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I-TASSER results for job id Rv1808

[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 3 1nkzA BCL Rep, Mult 89,92,93,96,97,100,151
20.04 3 2iegB FRY Rep, Mult 120,121,131,135
30.03 2 3cejB AVF Rep, Mult 104,105,106,109
40.03 2 1rzhL BCL Rep, Mult 92,97
50.03 2 3cemA AVD Rep, Mult 6,7,8,12
60.03 2 1exvA 700 Rep, Mult 104,106,150,154
70.03 2 3cvsC NUC Rep, Mult 130,131,132
80.01 1 4f8hA LMD Rep, Mult 90,93
90.01 1 1p2bA GLC Rep, Mult 38,39,41,42,79,82,86
100.01 1 3m9iA 3PE Rep, Mult 94,98
110.01 1 3arcJ III Rep, Mult 75,76
120.01 1 1c8lA CFF Rep, Mult 3,18,20
130.01 1 3cejA AVF Rep, Mult 110,111,112,116
140.01 1 3qfeA CA Rep, Mult 155,158
150.01 1 2w0sB BVP Rep, Mult 24,28,31
160.01 1 1gfzA CFF Rep, Mult 50,55,57
170.01 1 4bjwB I3C Rep, Mult 79,80
180.01 1 2h8pC GOA Rep, Mult 153,154
190.01 1 3bd7A CKB Rep, Mult 18,20,21,22
200.01 1 1dxoA DQN Rep, Mult 57,87

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
10.0601z0hB0.2757.150.0210.4673.4.24.69137,140
20.0603k1dA0.3456.770.0390.5652.4.1.18100,102
30.0603h0gA0.3407.530.0340.5992.7.7.6202
40.0601cc1L0.3596.560.0580.5571.12.99.650
50.0601fa9A0.2877.330.0370.4822.4.1.1NA
60.0602ebsB0.3427.000.0500.5753.2.1.150NA
70.0601kqfA0.2967.220.0510.5111.2.1.2NA
80.0601h2rL0.3757.180.0500.6191.12.2.141
90.0602wpnB0.3586.520.0640.5531.12.7.292,96
100.0601ffuB0.2917.160.0350.4941.2.99.2NA
110.0602e9bA0.3406.610.0480.5433.2.1.4152,71
120.0601yiqA0.3306.500.0610.5161.1.99.-NA
130.0602pflA0.3377.710.0430.6162.3.1.54NA
140.0601t3qB0.3356.450.0590.5261.3.99.17NA
150.0603f41A0.3377.030.0370.5653.1.3.8155
160.0602e8yA0.3366.640.0330.5403.2.1.41NA
170.0602frvD0.3687.160.0590.6191.12.2.195
180.0603ebgA0.3306.460.0240.5183.4.11.-NA
190.0603c46B0.3037.170.0360.5092.7.7.6NA

(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
00.300.7044.330.100.864ut1A GO:0005198 GO:0009424 GO:0044780
10.250.7284.030.090.872d4yA GO:0005198 GO:0005576 GO:0009288 GO:0009424 GO:0044780 GO:0071973
20.090.2726.980.050.452wssA 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
30.060.3955.740.070.572p7nA GO:0009405
40.060.2877.330.040.481fa9A GO:0000166 GO:0002060 GO:0003824 GO:0004645 GO:0005524 GO:0005536 GO:0005737 GO:0005829 GO:0005886 GO:0005975 GO:0005977 GO:0005980 GO:0006015 GO:0008144 GO:0008152 GO:0008184 GO:0016208 GO:0016740 GO:0016757 GO:0019842 GO:0030170 GO:0030246 GO:0032052 GO:0042593 GO:0042803 GO:0070062 GO:0070266
50.060.3056.620.040.481ygpA GO:0004645 GO:0005737 GO:0005975 GO:0005977 GO:0005980 GO:0008184 GO:0016740 GO:0016757 GO:0030170
60.060.3395.770.030.482izpA GO:0005576 GO:0009405
70.060.3154.640.070.402j0oA GO:0005576 GO:0009405
80.060.3295.480.060.472ym9A GO:0005576 GO:0009405
90.060.3777.230.040.654bqfB GO:0003824 GO:0004645 GO:0005737 GO:0005829 GO:0005975 GO:0005980 GO:0008152 GO:0008184 GO:0009414 GO:0009507 GO:0016740 GO:0016757 GO:0030170 GO:0046686
100.060.3737.200.040.642qllA GO:0000166 GO:0002060 GO:0003824 GO:0004645 GO:0005524 GO:0005536 GO:0005737 GO:0005829 GO:0005886 GO:0005975 GO:0005977 GO:0005980 GO:0006015 GO:0008144 GO:0008152 GO:0008184 GO:0016208 GO:0016740 GO:0016757 GO:0019842 GO:0030170 GO:0030246 GO:0032052 GO:0042593 GO:0042803 GO:0070062 GO:0070266
110.060.3097.430.040.541e1yA GO:0000166 GO:0003824 GO:0004645 GO:0005975 GO:0005977 GO:0008152 GO:0008184 GO:0016740 GO:0016757 GO:0030170
120.060.2926.810.040.472c4mC GO:0004645 GO:0005975 GO:0008184 GO:0016740 GO:0016757 GO:0030170
130.060.2786.690.040.453peiA GO:0004177 GO:0005622 GO:0005737 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0019538 GO:0030145 GO:0046872
140.060.3847.190.040.651ahpA GO:0003824 GO:0004645 GO:0005737 GO:0005829 GO:0005975 GO:0005980 GO:0008152 GO:0008184 GO:0016740 GO:0016757 GO:0030170 GO:0030980 GO:0031220
150.060.2726.890.040.455fp2A GO:0004872 GO:0005506 GO:0006810 GO:0009279 GO:0015891 GO:0016020
160.060.3677.310.020.634l22A GO:0004645 GO:0005975 GO:0008184 GO:0016740 GO:0016757 GO:0030170
170.060.2507.630.060.454n0rA GO:0005975
180.060.3827.280.040.663gpbA GO:0000166 GO:0003824 GO:0004645 GO:0005975 GO:0005977 GO:0008152 GO:0008184 GO:0016740 GO:0016757 GO:0030170


Consensus prediction of GO terms
 
Molecular Function GO:0005198
GO-Score 0.48
Biological Processes GO:0097588 GO:0044780
GO-Score 0.50 0.48
Cellular Component GO:0009424
GO-Score 0.48

(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.