 0.34 0.31
Biological Processes GO:0055114 GO:1901170 GO:0042178
GO-Score 0.67 0.33 0.31
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.