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I-TASSER results for job id Rv2395B

[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 5 1txcB 2AN Rep, Mult 8,30,42,47,48
20.07 3 1xrmA III Rep, Mult 1,4
30.07 3 1ib4B MAN Rep, Mult 21,25
40.05 2 2o8mB III Rep, Mult 34,39
50.04 2 1aztB MG Rep, Mult 20,47,48
60.04 2 4y2nB MG Rep, Mult 39,49
70.02 1 2m0oA III Rep, Mult 12,20,21,23,26,43,44,45,47
80.02 1 1zaoA MN Rep, Mult 36,47
90.02 1 3nmuC NUC Rep, Mult 35,36
100.02 1 3j0qL NUC Rep, Mult 18,19
110.02 1 4polA COM Rep, Mult 25,26
120.02 1 3bwxA CA Rep, Mult 9,12
130.02 1 2g77A AF3 Rep, Mult 14,53

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
10.0601ucyE0.4043.500.0200.8523.4.21.543
20.0601bbrH0.2853.980.0630.6673.4.21.515
30.0601ah5A0.4403.410.0800.8522.5.1.61,4.3.1.8NA
40.0601bsgA0.4493.640.0610.8893.5.2.6NA
50.0601ybqA0.4443.500.0830.8153.4.19.19
60.0601f1sA0.4453.230.0000.7594.2.2.1NA
70.0601jwtA0.4423.620.0190.9073.4.21.5NA
80.0602c4bA0.4713.100.0410.8703.1.27.3NA
90.0601ay7A0.4243.650.0610.8703.1.27.3NA
100.0602puxB0.4363.480.0200.8893.4.21.5NA
110.0603d5gB0.4463.610.0580.8893.1.4.817
120.0601n4oB0.4023.640.0600.9073.5.2.6NA
130.0601onxA0.4473.470.0830.8153.4.19.-NA
140.0601bujA0.4622.970.0410.8703.1.27.-25
150.0603a3iA0.4423.360.0820.8523.4.16.438
160.0601madH0.4423.310.0680.7781.4.99.39
170.0601cefA0.4652.940.0450.8153.4.16.4NA
180.0601jqjA0.4323.770.0630.8702.7.7.717,28,30,48
190.0601c54A0.4613.250.0960.9263.1.27.3NA

(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
00.140.4783.120.070.831lqmH
10.070.5122.940.000.891xv2C GO:0045151 GO:0047605
20.070.2934.060.040.634bt2A GO:0016829 GO:0016831 GO:0045151 GO:0047605
30.070.4433.710.020.851dy6A GO:0008800 GO:0016787 GO:0030655 GO:0046677
40.070.4313.310.120.802wpwA GO:0008080 GO:0033050
50.070.3013.850.080.633dkqB GO:0005506 GO:0016491 GO:0016705 GO:0016706 GO:0031418 GO:0046872 GO:0051213 GO:0055114
60.070.4153.520.040.831fusA GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0004540 GO:0016787 GO:0046589 GO:0090305 GO:0090501 GO:0090502
70.070.4043.510.040.853f2oB GO:0000209 GO:0004842 GO:0005737 GO:0005829 GO:0016567 GO:0035556
80.070.4423.330.040.891sqhA GO:0016740 GO:0016746 GO:0016747
90.070.3184.180.100.673dkqA GO:0005506 GO:0016491 GO:0016705 GO:0016706 GO:0031418 GO:0046872 GO:0051213 GO:0055114
100.070.4123.570.120.892blmA GO:0005886 GO:0008800 GO:0016020 GO:0016787 GO:0030655 GO:0046677
110.070.3893.920.100.914yfmA GO:0008800 GO:0016787 GO:0030655 GO:0046677
120.070.4023.640.060.911n4oB GO:0008800 GO:0016787 GO:0030655 GO:0046677
130.060.5043.070.060.912kaaA GO:0003723 GO:0004540 GO:0090501
140.060.4293.250.090.813whoA GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0004540 GO:0016787 GO:0046589 GO:0090305 GO:0090501 GO:0090502
150.060.4093.680.060.893lezA GO:0008800 GO:0016787 GO:0030655 GO:0046677 GO:0046872
160.060.3214.070.100.671y44A GO:0004518 GO:0004519 GO:0008033 GO:0008270 GO:0016787 GO:0016891 GO:0034414 GO:0042779 GO:0042781 GO:0046872 GO:0090502
170.060.2694.420.070.704d2oB GO:0008800 GO:0016787 GO:0030655 GO:0046677
180.060.3124.370.060.781iuzA GO:0005507 GO:0009055 GO:0009507 GO:0009535 GO:0009536 GO:0009579 GO:0016020 GO:0046872 GO:0051607 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0047605 GO:0008800 GO:0008080
GO-Score 0.13 0.07 0.07
Biological Processes GO:0045151 GO:0046677 GO:0033050 GO:0030655
GO-Score 0.13 0.07 0.07 0.07
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.