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I-TASSER results for job id Rv2896c

[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
10.06 2 1g42A CP2 Rep, Mult 184,186
20.06 2 1uh3A GLC Rep, Mult 143,238,263
30.06 2 1uh2A GLC Rep, Mult 233,234,236,237,257
40.04 1 3maj0 III Rep, Mult 139,263,264,265,267,276,279,280,285,287,291
50.03 1 1e3dB FSX Rep, Mult 14,167
60.03 1 1g20B SF4 Rep, Mult 126,127
70.03 1 2xn1A TRS Rep, Mult 124,126,128,155,157,158,181
80.03 1 1i9dA SO3 Rep, Mult 224,258
90.03 1 1oi6A TMP Rep, Mult 189,224
100.03 1 1j0jB GLC Rep, Mult 159,200,201
110.03 1 2gk6A MG Rep, Mult 133,239
120.03 1 2gjnA NIS Rep, Mult 161,167,272
130.03 1 1lbyA F6P Rep, Mult 224,226
140.03 1 4ljrA NUC Rep, Mult 130,221

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
10.0602z8yD0.3905.350.0970.5351.2.7.4,1.2.99.2240,247,263
20.0603bg3A0.3986.240.0630.6176.4.1.1NA
30.0601ea9C0.4096.860.0500.6843.2.1.54NA
40.0602zidA0.3836.270.0750.5893.2.1.70178
50.0602jkpB0.4216.870.0920.7023.2.1.20NA
60.0602iufA0.3925.750.0890.5711.11.1.6NA
70.0601ahpA0.3956.770.0370.6502.4.1.1NA
80.0601zjaA0.3856.310.0670.5945.4.99.11NA
90.0603i39X0.3845.360.0900.5271.2.99.2263
100.0601j0kA0.3996.930.0440.6713.2.1.135249
110.0602qf7B0.3546.670.0610.5686.4.1.1NA
120.0602azdB0.3936.860.0420.6612.4.1.1246,274
130.0601cf9A0.3885.770.0510.5661.11.1.6NA
140.0601iphA0.3935.580.0440.5581.11.1.6128,162
150.0601ygpA0.3895.420.0600.5402.4.1.1NA
160.0601ofdA0.3637.140.0510.6301.4.7.1NA
170.0601sy7A0.3935.610.0630.5601.11.1.6NA
180.0601od2A0.3636.840.0570.6026.3.4.14,6.4.1.2161
190.0601m53A0.3826.450.0430.5995.4.99.12NA

(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
00.480.8711.150.340.893majA GO:0009294
10.400.6412.640.280.713uqzA GO:0009294
20.340.4952.210.260.534ljkF GO:0009294
30.070.4267.020.090.725f7sB GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246
40.060.4177.170.060.723lppA GO:0003824 GO:0004553 GO:0004558 GO:0004574 GO:0004575 GO:0005794 GO:0005886 GO:0005903 GO:0005975 GO:0008152 GO:0016020 GO:0016021 GO:0016324 GO:0016787 GO:0016798 GO:0030246 GO:0044245 GO:0070062
50.060.4236.890.070.695aedA GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246
60.060.4307.230.070.754kwuA GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246 GO:0046872
70.060.4186.880.050.693tonA GO:0000023 GO:0003824 GO:0004339 GO:0004553 GO:0004558 GO:0005886 GO:0005975 GO:0005983 GO:0008152 GO:0016020 GO:0016021 GO:0016160 GO:0016324 GO:0016787 GO:0016798 GO:0030246 GO:0032450 GO:0044245 GO:0070062
80.060.4157.270.050.722g3mF GO:0000023 GO:0003824 GO:0004553 GO:0004558 GO:0005737 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246 GO:0032450
90.060.4147.120.050.703nsxA GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246
100.060.4147.350.060.735f7cC GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246
110.060.4137.280.060.725f7cA GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246
120.060.4077.290.070.724xpqA GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246
130.060.3847.400.050.685djwA GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246
140.060.4226.780.060.693l4uA GO:0000023 GO:0003824 GO:0004339 GO:0004553 GO:0004558 GO:0005886 GO:0005975 GO:0005983 GO:0008152 GO:0016020 GO:0016021 GO:0016160 GO:0016324 GO:0016787 GO:0016798 GO:0030246 GO:0032450 GO:0044245 GO:0070062
150.060.4217.250.060.744ba0A GO:0003824 GO:0004553 GO:0005975 GO:0016740 GO:0016757 GO:0030246 GO:0033825
160.060.4556.960.040.764amwA GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0016829 GO:0030246 GO:0047457
170.060.4287.140.040.732xvgA GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246
180.060.3477.290.060.614g9iA GO:0003725 GO:0008270 GO:0016743 GO:0046872 GO:0046944


Consensus prediction of GO terms
 
Molecular Function GO:0030246 GO:0004558 GO:0004574 GO:0004575
GO-Score 0.13 0.07 0.07 0.07
Biological Processes GO:0009294
GO-Score 0.80
Cellular Component GO:0070062 GO:0005903 GO:0005794 GO:0016021 GO:0016324
GO-Score 0.07 0.07 0.07 0.07 0.07

(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.