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I-TASSER results for job id Rv0008c

[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
10.10 6 3p1oA III Rep, Mult 54,57,58,61,64,114,117,118
20.05 3 3cu8A III Rep, Mult 47,51,54,55,60,64,114,115,143
30.05 3 3qvdA FE Rep, Mult 22,25,55
40.05 3 2wh0C III Rep, Mult 30,31,81,85,88,89
50.05 3 5fvkA III Rep, Mult 19,20,23,24,27,31,34,37,49,62,63,66,68,70,71,74,78,82,85
60.03 2 1yklG DHB Rep, Mult 25,26
70.03 2 1qjbB III Rep, Mult 23,30,31,76,80,83
80.03 2 1qjaA III Rep, Mult 50,51,54,57,58,104,107,111,114,115
90.02 1 3l26B MG Rep, Mult 136,137
100.02 1 1ysaC NUC Rep, Mult 46,47,50,53,57
110.02 1 3u7qB IMD Rep, Mult 75,78
120.02 1 2nofA NUC Rep, Mult 31,41,56,57
130.02 1 3bz1Z CLA Rep, Mult 83,87
140.02 1 1fp4B CA Rep, Mult 57,58
150.02 1 3j000 PEV Rep, Mult 15,17,26

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
10.0661wcrA0.4802.340.0770.5722.7.1.69NA
20.0602f6dA0.5523.650.0430.7653.2.1.333,44,86
30.0601qleA0.4994.610.0420.8351.9.3.1NA
40.0601jk0A0.5584.090.0710.8141.17.4.1NA
50.0602eabA0.5893.920.0430.8553.2.1.63NA
60.0602vn4A0.5534.190.1070.8623.2.1.3NA
70.0601uzrB0.5743.810.0660.8211.17.4.1NA
80.0601hzfA0.5513.560.0510.7593.4.21.43NA
90.0601smsA0.5513.840.0430.7861.17.4.1NA
100.0601h0nA0.5693.760.0370.7931.17.4.1NA
110.0602bq1I0.5733.750.0660.8211.17.4.1NA
120.0601i1iP0.5694.230.0500.8833.4.24.16NA
130.0601ut9A0.5573.780.0670.8213.2.1.4NA
140.0601biqB0.5683.750.0700.7931.17.4.1NA
150.0601gaiA0.5634.460.1010.8903.2.1.3NA
160.0601rw9A0.5434.500.1010.8694.2.2.5NA
170.0601j0mA0.5424.330.0830.8354.2.2.1223
180.0603e04D0.5533.220.0550.7104.2.1.283
190.0601g87B0.5673.810.0290.8413.2.1.4NA
200.0603gtdA0.5443.430.0480.7104.2.1.2100

(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
00.100.6943.110.080.904moaA GO:0005102 GO:0006952 GO:0009405 GO:0030435
10.090.6413.260.060.841dlcA GO:0005102 GO:0006952 GO:0009405 GO:0030435
20.090.6443.190.080.841ciyA GO:0005102 GO:0006952 GO:0009405 GO:0030435
30.090.6433.340.080.854w8jA GO:0005102 GO:0006952 GO:0009405 GO:0030435
40.070.6393.390.080.841ji6A GO:0005102 GO:0006952 GO:0009405 GO:0030435
50.070.6123.230.090.811i5pA GO:0005102 GO:0006952 GO:0009405 GO:0030435
60.070.5463.040.070.723eb7A GO:0005102 GO:0006952 GO:0009405 GO:0030435
70.070.6613.180.090.844d8mA GO:0009405 GO:0030435
80.070.6503.530.090.882c9kA GO:0005102 GO:0006952 GO:0009405 GO:0030435
90.070.5043.290.060.673ck6E GO:0005886 GO:0016020 GO:0016021 GO:0030001 GO:0046873 GO:0055085
100.060.4884.430.080.754uvkA GO:0000755 GO:0003682 GO:0005634 GO:0005829 GO:0006473 GO:0007064 GO:0009847 GO:0031505 GO:0031618 GO:0031934 GO:0034990 GO:1990707
110.060.4035.200.060.713pa8A GO:0009405 GO:0016740 GO:0016757
120.060.4253.150.030.542y4uA GO:0004860 GO:0005737 GO:0005783 GO:0005788 GO:0005790 GO:0005829 GO:0006417 GO:0006986 GO:0016020 GO:0019901 GO:0031205 GO:0036494 GO:0036498 GO:0043066 GO:0051087 GO:0051603 GO:0051607 GO:0051787 GO:0070062 GO:0070417 GO:1903561 GO:1903912 GO:1904030
130.060.3066.070.090.651gnzA GO:0030246 GO:0046872
140.060.3804.780.020.611v6yA GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0031176
150.060.3814.700.060.623t2dA GO:0046872
160.060.3724.670.020.611isvA GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0031176
170.060.3584.450.020.534k3vB GO:0006810 GO:0007155 GO:0030001 GO:0046872
180.060.3634.760.060.631ig0B GO:0000166 GO:0004788 GO:0005524 GO:0009229 GO:0016301 GO:0016310 GO:0016740 GO:0030975


Consensus prediction of GO terms
 
Molecular Function GO:0005102
GO-Score 0.37
Biological Processes GO:0006952 GO:0030435 GO:0009405
GO-Score 0.37 0.37 0.37
Cellular Component
GO-Score

(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.