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I-TASSER results for job id Rv3065

[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
10.06 2 3vr8G EPH Rep, Mult 4,54,58,59,95,99
20.06 2 1xvgA BRJ Rep, Mult 13,14,17,66,69,70
30.03 1 2w0fC HX0 Rep, Mult 69,70,97,101
40.03 1 5c65A 37X Rep, Mult 7,41
50.03 1 3ifxA MTN Rep, Mult 45,46
60.03 1 2q68A CA Rep, Mult 80,81
70.03 1 3v5uA CA Rep, Mult 15,24,25,26,30
80.03 1 1xvfA 3CL Rep, Mult 3,7,66
90.03 1 3m6zA MG Rep, Mult 13,20
100.03 1 2c6nB NDG Rep, Mult 17,20,21,24
110.03 1 3fk7A 4DM Rep, Mult 69,73
120.03 1 1ta9A GOL Rep, Mult 6,9,61,66
130.03 1 1xveA 3BB Rep, Mult 4,9,10,47,50
140.03 1 2ih1C 1EM Rep, Mult 83,87,91
150.03 1 3klzD FMT Rep, Mult 81,87

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
10.0601h0nA0.5604.000.0400.8601.17.4.1NA
20.0601kq3A0.5463.780.0480.8781.1.1.6NA
30.0603bkkA0.5713.750.0200.8693.4.15.1NA
40.0601jq5A0.5573.730.0580.8691.1.1.6NA
50.0601schA0.5373.340.0490.8041.11.1.7NA
60.0603g61A0.5733.920.0380.9633.6.3.4441,66
70.0601biqB0.5384.220.0810.8601.17.4.1NA
80.0602hi4A0.5364.170.0690.8781.14.14.1NA
90.0602j2fA0.5563.810.0570.8221.14.19.2,1.14.99.6NA
100.0601smsA0.5404.150.0910.8511.17.4.1NA
110.0602vuxB0.5544.120.0400.8601.17.4.1NA
120.0603ee4A0.5342.980.0290.7381.17.4.1NA
130.0603hq2B0.5324.050.0400.8693.4.24.-13
140.0601csmA0.5502.900.0820.7665.4.99.521
150.0601ta9B0.5753.620.0470.8881.1.1.6NA
160.0602c6fA0.5763.770.0200.8783.4.15.1NA
170.0601fziA0.5794.080.0380.9631.14.13.25NA
180.0601j38A0.5713.560.0310.8413.4.15.1NA
190.0603hf1B0.5583.940.0400.8511.17.4.1NA

