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I-TASSER results for job id Rv1332

[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
10.11 7 3g1mA RF3 Rep, Mult 60,74,75,78,79,136,137,140,167,170,171,174,203
20.05 3 3whbA DCC Rep, Mult 49,52,53,56,123,126,127,130,131,133,134,160,161,163,164,167,171
30.05 3 2uxuB NAR Rep, Mult 56,78,95,139,162,163,166,170
40.03 2 3jwrA IBM Rep, Mult 88,91
50.03 2 1usyF HIS Rep, Mult 203,207
60.03 2 1jumA BER Rep, Mult 55,56,59,80,131,134,167
70.03 2 4ojjC MG Rep, Mult 45,121
80.03 2 1jt0A QNA Rep, Mult 95,167,169,170,173,174
90.02 1 1gzmA C8E Rep, Mult 57,60
100.02 1 3fz3A CA Rep, Mult 28,170,171
110.02 1 4ev6E MG Rep, Mult 60,136
120.02 1 3hiyB MG Rep, Mult 88,97
130.02 1 3c9iB XE Rep, Mult 210,214
140.02 1 1jt0C QNA Rep, Mult 142,160,161,162,165,166
150.02 1 1bjyB CTC Rep, Mult 169,173,176
160.02 1 2wtfA CA Rep, Mult 105,108

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
10.0603ffzA0.4206.050.0640.7613.4.24.69NA
20.0601auiA0.4135.960.0310.7343.1.3.16126
30.0603c8yA0.4184.850.0590.6421.12.7.273,171,186
40.0601xzwB0.4245.940.0750.7523.1.3.2NA
50.0601kbpA0.4135.950.0400.7293.1.3.2NA
60.0601wdpA0.4125.300.0700.6653.2.1.2NA
70.0602qtcB0.3885.890.0770.6471.2.4.1113
80.0602fonB0.4174.890.0200.6421.3.3.6NA
90.0601cb7B0.4204.710.0710.6195.4.99.1NA
100.0602qf7A0.4265.740.0340.7346.4.1.1NA
110.0602uv8G0.4255.250.0580.6792.3.1.86NA
120.0602a06C0.3635.660.0600.6151.10.2.2174
130.0603gpbA0.4155.880.0740.7022.4.1.193
140.0601y7910.4445.090.0560.6793.4.15.545
150.0602pywA0.4385.190.0510.7022.7.1.100NA
160.0602uxwA0.4326.130.0460.7891.3.99.-NA
170.0602qllA0.4045.730.0560.6882.4.1.193
180.0602z1qB0.4206.040.0330.7661.3.99.3NA
190.0601w07B0.4295.300.0210.6791.3.3.6NA

(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
00.210.6643.610.130.873e7qB GO:0003677 GO:0003700 GO:0006351 GO:0006355
10.190.6183.990.060.822qibA GO:0003677 GO:0003700 GO:0006351 GO:0006355
20.180.6264.200.150.872uxhA GO:0003677 GO:0006351 GO:0006355
30.170.6033.640.080.783g7rB GO:0003677 GO:0003700 GO:0006351 GO:0006355
40.140.6004.100.060.823kz9B GO:0003677 GO:0006351 GO:0006355
50.130.6223.670.100.814ichA GO:0003677 GO:0006351 GO:0006355
60.120.6003.660.090.782np5A GO:0003677 GO:0006351 GO:0006355
70.100.5923.810.070.793crjA GO:0003677
80.100.6094.060.090.832id6A GO:0003677 GO:0006351 GO:0006355
90.100.6044.100.060.832pbxA
100.080.6303.760.070.832fbqA GO:0000976 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0044212 GO:0045893 GO:0050714
110.080.6323.980.060.853c07A GO:0003677 GO:0006351 GO:0006355
120.080.6353.820.060.853vibC GO:0003677 GO:0006351 GO:0006355
130.070.6124.080.080.843p9tA GO:0003677 GO:0006351 GO:0006355
140.070.6003.610.080.792g3bA GO:0003677 GO:0006351 GO:0006355
150.070.5853.850.140.784l62A GO:0000976 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355
160.070.5883.770.070.773knwA GO:0003677 GO:0006351 GO:0006355
170.070.5714.370.060.811rktA GO:0003677 GO:0006351 GO:0006355
180.070.5864.030.100.783f1bA GO:0003677 GO:0006351 GO:0006355


Consensus prediction of GO terms
 
Molecular Function GO:0003677 GO:0003700
GO-Score 0.62 0.47
Biological Processes GO:0006355
GO-Score 0.62
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.