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I-TASSER results for job id Rv2884

[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
10.42 61 1peyA MN Rep, Mult 27,67,69,115
20.19 31 1wb3C DXC Rep, Mult 68,69,75,91,93
30.10 16 1f4vA III Rep, Mult 95,97,98,101,105,109,110,111,112,113,114,125,128
40.02 4 1gxpA NUC Rep, Mult 166,167,168,193,198,199,200,203,206,207,210,227
50.01 2 3myyA BEF Rep, Mult 45,46,51,55
60.01 2 1ffwA PON Rep, Mult 27,28,29
70.01 2 1zdmA XE Rep, Mult 25,26,35,65,66,67,91
80.01 2 3p27A GDP Rep, Mult 26,27,28,31,32,33,34
90.01 3 3gwgA MG Rep, Mult 31,115
100.01 2 2z33A NUC Rep, Mult 185,202,205,209,212,225,227,228,231
110.01 2 3cw2B III Rep, Mult 94,96,100,102,105,112,113,114,117,118,120,121,129
120.00 1 1wb1A UUU Rep, Mult 93,115,116
130.00 1 2a9rA MG Rep, Mult 24,26,32,45,46,47
140.00 1 3olvA BEF Rep, Mult 47,51
150.00 1 2pmuB GLY Rep, Mult 190,191,193,194
160.00 1 2flkA CXS Rep, Mult 119,120,123
170.00 1 1xhfB BF2 Rep, Mult 83,85
180.00 1 3chyA SO4 Rep, Mult 111,112,125,128
190.00 1 1nxtA XE Rep, Mult 76,77,80,107

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
10.0602vk1A0.4825.310.0770.7344.1.1.1NA
20.0601etuA0.2275.780.0520.3693.6.5.3NA
30.0601f60A0.4874.870.0460.7143.6.5.3NA
40.0603ey9A0.4615.100.0570.6861.2.2.2194
50.0602ji8A0.4485.490.0410.7304.1.1.831
60.0601zpdA0.4845.060.0720.7304.1.1.1NA
70.0602wvhA0.4815.170.0710.7304.1.1.126
80.0601d2eA0.4705.080.0950.7223.6.5.3NA
90.0601ovmA0.4765.080.0680.7264.1.1.74168
100.0603dnyT0.4685.070.0740.6713.6.5.367
110.0601ob2A0.4974.600.0780.6943.6.1.48NA
120.0602djiA0.4665.470.0380.7221.2.3.3104,130
130.0602vycA0.5054.330.0830.6594.1.1.19NA
140.0601wdlA0.4525.400.0470.7025.3.3.8,5.1.2.3,4.2.1.17,1.1.1.3575,105
150.0601ybhA0.4585.430.0770.7142.2.1.6219
160.0602x58A0.4415.810.0550.7185.3.3.8,4.2.1.17,1.1.1.3589,130
170.0602ji6A0.4535.180.0550.6984.1.1.8NA
180.0602vbiA0.4745.190.0660.7224.1.1.1NA
190.0601ovmC0.4745.230.0800.7224.1.1.74NA

(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
00.360.4421.780.130.472jk1A GO:0000160 GO:0000166 GO:0003677 GO:0005524 GO:0005737 GO:0006351 GO:0006355 GO:0008134 GO:0043565
10.360.4292.060.140.471dbwB GO:0000160 GO:0003677 GO:0005737 GO:0006351 GO:0006355 GO:0009399 GO:0046872
20.270.4452.510.150.501l5yB GO:0000160 GO:0000166 GO:0003677 GO:0005524 GO:0005737 GO:0006351 GO:0006355 GO:0008134 GO:0043565
30.250.4442.920.070.511yioA GO:0000160 GO:0003677 GO:0005622 GO:0006351 GO:0006355 GO:0046872
40.230.4592.700.190.521ys6B GO:0000160 GO:0000287 GO:0003677 GO:0005509 GO:0005737 GO:0005829 GO:0005886 GO:0006351 GO:0006355 GO:0044110
50.230.4471.710.130.474knyB GO:0000160 GO:0000986 GO:0001131 GO:0003677 GO:0005737 GO:0006351 GO:0006355
60.220.4422.150.110.482v0nA GO:0000160 GO:0000166 GO:0004871 GO:0005525 GO:0005737 GO:0007049 GO:0007165 GO:0016740 GO:0030154 GO:0046872 GO:0052621
70.220.4501.440.130.473cfyA GO:0000160 GO:0000166 GO:0003677 GO:0005524 GO:0005622 GO:0006351 GO:0006355 GO:0008134 GO:0043565
80.210.4422.360.100.483lufB GO:0000160 GO:0005622 GO:0046872
90.200.4663.300.220.542gwrA GO:0000160 GO:0003677 GO:0005737 GO:0005886 GO:0006351 GO:0006355 GO:0006468 GO:0044117 GO:0045893 GO:0046872
100.180.4402.040.110.481i3cA GO:0000160 GO:0005622
110.170.4762.640.130.541a04A GO:0000160 GO:0000166 GO:0003677 GO:0005524 GO:0005829 GO:0006351 GO:0006355 GO:0010468 GO:0042128 GO:0090352
120.160.4522.180.080.503breB GO:0000160 GO:0005622
130.150.4443.200.090.522hqrA GO:0000160 GO:0003677 GO:0005622 GO:0006351 GO:0006355
140.150.4664.790.170.645ed4E GO:0000160 GO:0003677 GO:0005622 GO:0005886 GO:0006351 GO:0006355 GO:0006979 GO:0009247 GO:0009405 GO:0010628 GO:0044315 GO:0045892 GO:0045893 GO:0046889
150.140.4723.180.130.563q9sA GO:0000160 GO:0003677 GO:0005622 GO:0006351 GO:0006355
160.140.4431.990.140.483t8yB GO:0000156 GO:0000160 GO:0004871 GO:0005737 GO:0006935 GO:0007165 GO:0008984 GO:0016787
170.070.5024.660.080.693sy8B GO:0000160 GO:0005622 GO:0045892 GO:0046872
180.070.4773.720.090.584gvpA GO:0000160 GO:0003677 GO:0005737 GO:0006351 GO:0006355 GO:0046677
190.070.4403.210.180.531s8nA GO:0000160 GO:0003723 GO:0005618 GO:0005622 GO:0005886 GO:0006351 GO:0006355 GO:0031564 GO:0040007


Consensus prediction of GO terms
 
Molecular Function GO:0005524 GO:0043565 GO:0008134 GO:0046872
GO-Score 0.53 0.53 0.53 0.52
Biological Processes GO:0000160 GO:0006355 GO:0044403 GO:0040007 GO:0009399
GO-Score 0.83 0.83 0.45 0.45 0.36
Cellular Component GO:0044444 GO:0071944 GO:0016020
GO-Score 0.45 0.45 0.34

(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.