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I-TASSER results for job id Rv2418c

[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
10.25 13 3dt9A GD7 Rep, Mult 16,17,86,87,217,218
20.04 2 3bqmB BQM Rep, Mult 11,35,39,46,81,157,159,160,161,195,196,197,198,232
30.04 2 2hsjA MG Rep, Mult 189,192,194
40.04 2 4aljF GLU Rep, Mult 9,78,157,194,235
50.02 1 3lsjA COA Rep, Mult 218,219,224
60.02 1 3dc7C NA Rep, Mult 194,195,196,233
70.02 1 3anvA 2RA Rep, Mult 22,218
80.02 1 1xp3A ZN Rep, Mult 166,215,218
90.02 1 1y10C CA Rep, Mult 212,215
100.02 1 1r3nA BIB Rep, Mult 175,213

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
10.1542q0sH0.5933.350.1220.7213.1.1.2218
20.0901ivnA0.5733.320.1890.7093.1.1.5,17,218
30.0671bwpA0.5773.280.1000.7003.1.1.4717,86,215,218
40.0671vyhA0.5763.300.1240.7003.1.1.4717,215,218
50.0601a4uB0.5384.110.0910.7171.1.1.185,142,159
60.0601ahiA0.5404.520.0970.7371.1.1.159144
70.0603gr6D0.5384.590.0490.7411.3.1.9NA
80.0603kvnX0.6523.630.1290.8263.1.1.118,85
90.0601ae1B0.5384.370.0840.7371.1.1.206NA
100.0601zemA0.5424.410.0730.7331.1.1.9161
110.0601pp4A0.6333.760.1590.7983.1.1.-NA
120.0601xg5C0.5424.490.0910.7651.-.-.-164
130.0601ipeA0.5404.490.0680.7451.1.1.236NA
140.0601aknA0.5374.610.0750.7693.1.1.13,3.1.1.3NA
150.0601deoA0.6323.600.1590.7893.1.1.-17,215,218
160.0601k2wA0.5424.240.0580.7291.1.1.14164
170.0601ahiB0.5424.420.0980.7371.1.1.15985,225
180.0602dtdA0.5374.470.0930.7331.1.1.118164,174
190.0602p91A0.5394.720.0450.7451.3.1.9NA
200.0602waaA0.5763.490.1640.7213.1.1.7249,226,228
210.0602vptA0.5773.000.1620.6843.1.1.72218
220.0602b4qA0.5394.410.0890.7411.1.1.100NA
230.0601h5qA0.5394.390.0740.7291.1.1.138NA

(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
00.280.7342.430.170.834jhlA GO:0000272 GO:0005737 GO:0005975 GO:0016787 GO:0045493 GO:0046555 GO:0052689
10.230.6902.360.160.783rjtA
20.150.5832.870.170.693x0hA GO:0004553 GO:0005576 GO:0005975 GO:0030248
30.140.5912.770.160.694rshA GO:0016020 GO:0016021
40.070.6173.460.140.762o14A GO:0016787
50.070.6143.120.160.721yzfA GO:0016787
60.070.6153.450.150.763dc7A
70.070.6013.240.150.724ppyA GO:0016787
80.070.5943.100.150.704hf7A GO:0016787
90.070.6123.280.130.741z8hA
100.070.5733.320.190.711ivnA GO:0004620 GO:0004622 GO:0006508 GO:0006629 GO:0008233 GO:0016290 GO:0016298 GO:0016787 GO:0030288 GO:0042597 GO:0042802 GO:0047617
110.070.5723.300.150.683p94A
120.060.4235.670.090.664zrxA GO:0004560 GO:0005975
130.060.4123.610.090.534m1sC GO:0000165 GO:0000166 GO:0001934 GO:0002223 GO:0003924 GO:0005525 GO:0005737 GO:0005739 GO:0005829 GO:0005886 GO:0005925 GO:0007165 GO:0007173 GO:0007264 GO:0007265 GO:0007411 GO:0008284 GO:0008542 GO:0010628 GO:0016020 GO:0019002 GO:0019003 GO:0019221 GO:0021897 GO:0030036 GO:0030275 GO:0031234 GO:0031647 GO:0032228 GO:0032403 GO:0035022 GO:0035176 GO:0038002 GO:0038095 GO:0038128 GO:0043406 GO:0043524 GO:0045121 GO:0045596 GO:0048169 GO:0048873 GO:0050900 GO:0051000 GO:0051092 GO:0051146 GO:0051384 GO:0051385 GO:0060441
140.060.4304.020.070.592mscB GO:0000166 GO:0005525 GO:0005622 GO:0007165 GO:0007264 GO:0016020 GO:0046872
150.060.3505.640.060.564e3qA GO:0003824 GO:0008483 GO:0030170
160.060.3186.070.040.551dk5A GO:0005509 GO:0005544
170.060.2876.410.040.522i99A GO:0000122 GO:0003714 GO:0005634 GO:0005737 GO:0005739 GO:0005782 GO:0006554 GO:0007605 GO:0016491 GO:0042403 GO:0042562 GO:0042803 GO:0047127 GO:0050661 GO:0055114 GO:0070062 GO:0070324 GO:0070327
180.060.2545.160.090.384rckA GO:0016020 GO:0016021 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0052689
GO-Score 0.55
Biological Processes GO:0045491 GO:0000272
GO-Score 0.55 0.55
Cellular Component GO:0044424
GO-Score 0.55

(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.