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I-TASSER results for job id Rv3796

[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
10.52 40 4qn9A ZN Rep, Mult 124,125,276,341
20.13 11 2e7yA ZN Rep, Mult 120,122,251,276
30.02 2 3iemA SSU Rep, Mult 61,63,85,102,103,104,370,372
40.01 1 2fk6A NUC Rep, Mult 88,109,111,138,139,207,208,210,221,222,224,225,228
50.01 1 2cbnA ZN Rep, Mult 120,122,188,276
60.01 1 1zkp0 III Rep, Mult 70,71,75,97,101,104,122,123,124,128,130,131,134,135,138,344,345
70.01 1 3iemB SSU Rep, Mult 61,63,85,90,110,112,135,370,372
80.01 1 2cbn0 III Rep, Mult 71,72,78,97,98,100,101,104,105,121,122,127,128,130,131,134,135,157,158,164,165,166

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
10.3161y44A0.6261.720.2960.6593.1.26.1165,69
20.2832fk6A0.6371.680.2830.6693.1.26.1169
30.0603hnnA0.4074.930.0740.5441.-.-.-NA
40.0601a0cA0.4116.810.0440.6855.3.1.5341
50.0602cbnA0.6351.810.2540.6723.1.26.1169,122,124
60.0601e3xA0.4046.680.0730.6513.2.1.194
70.0601ofdA0.3517.090.0690.6031.4.7.1NA
80.0601qbaA0.4267.160.0390.7413.2.1.5276
90.0601a0dD0.4116.740.0320.6835.3.1.5NA
100.0601llwA0.4166.850.0750.7011.4.7.1NA
110.0603m07A0.4086.280.0530.6453.2.1.141286,292,320
120.0601bplB0.2486.900.0720.4243.2.1.1271
130.0601fa2A0.4126.780.0600.6833.2.1.2128
140.0601w9xA0.4076.410.0600.6403.2.1.1NA
150.0603elqB0.4066.720.0450.6882.8.2.22NA
160.0601bliA0.4046.620.0730.6513.2.1.1276,296
170.0601a0eD0.4116.810.0440.6885.3.1.5NA
180.0601a0eA0.4116.810.0440.6885.3.1.5NA
190.0601ug9A0.4046.460.0500.6563.2.1.70NA
200.0601veoA0.4245.820.0550.6323.2.1.294
210.0603bh4B0.4116.390.0640.6453.2.1.1NA

(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
00.410.5512.540.180.612e7yA GO:0016787 GO:0034414 GO:0042781 GO:0046872
10.220.5562.710.180.621ww1A GO:0016787 GO:0034414 GO:0042781 GO:0046872
20.200.6112.680.220.673zwfA GO:0004518 GO:0004519 GO:0005634 GO:0005737 GO:0005829 GO:0008033 GO:0016787 GO:0016891 GO:0034414 GO:0042779 GO:0042781 GO:0046872 GO:0090502
30.200.6351.810.250.672cbnA 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
40.160.5902.570.170.651zkpA GO:0046872
50.100.5123.860.140.623a4yA GO:0003723 GO:0004518 GO:0004519 GO:0005737 GO:0006364 GO:0016787 GO:0046872 GO:0090305
60.070.6371.680.280.672fk6A GO:0004518 GO:0004519 GO:0008033 GO:0008270 GO:0016787 GO:0016891 GO:0034414 GO:0042779 GO:0042781 GO:0046872 GO:0090502
70.070.6361.710.290.671y44A GO:0004518 GO:0004519 GO:0008033 GO:0008270 GO:0016787 GO:0016891 GO:0034414 GO:0042779 GO:0042781 GO:0046872 GO:0090502
80.070.5373.830.160.652i7vA 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
90.070.5353.820.160.652i7tA 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
100.070.5263.170.160.613g1pB GO:0008081 GO:0016787 GO:0019700 GO:0030145 GO:0046872
110.070.5023.930.110.612p4zB GO:0016787 GO:0046872
120.060.4365.280.140.594xukA GO:0016787
130.060.4345.240.140.591p9eA GO:0016787 GO:0046872
140.060.4004.950.170.534le6A GO:0004063 GO:0016311 GO:0016787 GO:0046872
150.060.4055.010.090.551e5dA GO:0009055 GO:0010181 GO:0016491 GO:0022904 GO:0046872 GO:0055114
160.060.3864.020.110.472qedA GO:0004416 GO:0016787 GO:0019243 GO:0046872
170.060.3734.340.130.473adrA GO:0008270 GO:0046872
180.060.2707.610.040.513c6gB GO:0004497 GO:0005506 GO:0005783 GO:0005789 GO:0006766 GO:0008395 GO:0010038 GO:0010164 GO:0010212 GO:0016020 GO:0016491 GO:0016705 GO:0020037 GO:0030343 GO:0031090 GO:0036378 GO:0042359 GO:0043231 GO:0046872 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0042781 GO:0004527 GO:0046914
GO-Score 0.70 0.40 0.40
Biological Processes GO:0034414
GO-Score 0.70
Cellular Component GO:0043231 GO:0044444
GO-Score 0.41 0.41

(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.