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I-TASSER results for job id Rv2752c

[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 1 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
10.41 31 3bv6F FE Rep, Mult 85,86,170,397
20.31 25 3idzC ZN Rep, Mult 81,83,148,170,375
30.18 12 3t3oA NUC Rep, Mult 27,49,58,59,85,237,238,239,240,241,263,264,265,305,308,310,312,317,341,344,371,373,374,375,397
40.12 7 4xwwA MN Rep, Mult 56,58,450
50.04 7 3iemA NUC Rep, Mult 17,19,35,40,66,67,426,428
60.04 6 3ielA U5P Rep, Mult 27,204,205,238,242,338,339,373,374,375,399,402
70.04 3 3bk2A U5P Rep, Mult 27,84,85,238,241,339,340,341,342,371,373,374,375
80.03 4 3p2uA VO4 Rep, Mult 83,85,148,170,375,397
90.02 4 3ie1D NUC Rep, Mult 49,83,84,85,118,119,121,122,148,170,238,239,242,264,265,305,306,309,310,397
100.02 3 3iemC NUC Rep, Mult 27,83,204,238,339,375,399
110.01 1 3zq4D CA Rep, Mult 471,547
120.01 1 3zq4C CA Rep, Mult 470,471
130.01 2 3iemB SSU Rep, Mult 27,49,50,84,85,204,238,239,240,265,375,397,399,402
140.00 1 3af6A NUC Rep, Mult 411,419,420
150.00 1 2cbn0 III Rep, Mult 47,65,82,83,88,89,91,92,95,96,150
160.00 1 3iemC NUC Rep, Mult 118,122,123,238,239,242,265,306,311

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
10.0603bicA0.3546.610.0720.5165.4.99.2NA
20.0603itkC0.3445.770.0750.4621.1.1.22149
30.0603ictA0.3497.580.0580.5661.8.1.14107,273
40.0602cbnA0.3772.970.1550.4183.1.26.1130,83,85,91,93
50.0602pffB0.3687.920.0750.6112.3.1.8688,104
60.0602fgeA0.3387.850.0350.5653.4.24.-NA
70.0602wbaA0.3267.350.0680.5201.8.1.12345
80.0603f93A0.3647.300.0500.5743.2.1.-NA
90.0602b0tA0.3317.140.0370.5071.1.1.4289
100.0602vkzG0.3557.530.0540.5702.3.1.38,3.1.2.1423
110.0602w00B0.3277.430.0540.5183.1.21.3108,146
120.0602dkfA0.6003.340.1930.6793.1.-.-NA
130.0603igyB0.3496.900.0590.5235.4.2.185
140.0601feaA0.3247.440.0680.5251.8.1.12397
150.0602i7tA0.5603.870.1440.6613.1.27.-50,239,306,373,375
160.0602i7vA0.6043.830.1390.7103.1.27.-85,170
170.0602ipyA0.3077.540.0570.4894.2.1.3NA
180.0602uv8G0.3567.420.0510.5682.3.1.86NA
190.0602qr5A0.3387.240.0650.5343.4.19.1NA

(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
00.620.9022.600.370.973t3oA GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0004527 GO:0004534 GO:0005737 GO:0006364 GO:0006396 GO:0008270 GO:0016787 GO:0046872 GO:0090501 GO:0090502 GO:0090503
10.620.9660.830.370.973zq4A GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0004527 GO:0004534 GO:0005737 GO:0006364 GO:0006396 GO:0006397 GO:0008270 GO:0016787 GO:0046872 GO:0090501 GO:0090502 GO:0090503
20.580.7651.810.580.795a0tA GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0004527 GO:0004534 GO:0005737 GO:0006364 GO:0006396 GO:0008270 GO:0016787 GO:0046872 GO:0090501 GO:0090502 GO:0090503
30.580.9271.840.370.974xwwA GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0004527 GO:0004534 GO:0005737 GO:0006364 GO:0006396 GO:0008270 GO:0016787 GO:0046872 GO:0090501 GO:0090502 GO:0090503
40.440.6023.030.190.672az4B GO:0046872
50.420.6183.600.160.712xr1B GO:0003676 GO:0003723 GO:0046872
60.420.6143.720.150.723af5A GO:0003676 GO:0003723 GO:0046872
70.410.6043.830.140.712i7vA GO:0000398 GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0005634 GO:0005654 GO:0005847 GO:0006369 GO:0006378 GO:0006379 GO:0006397 GO:0006398 GO:0006406 GO:0008409 GO:0016787 GO:0030529 GO:0031124 GO:0046872 GO:0090305 GO:0090502
80.330.6103.290.190.693a4yA GO:0003723 GO:0004518 GO:0004519 GO:0005737 GO:0006364 GO:0016787 GO:0046872 GO:0090305
90.320.3583.270.160.403g1pB GO:0008081 GO:0016787 GO:0019700 GO:0030145 GO:0046872
100.220.3772.970.150.422cbnA GO:0004518 GO:0004519 GO:0004527 GO:0004532 GO:0008033 GO:0008270 GO:0016787 GO:0016891 GO:0034414 GO:0042779 GO:0042781 GO:0046872 GO:0090502 GO:0090503
110.160.3782.920.190.421y44A GO:0004518 GO:0004519 GO:0008033 GO:0008270 GO:0016787 GO:0016891 GO:0034414 GO:0042779 GO:0042781 GO:0046872 GO:0090502
120.090.3553.580.170.412p4zB GO:0016787 GO:0046872
130.070.6113.800.160.722ycbB GO:0003676 GO:0003723 GO:0046872
140.070.5603.870.140.662i7tA GO:0000398 GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0005634 GO:0005654 GO:0005847 GO:0006369 GO:0006378 GO:0006379 GO:0006397 GO:0006398 GO:0006406 GO:0008409 GO:0016787 GO:0030529 GO:0031124 GO:0046872 GO:0090305 GO:0090502
150.070.4993.470.160.574b87A GO:0000784 GO:0003684 GO:0005634 GO:0005654 GO:0005730 GO:0006281 GO:0006303 GO:0006974 GO:0007049 GO:0007067 GO:0031848 GO:0035312 GO:0036297 GO:0051301 GO:0090305
160.070.4843.320.170.555ahoA GO:0000075 GO:0000723 GO:0000781 GO:0000784 GO:0003684 GO:0004518 GO:0004527 GO:0005634 GO:0005694 GO:0005737 GO:0005813 GO:0005815 GO:0005856 GO:0006281 GO:0006303 GO:0006974 GO:0008409 GO:0016787 GO:0031627 GO:0031848 GO:0031860 GO:0035312 GO:0036297 GO:0090305
170.060.3403.630.140.393h3eA GO:0016787 GO:0046872
180.060.3773.110.180.422fk6A GO:0004518 GO:0004519 GO:0008033 GO:0008270 GO:0016787 GO:0016891 GO:0034414 GO:0042779 GO:0042781 GO:0046872 GO:0090502


Consensus prediction of GO terms
 
Molecular Function GO:0008270 GO:0004521 GO:0004534 GO:0003723
GO-Score 0.97 0.97 0.97 0.97
Biological Processes GO:0090503 GO:0090502 GO:0006364 GO:0006397
GO-Score 0.97 0.97 0.97 0.61
Cellular Component GO:0005737
GO-Score 0.97

(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.