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I-TASSER results for job id Rv3018c

[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
10.04 2 4amjA 2CV Rep, Mult 126,146,150,153
20.04 2 1lphD IPH Rep, Mult 93,97
30.04 2 5d92A 8K6 Rep, Mult 78,82
40.04 2 3r6wA NFZ Rep, Mult 80,100,128
50.04 2 3ar3A PTY Rep, Mult 83,86,90,94,274
60.04 2 3pyoN MG Rep, Mult 26,30
70.04 2 3ar2A NA Rep, Mult 154,155,157,158,161
80.02 1 1vgiA XE Rep, Mult 44,48,129
90.02 1 3ar9A NA Rep, Mult 48,49,54,55,56
100.02 1 3ar4A PTY Rep, Mult 146,153,157
110.02 1 3l26B MG Rep, Mult 18,22,23
120.02 1 3vh7E MG Rep, Mult 97,100
130.02 1 2r9rB PGW Rep, Mult 44,48
140.02 1 2w0sB BVP Rep, Mult 27,31,34
150.02 1 3wmgA DMU Rep, Mult 99,103
160.02 1 3iilA MG Rep, Mult 11,12
170.02 1 2rh1A CLR Rep, Mult 124,154
180.02 1 1ystM BPH Rep, Mult 100,103,104,107

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
10.0601jroB0.3347.370.0540.5621.1.1.204NA
20.0602zxqA0.3397.690.0490.6043.2.1.97NA
30.0601fo4A0.3057.570.0450.5351.17.1.4NA
40.0601mhsA0.3477.010.0440.5623.6.3.6NA
50.0601ojnA0.3496.350.0610.5284.2.2.193
60.0602vuaA0.2677.020.0200.4353.4.24.69138,140
70.0602azdB0.3347.430.0520.5712.4.1.1141
80.0603iayA0.3496.870.0390.5602.7.7.7NA
90.0601w6jA0.3337.460.0410.5765.4.99.7NA
100.0601e6yA0.3336.870.0690.5412.8.4.1230
110.0601vlbA0.3347.150.0670.5581.2.99.762
120.0601ahpA0.3377.410.0570.5742.4.1.1NA
130.0602np0A0.3646.310.0300.5513.4.24.6912,157
140.0601dgjA0.3357.060.0800.5531.2.-.-NA
150.0602e1qA0.3357.220.0690.5621.17.3.2,1.17.1.4NA
160.0601ynnJ0.2266.290.0230.3432.7.7.6125,137
170.0601eulA0.3017.260.0400.5093.6.3.8280
180.0603eqlD0.2786.870.0570.4452.7.7.696
190.0601ynnD0.3096.630.0580.4842.7.7.6118,156,172,185

(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
00.290.8183.420.100.934ut1A GO:0005198 GO:0009424 GO:0044780
10.190.8472.870.090.932d4yA GO:0005198 GO:0005576 GO:0009288 GO:0009424 GO:0044780 GO:0071973
20.060.3857.350.040.662yajC GO:0003824 GO:0008152 GO:0016829 GO:0043722
30.060.3767.340.060.645i2gA GO:0003824 GO:0008152
40.060.3747.210.050.634mtjA GO:0003824 GO:0008152
50.060.3757.240.050.635i2aB GO:0003824 GO:0008152
60.060.3577.270.040.612f3oA GO:0003824 GO:0008152 GO:0016829
70.060.3337.450.040.581cm5A GO:0003824 GO:0005737 GO:0005829 GO:0005975 GO:0006006 GO:0006567 GO:0008152 GO:0008861 GO:0016020 GO:0016740 GO:0016746
80.060.3647.120.060.615bweA GO:0003824 GO:0008152
90.060.2777.610.040.503r0xA GO:0003941 GO:0005737 GO:0006520 GO:0006563 GO:0008721 GO:0016829 GO:0016836 GO:0030170 GO:0030378 GO:0036088 GO:0046416 GO:0070179
100.060.2667.040.050.433peiA GO:0004177 GO:0005622 GO:0005737 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0019538 GO:0030145 GO:0046872
110.060.2527.110.040.424n0rA GO:0005975
120.060.2657.400.070.462wssA GO:0000166 GO:0005524 GO:0005739 GO:0005743 GO:0005753 GO:0005886 GO:0006754 GO:0006810 GO:0006811 GO:0015986 GO:0015991 GO:0015992 GO:0016020 GO:0016820 GO:0033178 GO:0045261 GO:0046034 GO:0046933 GO:0046961
130.060.2407.070.040.395jc7A GO:0003677 GO:0005524 GO:0016787 GO:0016817
140.060.2667.020.090.432pljA GO:0003824 GO:0004586 GO:0006596 GO:0016829
150.060.2357.820.050.422ahuA GO:0008152 GO:0008410 GO:0008775 GO:0016740 GO:0046459 GO:0046952 GO:0051289
160.060.2466.390.070.384jz7C GO:0000166 GO:0005829 GO:0006525 GO:0008804 GO:0016301 GO:0016310 GO:0016740 GO:0019546
170.060.2376.230.040.352aekA GO:0016106 GO:0016829 GO:0045482
180.060.2387.360.060.411n8pA GO:0003824 GO:0003962 GO:0004123 GO:0005737 GO:0008652 GO:0016829 GO:0019343 GO:0019344 GO:0019346 GO:0030170 GO:0042802 GO:0044540 GO:0071266 GO:0080146


Consensus prediction of GO terms
 
Molecular Function GO:0005198
GO-Score 0.43
Biological Processes GO:0044780 GO:0097588
GO-Score 0.43 0.38
Cellular Component GO:0009424
GO-Score 0.43

(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.