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I-TASSER results for job id Rv2696c

[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
10.07 4 3a68A CA Rep, Mult 187,190
20.06 3 2ushA WO4 Rep, Mult 167,171,199
30.04 2 2bsqH NUC Rep, Mult 197,199
40.04 2 3eu4A CA Rep, Mult 65,101,113,187
50.02 1 2x7qA CA Rep, Mult 147,149
60.02 1 2ya0A NA Rep, Mult 19,72,93,94
70.02 1 1ti1A D12 Rep, Mult 77,82,211,218
80.02 1 2i89B MG Rep, Mult 161,162
90.02 1 5esrA MG Rep, Mult 18,223
100.02 1 1r4wC GSH Rep, Mult 113,114,115,161,163,164
110.02 1 2uwfA CA Rep, Mult 71,149
120.02 1 1yklG DHB Rep, Mult 52,53
130.02 1 2d32D CYS Rep, Mult 83,128,129,132
140.02 1 4dw5A BMA Rep, Mult 216,217
150.02 1 2gxsB CA Rep, Mult 119,123
160.02 1 3dksC III Rep, Mult 79,80,100,101,196
170.02 1 2y8nA SF4 Rep, Mult 168,171
180.02 1 1n24B MG Rep, Mult 194,208
190.02 1 2d32B MG Rep, Mult 45,53,56
200.02 1 2d32A CYS Rep, Mult 104,187,189,192

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
10.0602zjfA0.3746.230.0770.6493.3.2.3190
20.0601zjaA0.3836.100.0770.6455.4.99.11NA
30.0601ti6A0.3866.370.0570.6871.97.1.2NA
40.0601yq2A0.3736.420.0440.6643.2.1.23123
50.0601llwA0.3726.340.0360.6561.4.7.1NA
60.0602vtfA0.3946.320.0560.6913.2.1.9693,95,120
70.0602je8B0.3436.320.0560.6143.2.1.25NA
80.0602qnoA0.3256.220.0200.5753.2.1.4NA
90.0603l4uA0.3816.130.0760.6523.2.1.20,3.2.1.3116
100.0603fn9C0.3786.060.0460.6493.2.1.23NA
110.0603a1kA0.3166.730.0450.5913.5.1.492
120.0601bf2A0.4015.700.0480.6523.2.1.68NA
130.0602wanA0.3965.880.0480.6563.2.1.41194
140.0602prmA0.3786.470.0740.6791.3.5.238
150.0602jiiB0.3815.920.0540.6452.7.11.1NA
160.0601yzxB0.4413.440.0800.5442.5.1.18NA
170.0602zueA0.3755.820.0480.6296.1.1.19NA
180.0602b4kA0.3785.640.0430.6023.1.1.43NA
190.0601cygA0.3925.870.0770.6492.4.1.19NA

(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
00.290.7802.140.120.864pwoA GO:0016020 GO:0016021
10.070.5153.670.050.653f4tA GO:0003756 GO:0019153 GO:0055114
20.070.5063.140.090.613eu3A GO:0016491 GO:0030420 GO:0055114
30.070.4793.720.140.614ihuB GO:0005618 GO:0005886 GO:0009986 GO:0016020 GO:0016021 GO:0040007
40.070.4713.960.090.624k2dA GO:0015035 GO:0042597 GO:0045454 GO:0055114
50.070.4813.240.080.594gxzA GO:0005623 GO:0015035 GO:0045454 GO:0055114
60.070.4943.230.060.614xvwA GO:0005623 GO:0045454
70.070.4614.020.080.623h93A GO:0015035 GO:0042597 GO:0045454 GO:0055114
80.070.4723.870.090.612remC GO:0042597 GO:0045454
90.070.4514.510.090.643a3tA GO:0005623 GO:0045454
100.070.4664.060.070.623gmfA GO:0016020 GO:0016021 GO:0016853
110.070.4713.420.070.584n30A GO:0016853
120.070.4713.210.150.583gykA
130.060.4233.390.090.533bciA GO:0016853
140.060.4304.140.090.583l9vA GO:0015035 GO:0016853 GO:0042597 GO:0045454 GO:0055114
150.060.4143.680.060.532h0hB GO:0003756 GO:0015035 GO:0042597 GO:0055114
160.060.4023.330.090.504xvwL GO:0005623 GO:0045454
170.060.4024.140.070.543hd5A GO:0015035 GO:0042597 GO:0045454 GO:0055114
180.060.2826.870.050.534werA GO:0000166 GO:0003951 GO:0008152 GO:0016301 GO:0016310


Consensus prediction of GO terms
 
Molecular Function GO:0015035 GO:0019153 GO:0003756
GO-Score 0.07 0.07 0.07
Biological Processes GO:0044710
GO-Score 0.37
Cellular Component GO:0016021
GO-Score 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.