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I-TASSER results for job id Rv1232c

[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
10.39 13 2zy9A MG Rep, Mult 247,248,402,405
20.13 5 2zy9A MG Rep, Mult 251,254,289
30.06 4 2yvxB MG Rep, Mult 374,414,417,418
40.05 3 2zy9A MG Rep, Mult 381,382,384
50.04 2 2yvxD MG Rep, Mult 402,404,405
60.03 2 2yvxC MG Rep, Mult 372,374,414
70.03 2 2zy9B MG Rep, Mult 220,408
80.02 1 2ouxA MG Rep, Mult 323,325,387,388,389
90.02 1 2yvy0 III Rep, Mult 190,312,315,318,321,322,343,344,345,348,382,383,384,403,404,407
100.02 1 2ouxB MG Rep, Mult 285,413
110.02 1 2yvxA MG Rep, Mult 405,409

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
10.0601dl2A0.3716.640.0470.5843.2.1.113NA
20.0601dgjA0.3697.170.0300.6281.2.-.-NA
30.0602cqsA0.4007.070.0730.6602.4.1.20NA
40.0602pflA0.3646.530.0430.5632.3.1.54282,406
50.0601z1wA0.3795.690.0660.5423.4.11.-NA
60.0601w6jA0.3746.710.0550.5955.4.99.7NA
70.0601fa9A0.3787.600.0420.6672.4.1.1NA
80.0603b9jJ0.2187.070.0540.3591.17.1.4,1.17.3.2186
90.0601g72A0.3707.030.0470.6091.1.99.8NA
100.0602ivfA0.3677.360.0310.6301.17.99.2NA
110.0601vlbA0.3647.630.0510.6371.2.99.7NA
120.0601kv9A0.3787.360.0390.6441.1.99.-116
130.0601kb0A0.3687.580.0450.6441.1.99.-NA
140.0601fo4A0.4007.400.0500.6831.17.1.4NA
150.0601lrwC0.3796.850.0280.6051.1.99.8245
160.0601nxcA0.3726.660.0570.5893.2.1.113NA
170.0601w6sC0.3776.190.0440.5681.1.99.850
180.0601g87B0.3637.130.0290.5983.2.1.4NA
190.0602ckjA0.3847.730.0450.6781.17.1.4,1.17.3.2NA

(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
00.320.5602.460.280.612yvxA GO:0000287 GO:0005886 GO:0006810 GO:0006812 GO:0008324 GO:0015095 GO:0015693 GO:0016020 GO:0016021 GO:0042803 GO:0046872 GO:0098655 GO:1903830
10.190.5741.130.220.592ouxA GO:0005886 GO:0006810 GO:0006812 GO:0008324 GO:0015095 GO:0015693 GO:0016020 GO:0016021 GO:0046872 GO:0098655 GO:1903830
20.110.2592.490.160.283fv6B GO:0003677 GO:0006351 GO:0006355 GO:0045013
30.080.3362.840.210.373kxrA GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655
40.060.3395.150.080.453ddjA GO:0000166 GO:0003824
50.060.3285.360.080.442v8qE GO:0000166 GO:0004679 GO:0005524 GO:0005654 GO:0006468 GO:0006629 GO:0006631 GO:0006633 GO:0016208 GO:0019901 GO:0031588 GO:0042304 GO:0043234 GO:0043531 GO:0050790 GO:0051291
60.060.3225.020.090.413lfzA
70.060.3044.110.130.362yzqA GO:0003824 GO:0046872 GO:0051536 GO:0051539
80.060.2905.160.080.374qfsC GO:0000166 GO:0004679 GO:0005524 GO:0005654 GO:0006468 GO:0006629 GO:0006631 GO:0006633 GO:0016208 GO:0019901 GO:0031588 GO:0042304 GO:0043234 GO:0043531 GO:0050790 GO:0051291
90.060.2793.110.220.315aweA GO:0003824
100.060.3195.080.100.421zfjA GO:0000166 GO:0003824 GO:0003938 GO:0006164 GO:0006177 GO:0016491 GO:0046872 GO:0055114
110.060.3254.090.170.394dqwA GO:0000166 GO:0003824 GO:0003938 GO:0005524 GO:0006164 GO:0006177 GO:0016491 GO:0046872 GO:0055114
120.060.2596.980.070.424lzdA GO:0003677 GO:0003887 GO:0005634 GO:0005654 GO:0006281 GO:0006303 GO:0006310 GO:0006974 GO:0016446 GO:0016740 GO:0016779 GO:0030183 GO:0034061 GO:0046872 GO:0071897
130.060.2677.430.030.464fxsA GO:0000166 GO:0003824 GO:0003938 GO:0006164 GO:0006177 GO:0009152 GO:0016491 GO:0046872 GO:0055114
140.060.3275.020.110.424z87A GO:0000166 GO:0003824 GO:0003938 GO:0005737 GO:0005829 GO:0006164 GO:0006177 GO:0016491 GO:0046872 GO:0055114
150.060.2602.340.240.284gqyA GO:0009507 GO:0009536 GO:0009570 GO:0045454
160.060.2642.060.190.281yavB
170.060.2592.880.200.292o16B
180.060.2592.140.240.281vr9A GO:0008152 GO:0016597


Consensus prediction of GO terms
 
Molecular Function GO:0015095 GO:0042803 GO:0000287
GO-Score 0.45 0.32 0.32
Biological Processes GO:0098655 GO:0015693 GO:1903830
GO-Score 0.49 0.45 0.45
Cellular Component GO:0016021 GO:0005886
GO-Score 0.49 0.45

(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.