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I-TASSER results for job id Rv3073c

[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
10.08 5 3wmn2 BCL Rep, Mult 110,114
20.07 4 1r1rA III Rep, Mult 45,46,48,54,98
30.05 3 4glbB XXH Rep, Mult 34,35,44,103
40.05 3 2c0kA OXY Rep, Mult 107,111
50.05 3 1g42A CA Rep, Mult 31,34
60.03 2 6r1rA III Rep, Mult 86,87,88,89,90
70.03 2 7r1rA III Rep, Mult 72,73,75,76,81
80.03 2 1vf5S III Rep, Mult 114,115
90.02 1 2onkE MG Rep, Mult 56,62,66
100.02 1 3v09A UNK Rep, Mult 37,57
110.02 1 1peoA DCP Rep, Mult 50,51,55,65,66
120.02 1 1cgpA CMP Rep, Mult 76,79
130.02 1 2nq8C ZID Rep, Mult 65,69
140.02 1 3mjlB 2AI Rep, Mult 102,107

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
10.0602b7oA0.4764.490.0360.8222.5.1.54NA
20.0602qjgA0.4794.860.0690.8644.1.2.-NA
30.0602gewA0.4805.050.0800.8901.1.3.6NA
40.0601xasA0.4454.640.0350.7633.2.1.8NA
50.0601e6yA0.4974.030.0640.8222.8.4.175
60.0603hfwA0.4963.980.0340.8223.2.2.1977
70.0601hqfA0.5054.660.0550.8813.5.3.1NA
80.0603hwkE0.4794.280.0450.8052.3.3.1NA
90.0601wogA0.5194.470.0880.8733.5.3.1117
100.0602cvtA0.4964.510.0190.8561.17.4.1NA
110.0603gmzA0.5054.530.0360.8643.5.3.147,89
120.0601peuA0.5184.350.0280.8811.17.4.145
130.0603f0zA0.4864.580.0740.8984.2.99.18NA
140.0603m1rA0.5184.690.1030.8813.5.3.873
150.0601e6vA0.4824.300.1050.8562.8.4.1NA
160.0605r1rA0.4854.110.0710.8311.17.4.1104
170.0601xjjA0.5024.360.0570.8811.17.4.1100
180.0602wghB0.4954.440.0270.8561.17.4.145
190.0601v0nA0.4644.260.0650.7973.2.1.8NA

