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I-TASSER results for job id Rv2609c

[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
10.26 14 2a8pA MN Rep, Mult 218,219,234,238,294
20.10 6 3ffuA MG Rep, Mult 234,237,238
30.08 5 2qjoA APR Rep, Mult 178,180,182,197,218,219,220,234,238,268,316,320
40.03 2 1a9x1 III Rep, Mult 113,115,116,138,139
50.02 1 1su2A MG Rep, Mult 180,218,219,270
60.02 1 2qjtB MN Rep, Mult 220,222,233,234
70.02 1 2ckjD PO4 Rep, Mult 193,236,239,286

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
10.0862r5wB0.6614.470.0890.8522.7.7.1NA
20.0852qjoB0.6664.500.1080.8602.7.7.186,93
30.0602nz2A0.3736.170.0570.5936.3.4.5NA
40.0602ow6A0.3876.720.0310.6523.2.1.114NA
50.0602cqsA0.3426.860.0330.5782.4.1.20225
60.0601dl2A0.3786.520.0600.6243.2.1.11328
70.0601w6jA0.3836.270.0680.6215.4.99.7215,218
80.0602nq5A0.3737.330.0470.6752.1.1.14NA
90.0601nxcA0.3896.540.0530.6383.2.1.113NA
100.0601gqqA0.3136.600.0660.5246.3.2.8NA
110.0602vkzG0.3946.410.0290.6382.3.1.38,3.1.2.1469,90,92
120.0601f20A0.2706.940.0340.4641.14.13.3935,110
130.0602f00B0.3806.480.0970.6186.3.2.8NA
140.0602a6tA0.3683.970.1320.4533.6.1.30234,237
150.0603ecqB0.3757.020.0680.6523.2.1.97NA
160.0601gqyB0.3846.300.0670.6136.3.2.8NA
170.0603bcbA0.3786.010.0540.5812.9.1.2115
180.0601t3tA0.3776.690.0710.6326.3.5.3138
190.0603b9jC0.3356.960.0410.5781.17.3.2,1.17.1.4NA
200.0601t7lA0.3126.080.0660.4902.1.1.14NA
210.0601hxgA0.3836.510.0530.6504.2.3.9,4.1.99.7NA

(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
00.370.6614.470.090.852r5wB GO:0000166 GO:0000309 GO:0003824 GO:0009058 GO:0016740 GO:0016779 GO:0016787 GO:0046872
10.180.3513.230.130.413cngC GO:0016787 GO:0046872
20.110.3343.010.170.383gg6A GO:0000287 GO:0005829 GO:0009117 GO:0016787 GO:0034656 GO:0044715 GO:0044716 GO:0044717 GO:0046057 GO:0046067 GO:0046712 GO:0046872
30.080.6664.500.110.862qjoB GO:0000166 GO:0000309 GO:0003824 GO:0005524 GO:0005737 GO:0008152 GO:0009058 GO:0009435 GO:0016740 GO:0016779 GO:0016787 GO:0019363
40.070.3442.660.190.393dkuA GO:0016787
50.060.3764.220.070.484hfqA GO:0016787
60.060.3714.650.090.482gb5A GO:0000210 GO:0000287 GO:0008270 GO:0016787 GO:0030145 GO:0035529 GO:0046872
70.060.3603.180.140.423i9xA GO:0016787
80.060.3653.070.180.421su2A GO:0000166 GO:0005524 GO:0016787
90.060.3633.260.130.435bonA GO:0005829 GO:0006203 GO:0008413 GO:0016787 GO:0017110 GO:0034656 GO:0035539 GO:0046872
100.060.3653.390.090.432fmlA GO:0016787
110.060.3493.000.110.403fcmB GO:0016787
120.060.3412.940.140.393grnA GO:0016787
130.060.3383.660.160.412gt4A GO:0000287 GO:0008727 GO:0009103 GO:0016787 GO:0030145 GO:0046872 GO:0047917
140.060.3403.260.160.402pqvB GO:0016787
150.060.3333.190.140.392i8tB GO:0000287 GO:0008727 GO:0016787 GO:0046872
160.060.3432.830.180.392b0vA GO:0016787
170.060.3343.570.090.404zbpB GO:0000210 GO:0005634 GO:0005737 GO:0005886 GO:0016020 GO:0016787 GO:0046872 GO:0047631
180.060.3383.160.160.393fk9A GO:0016787


Consensus prediction of GO terms
 
Molecular Function GO:0016787 GO:0046872 GO:0000166 GO:0000309
GO-Score 0.61 0.55 0.42 0.42
Biological Processes GO:0009058
GO-Score 0.42
Cellular Component GO:0005829
GO-Score 0.11

(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.