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I-TASSER results for job id Rv1773c

[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
10.74 21 2o9aD PYR Rep, Mult 142,147,148,149,192,200,202,218,220
20.02 1 2o9a0 III Rep, Mult 131,136,196,199,200,221,222,224
30.02 1 2ia20 III Rep, Mult 16,18,19,20,22,23,26,27,29,34,54,58,59,61,62,64,75,76,77,78,79,80,141

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
10.0602v2fF0.4424.410.0560.6173.4.16.4207
20.0601rp5A0.4715.240.0970.7183.4.-.-NA
30.0603eqvA0.4775.110.0610.7183.4.16.4NA
40.0602q8nB0.4076.050.0590.7065.3.1.9NA
50.0603hz6A0.4146.420.0820.7462.7.1.17139,148,219
60.0601sj2A0.3435.970.0360.5931.11.1.6,1.11.1.721
70.0601pn0C0.4056.020.0630.6901.14.13.7NA
80.0603flcX0.4106.510.0640.7582.7.1.30NA
90.0601a3wA0.4305.190.0400.6732.7.1.40NA
100.0603hztA0.2746.300.0420.4842.7.11.17147
110.0602d4wA0.4226.090.0560.7542.7.1.304
120.0602o9bA0.4243.730.0660.5322.7.13.3153
130.0601y9mA0.4365.710.0330.7143.2.1.80224
140.0601zaoA0.4445.370.0780.6982.7.11.1NA
150.0602zmfB0.4023.260.0560.4843.1.4.17112,153,241
160.0603fwlA0.4445.540.0850.7182.4.1.129NA
170.0601y4wA0.4325.790.0560.7143.2.1.8043
180.0602agsA0.4376.070.0800.7383.2.1.18162
190.0602zf5Y0.4176.320.0600.7542.7.1.30187,191,203

(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
00.490.9171.040.250.941mkmB GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0045892
10.350.7693.510.230.962o0yC GO:0003677 GO:0006351 GO:0006355
20.280.5962.050.300.653bjnA GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0045892
30.270.6042.100.210.661tf1A GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0006974 GO:0042802 GO:0045892
40.260.5812.010.140.643mq0B GO:0003677 GO:0006351 GO:0006355
50.240.5961.950.190.653r4kA GO:0003677 GO:0006351 GO:0006355
60.230.5902.460.200.652xrnB GO:0003677 GO:0006351 GO:0006355
70.230.6021.760.240.651ysqA GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0045892
80.220.5781.540.260.611yspA GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0045892
90.210.6041.750.230.652o99C GO:0003677 GO:0003700 GO:0005829 GO:0006097 GO:0006351 GO:0006355 GO:0045892
100.190.5832.170.200.653obfA GO:0003677 GO:0006351 GO:0006355
110.180.6041.720.170.652ia2A GO:0003677 GO:0006351 GO:0006355 GO:0045893 GO:0046278
120.140.5652.510.150.643d3oA GO:0003677 GO:0006351 GO:0006355
130.070.5971.880.150.652g7uA GO:0003677 GO:0006351 GO:0006355 GO:0045893 GO:0046278
140.060.3246.400.060.584moaA GO:0005102 GO:0006952 GO:0009405 GO:0030435
150.060.2875.470.080.463k2zB GO:0003677 GO:0004252 GO:0006260 GO:0006281 GO:0006351 GO:0006355 GO:0006508 GO:0006974 GO:0009432 GO:0016787 GO:0045892
160.060.2905.670.050.481ig0B GO:0000166 GO:0004788 GO:0005524 GO:0009229 GO:0016301 GO:0016310 GO:0016740 GO:0030975
170.060.3166.310.060.574ylfB GO:0004355 GO:0005737 GO:0016491 GO:0051536 GO:0055114
180.060.2763.380.070.332fxaB GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0030435 GO:0045892


Consensus prediction of GO terms
 
Molecular Function GO:0003677 GO:0003700 GO:0005515
GO-Score 0.87 0.73 0.54
Biological Processes GO:0045892 GO:0033554
GO-Score 0.73 0.54
Cellular Component GO:0044444
GO-Score 0.54

(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.