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I-TASSER results for job id Rv1087A

[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
10.18 10 4h8eA SO4 Rep, Mult 38,44,46
20.14 9 3th8B TH9 Rep, Mult 2
30.10 6 3djyA UUU Rep, Mult 62,64,66,67
40.07 4 3vuvA ZN Rep, Mult 84,87
50.06 5 3puwA ALF Rep, Mult 83,84,85
60.03 2 2e9cA B75 Rep, Mult 3,4
70.02 2 2vg2C DPO Rep, Mult 8,10,11,12,13,21,25
80.02 1 2vg2C PO4 Rep, Mult 46
90.02 1 1uehB OXN Rep, Mult 2,4,65
100.02 1 2e98A B29 Rep, Mult 4,5,6
110.01 1 2vg2C IPE Rep, Mult 45,50,53
120.01 1 4awuA 4CH Rep, Mult 90,94
130.01 1 1p0qA UUU Rep, Mult 32,34,58,76,81

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
10.0602wgdA0.4834.010.0450.8022.3.1.41NA
20.0601z8lA0.4874.440.0530.8873.4.17.21NA
30.0602fj0A0.4933.790.0750.8493.1.1.1NA
40.0601l7qA0.4934.410.0630.8963.1.1.1NA
50.0601lpsA0.4934.290.0530.8683.1.1.3NA
60.0601qlaD0.4664.630.0880.8961.3.99.193
70.0601tqyA0.4834.100.0450.8212.3.1.41NA
80.0601f6wA0.4923.940.0210.8403.1.1.13,3.1.1.3NA
90.0603eplB0.4954.210.0520.8682.5.1.874
100.0602pm8A0.5103.960.0330.8493.1.1.8NA
110.0603fedA0.3985.170.0770.8593.4.17.21NA
120.0602q28A0.4833.890.0570.7644.1.1.85
130.0603eifA0.4834.340.0520.8873.4.21.110NA
140.0602vg2D0.6262.600.2220.7832.5.1.31NA
150.0603b9xA0.4984.250.0980.8593.2.2.8NA
160.0601gz7A0.5024.550.0630.8873.1.1.3NA
170.0601c7jA0.3824.730.0530.7173.1.1.-NA
180.0603fz0B0.4824.270.0870.8403.2.2.1NA
190.0605acnA0.4934.230.1200.8304.2.1.3NA

(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
00.150.6202.710.200.781x07A GO:0000287 GO:0004659 GO:0005737 GO:0005829 GO:0007049 GO:0008360 GO:0008834 GO:0009252 GO:0016094 GO:0016740 GO:0016765 GO:0043164 GO:0046872 GO:0051301 GO:0071555
10.140.6222.670.260.784u82A GO:0000287 GO:0004659 GO:0016740 GO:0016765 GO:0046872
20.080.6312.490.240.772d2rA GO:0000287 GO:0004659 GO:0016740 GO:0016765 GO:0046872
30.070.6163.030.210.783ugsB GO:0000287 GO:0004659 GO:0016740 GO:0016765 GO:0046872
40.070.6262.600.220.782vg2D GO:0000287 GO:0004659 GO:0005829 GO:0005886 GO:0008834 GO:0016020 GO:0016094 GO:0016740 GO:0016765 GO:0030145 GO:0033850 GO:0040007 GO:0046872 GO:0050347
50.070.6142.730.320.784q9oA GO:0000287 GO:0004659 GO:0016740 GO:0016765 GO:0046872
60.070.6192.790.470.772vg1A GO:0000287 GO:0004659 GO:0005737 GO:0005829 GO:0005886 GO:0016020 GO:0016094 GO:0016740 GO:0016765 GO:0030145 GO:0033850 GO:0046872
70.070.6202.650.290.771f75A GO:0000287 GO:0004659 GO:0008834 GO:0016740 GO:0016765 GO:0046872
80.070.6182.620.200.763sgxB GO:0000287 GO:0004659 GO:0005737 GO:0005829 GO:0007049 GO:0008360 GO:0008834 GO:0009252 GO:0016094 GO:0016740 GO:0016765 GO:0043164 GO:0046872 GO:0051301 GO:0071555
90.070.3674.530.030.711iwpA GO:0003824 GO:0008152 GO:0016829 GO:0016836 GO:0031419 GO:0046405 GO:0050215
100.060.3284.890.060.665dbuJ GO:0003824 GO:0004139 GO:0005737 GO:0009264 GO:0016052 GO:0016829 GO:0046386
110.060.4554.510.030.865eixJ GO:0000166 GO:0000287 GO:0003677 GO:0003916 GO:0003918 GO:0005524 GO:0005694 GO:0005886 GO:0006259 GO:0006265 GO:0007059 GO:0016020 GO:0016853 GO:0019897 GO:0046872
120.060.4474.490.050.845eixA GO:0000166 GO:0000287 GO:0003677 GO:0003916 GO:0003918 GO:0005524 GO:0005694 GO:0005886 GO:0006259 GO:0006265 GO:0007059 GO:0016020 GO:0016853 GO:0019897 GO:0046872
130.060.3625.320.040.752d73A GO:0000272 GO:0004339 GO:0004558 GO:0005509 GO:0005886 GO:0005975 GO:0005983 GO:0008152 GO:0016787 GO:0016798 GO:0042597 GO:0046872
140.060.3645.160.090.773mvgA GO:0006952 GO:0016787 GO:0017148 GO:0030598
150.060.3525.160.040.744ohjB GO:0005576 GO:0009405
160.060.3625.220.060.743hdiA GO:0003824 GO:0004222 GO:0006508 GO:0008233 GO:0046872
170.060.3345.150.020.721z0xA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677
180.060.3724.150.050.663u7iB GO:0008752 GO:0009055 GO:0010181 GO:0016491 GO:0016652 GO:0016661 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0004659 GO:0000287
GO-Score 0.41 0.41
Biological Processes GO:0008299 GO:0016093 GO:0046165
GO-Score 0.41 0.41 0.41
Cellular Component GO:0044444
GO-Score 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.