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I-TASSER results for job id Rv1632c

[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
10.24 7 3exmA CA Rep, Mult 57,59,74,78
20.13 4 3exmA CA Rep, Mult 76,78,91
30.07 3 4ku8A GLY Rep, Mult 108,112
40.05 2 3jcuH CLA Rep, Mult 112,119
50.05 2 3exmA GP2 Rep, Mult 22,23,27,57,59,74,78,90,91
60.02 1 2xgxA AKG Rep, Mult 117,121
70.02 1 2d2cA CLA Rep, Mult 92,120
80.02 1 1gzmA C8E Rep, Mult 120,123

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
10.0603c6bA0.4594.530.0650.7353.1.2.12115
20.0601vb3A0.4634.950.0630.7894.2.3.1NA
30.0601rqxC0.4585.160.0220.8233.5.99.7NA
40.0601rw9A0.4684.860.0560.7824.2.2.5NA
50.0603exmA0.7412.980.1990.9253.6.1.657,73,94
60.0601tzmC0.4634.850.0150.8033.5.99.7NA
70.0601c8bA0.4714.010.0310.6733.4.24.7839
80.0602de6B0.4575.150.0470.7751.14.12.-NA
90.0601kb9A0.4565.070.0680.8031.10.2.2NA
100.0601tlbA0.4874.930.0590.8501.3.3.393,100,108
110.0601sqbB0.4615.100.0610.8301.10.2.2NA
120.0602v5aB0.4534.980.0620.7826.3.4.14123
130.0601aupA0.3485.010.0390.6261.4.1.2NA
140.0603cxhL0.4195.360.0520.8031.10.2.2NA
150.0602vqdA0.4565.080.0760.7966.3.4.14,6.4.1.282
160.0601larA0.4624.790.0540.7693.1.3.48115
170.0601ojnA0.4904.110.0550.7014.2.2.1NA
180.0601pa1A0.4724.930.0420.7893.1.3.4874
190.0601wgzA0.4564.670.0470.7553.4.24.66NA

(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
00.300.7352.850.200.913cbtA GO:0046872
10.070.4614.970.060.803d8kC GO:0003824 GO:0004722 GO:0006470
20.070.4874.930.060.851tlbA GO:0004109 GO:0005737 GO:0005829 GO:0006779 GO:0006782 GO:0006783 GO:0016491 GO:0042803 GO:0055114
30.070.4744.830.050.825eo6A GO:0004109 GO:0006779 GO:0006782 GO:0006783 GO:0016491 GO:0055114
40.070.4785.030.070.843dwrB GO:0004109 GO:0005737 GO:0006779 GO:0006782 GO:0006783 GO:0016491 GO:0042803 GO:0055114
50.070.4744.930.060.823dwsB GO:0004109 GO:0005737 GO:0006779 GO:0006782 GO:0006783 GO:0016491 GO:0042803 GO:0055114
60.070.4754.870.080.812aexA GO:0004109 GO:0005212 GO:0005737 GO:0005739 GO:0005743 GO:0005758 GO:0006779 GO:0006782 GO:0006783 GO:0010035 GO:0010039 GO:0010288 GO:0016020 GO:0016491 GO:0017085 GO:0042802 GO:0042803 GO:0046685 GO:0051597 GO:0055114
70.070.4204.510.030.643rt0A GO:0003824 GO:0004721 GO:0004722 GO:0005634 GO:0005737 GO:0006470 GO:0009738 GO:0016787 GO:0043169 GO:0046872
80.070.4134.970.020.671a6qA GO:0000122 GO:0000287 GO:0003824 GO:0004721 GO:0004722 GO:0004871 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0006470 GO:0006499 GO:0007050 GO:0010991 GO:0016020 GO:0016055 GO:0016311 GO:0016787 GO:0030145 GO:0030177 GO:0030512 GO:0030514 GO:0033192 GO:0035970 GO:0042347 GO:0043123 GO:0043124 GO:0043169 GO:0045893 GO:0046827 GO:0046872 GO:0070412 GO:0071560
90.070.3995.350.070.713acsA GO:0003824 GO:0005975 GO:0030246
100.070.4434.940.060.793nmnD GO:0003824 GO:0004721 GO:0004722 GO:0005634 GO:0005737 GO:0005886 GO:0006470 GO:0009408 GO:0009409 GO:0009737 GO:0009738 GO:0009787 GO:0009788 GO:0010119 GO:0016020 GO:0016787 GO:0019901 GO:0043169 GO:0046872
110.060.3854.830.050.674n0gA GO:0003824 GO:0004721 GO:0004722 GO:0005634 GO:0005829 GO:0006470 GO:0009409 GO:0009414 GO:0009737 GO:0009738 GO:0009788 GO:0010119 GO:0010360 GO:0016787 GO:0019901 GO:0043169 GO:0046872
120.060.4354.890.060.782p8eB GO:0000287 GO:0003824 GO:0004721 GO:0004722 GO:0005737 GO:0005829 GO:0006470 GO:0006499 GO:0016020 GO:0016787 GO:0030145 GO:0032688 GO:0035970 GO:0042347 GO:0043124 GO:0043169 GO:0046872 GO:0050687
130.060.3875.130.060.714da1A GO:0003824 GO:0004721 GO:0004722 GO:0005739 GO:0005759 GO:0006470 GO:0009083 GO:0016787 GO:0043169 GO:0046872
140.060.3985.390.070.713rrsA GO:0003824 GO:0005975 GO:0016740 GO:0016757 GO:0030246 GO:0047738
150.060.4235.280.070.792isnA
160.060.4015.000.060.701v7vA GO:0003824 GO:0005975 GO:0016740 GO:0030246 GO:0046872
170.060.4414.940.030.794lg5B GO:0003824 GO:0004721 GO:0004722 GO:0005634 GO:0005737 GO:0006470 GO:0009738 GO:0016787 GO:0043169 GO:0046872
180.060.3735.520.070.713qdeA GO:0003824 GO:0005975 GO:0016740 GO:0016757 GO:0030246 GO:0047738


Consensus prediction of GO terms
 
Molecular Function GO:0016634 GO:0046872
GO-Score 0.37 0.30
Biological Processes GO:0006783 GO:0046501
GO-Score 0.37 0.37
Cellular Component GO:0005829
GO-Score 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.