(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
00.070.5384.520.060.873pzlB GO:0016787 GO:0016813 GO:0046872
10.070.5074.360.020.862wghA GO:0000166 GO:0000278 GO:0003824 GO:0004748 GO:0005524 GO:0005635 GO:0005654 GO:0005737 GO:0005829 GO:0005971 GO:0006206 GO:0006260 GO:0008152 GO:0008584 GO:0009263 GO:0010212 GO:0015949 GO:0016491 GO:0017076 GO:0021846 GO:0042995 GO:0043025 GO:0051259 GO:0051290 GO:0055114 GO:0060041 GO:0070062
20.070.4814.650.050.882a0mA GO:0046872
30.070.5054.530.040.863gmzA GO:0000050 GO:0001889 GO:0001938 GO:0004053 GO:0005615 GO:0005634 GO:0005737 GO:0005741 GO:0005829 GO:0006525 GO:0006527 GO:0007565 GO:0007568 GO:0009611 GO:0009635 GO:0010042 GO:0010043 GO:0010269 GO:0010963 GO:0014075 GO:0016787 GO:0016813 GO:0019547 GO:0030145 GO:0030324 GO:0032496 GO:0032964 GO:0033189 GO:0033197 GO:0042493 GO:0043005 GO:0043025 GO:0043200 GO:0043434 GO:0046686 GO:0046872 GO:0048545 GO:0048678 GO:0051597 GO:0060056 GO:0060135 GO:0070062 GO:0070207 GO:0070301 GO:0071222 GO:0071353 GO:0071377 GO:0071549 GO:0071560
40.070.5064.780.130.894dz4B GO:0008783 GO:0016787 GO:0016813 GO:0046872
50.070.5004.540.060.853m1rD GO:0006547 GO:0006548 GO:0016787 GO:0016813 GO:0019556 GO:0019557 GO:0030145 GO:0046872 GO:0050415
60.070.5054.660.060.881hqfA GO:0000050 GO:0001889 GO:0001938 GO:0004053 GO:0005615 GO:0005634 GO:0005737 GO:0005741 GO:0006525 GO:0007565 GO:0007568 GO:0009611 GO:0009635 GO:0010042 GO:0010043 GO:0010269 GO:0010963 GO:0014075 GO:0016787 GO:0016813 GO:0019547 GO:0030145 GO:0030324 GO:0032496 GO:0032964 GO:0033189 GO:0033197 GO:0042493 GO:0043005 GO:0043025 GO:0043200 GO:0043434 GO:0046686 GO:0046872 GO:0048545 GO:0048678 GO:0051597 GO:0060056 GO:0060135 GO:0070062 GO:0070207 GO:0070301 GO:0071222 GO:0071353 GO:0071377 GO:0071549 GO:0071560
70.070.4814.880.130.881cevA GO:0000050 GO:0004053 GO:0006525 GO:0016787 GO:0016813 GO:0046872
80.070.4854.420.030.861zyzA GO:0000166 GO:0003824 GO:0004748 GO:0005524 GO:0005737 GO:0005971 GO:0006260 GO:0008152 GO:0009263 GO:0016491 GO:0055114
90.070.4864.800.130.882ef4A GO:0004053 GO:0006525 GO:0016787 GO:0046872
100.070.4964.510.020.862cvtA GO:0000166 GO:0003824 GO:0004748 GO:0005524 GO:0005737 GO:0005971 GO:0006260 GO:0008152 GO:0009263 GO:0016491 GO:0055114
110.070.4944.640.090.861gq6B GO:0016787 GO:0016813 GO:0033050 GO:0033972 GO:0046872
120.070.4974.880.050.894q3vC GO:0000050 GO:0004053 GO:0006525 GO:0016787 GO:0016813 GO:0046872
130.070.4854.770.060.873lhlA GO:0008783 GO:0016787 GO:0016813 GO:0046872
140.070.5044.620.060.874hzeA GO:0000050 GO:0001657 GO:0004053 GO:0005739 GO:0005759 GO:0006525 GO:0006809 GO:0006941 GO:0016787 GO:0016813 GO:0046872
150.070.5004.440.060.865hj9A GO:0004053 GO:0006525 GO:0016787 GO:0016813 GO:0046872
160.070.5124.270.010.865im3A GO:0000166 GO:0004748 GO:0005524 GO:0005971 GO:0006260 GO:0009263 GO:0016491 GO:0055114
170.070.5194.470.090.871wogA GO:0016787 GO:0016813 GO:0046872
180.070.4974.510.060.863mmrA GO:0004053 GO:0016787 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0043169 GO:0016810
GO-Score 0.48 0.37
Biological Processes GO:0009263 GO:0030324 GO:0010043 GO:0010042 GO:0021846 GO:0009635 GO:0071560 GO:0071377 GO:0001938 GO:0015949 GO:0033197 GO:0048678 GO:0001889 GO:0010269 GO:0032964 GO:0051290 GO:0070207 GO:0043200 GO:0000050 GO:0070301 GO:0014075 GO:0006260 GO:0055114 GO:0051597 GO:0010212 GO:0042493 GO:0071353 GO:0071549 GO:0008584 GO:0071222 GO:0007568 GO:0033189 GO:0060135 GO:0060056 GO:0019547 GO:0060041 GO:0010963 GO:0046686 GO:0000278 GO:0006206
GO-Score 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07
Cellular Component GO:0043025 GO:0070062 GO:0005971 GO:0005635 GO:0043005 GO:0005615 GO:0005654 GO:0005741
GO-Score 0.13 0.13 0.07 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.