(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
00.300.5562.340.230.722i68A GO:0005886 GO:0005887 GO:0006805 GO:0006810 GO:0006970 GO:0006974 GO:0015199 GO:0015220 GO:0015297 GO:0015307 GO:0015871 GO:0016020 GO:0016021 GO:0022857 GO:0031460 GO:0042493 GO:0046618 GO:0055085
10.100.5393.500.080.844mrrA GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0006811 GO:0016020 GO:0016021 GO:0016887 GO:0042626 GO:0046689 GO:0055085
20.100.6203.320.140.935c73A GO:0000166 GO:0005524 GO:0006810 GO:0016021 GO:0016887 GO:0042626 GO:0055085
30.090.5644.050.090.933b5wA GO:0000166 GO:0005319 GO:0005524 GO:0005886 GO:0006810 GO:0006869 GO:0008144 GO:0008289 GO:0015437 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0034040 GO:0042626 GO:0043190 GO:0055085 GO:1901264
40.090.6573.240.100.983wmgA GO:0000166 GO:0005524 GO:0006810 GO:0016020 GO:0016021 GO:0016887 GO:0042626 GO:0055085
50.080.5753.950.040.974m1mA GO:0000086 GO:0000166 GO:0002481 GO:0002485 GO:0002489 GO:0002591 GO:0005524 GO:0005886 GO:0006810 GO:0006855 GO:0008559 GO:0009986 GO:0015893 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0042623 GO:0042626 GO:0042908 GO:0046581 GO:0055085 GO:0070062 GO:0072089
60.070.4824.560.080.884mycA GO:0000166 GO:0005524 GO:0005739 GO:0005743 GO:0006810 GO:0006811 GO:0006879 GO:0016020 GO:0016021 GO:0016887 GO:0022857 GO:0042626 GO:0044281 GO:0055072 GO:0055085
70.070.4984.640.110.943qf4B GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0016020 GO:0016021 GO:0016887 GO:0042626 GO:0055085
80.070.5273.740.120.804ry2A GO:0005524 GO:0006508 GO:0006810 GO:0008233 GO:0008234 GO:0016020 GO:0016021 GO:0016887 GO:0022885 GO:0042626 GO:0043213 GO:0055085
90.070.5514.140.100.953b5xA GO:0000166 GO:0005319 GO:0005524 GO:0005886 GO:0006810 GO:0006869 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0034040 GO:0042626 GO:0043190 GO:0055085
100.070.5504.210.090.934ayxA GO:0000166 GO:0005215 GO:0005524 GO:0005739 GO:0005743 GO:0006810 GO:0016020 GO:0016021 GO:0016887 GO:0032592 GO:0042626 GO:0042803 GO:0055085
110.070.4563.830.090.795do7D GO:0005524 GO:0005886 GO:0006810 GO:0007584 GO:0007588 GO:0010949 GO:0015248 GO:0015914 GO:0015918 GO:0016020 GO:0016021 GO:0016324 GO:0016887 GO:0017127 GO:0030299 GO:0033344 GO:0042493 GO:0042626 GO:0042632 GO:0043190 GO:0043235 GO:0045796 GO:0046982 GO:0055085 GO:0055092
120.070.6173.560.100.964pl0B GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0016887 GO:0030153 GO:0042626 GO:0043213 GO:0055085
130.070.6223.470.070.954f4cA GO:0000166 GO:0005524 GO:0006810 GO:0006855 GO:0008559 GO:0010038 GO:0015562 GO:0016020 GO:0016021 GO:0016324 GO:0016787 GO:0016887 GO:0042626 GO:0042908 GO:0045087 GO:0050829 GO:0055085 GO:0093002
140.070.6083.510.090.934a82A GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0042626 GO:0055085
150.060.4123.670.050.584rfvA GO:0000103 GO:0000166 GO:0003824 GO:0003924 GO:0004020 GO:0004781 GO:0005524 GO:0005525 GO:0005829 GO:0005886 GO:0006790 GO:0008152 GO:0009336 GO:0010134 GO:0010438 GO:0016301 GO:0016310 GO:0016740 GO:0016779 GO:0034599 GO:0040007 GO:0070814
160.060.3634.260.060.643zqjD GO:0000166 GO:0003677 GO:0003824 GO:0004518 GO:0005524 GO:0005618 GO:0005737 GO:0005829 GO:0005886 GO:0006281 GO:0006289 GO:0006974 GO:0008270 GO:0009380 GO:0009381 GO:0009432 GO:0016887 GO:0046872 GO:0060543 GO:0090305
170.060.3873.740.020.583zqjF GO:0000166 GO:0003677 GO:0003824 GO:0004518 GO:0005524 GO:0005618 GO:0005737 GO:0005829 GO:0005886 GO:0006281 GO:0006289 GO:0006974 GO:0008270 GO:0009380 GO:0009381 GO:0009432 GO:0016887 GO:0046872 GO:0060543 GO:0090305
180.060.4252.770.030.575da9A GO:0000723 GO:0005089 GO:0005524 GO:0005634 GO:0006281 GO:0016887 GO:0030870 GO:0035023 GO:0043547


Consensus prediction of GO terms
 
Molecular Function GO:0015238 GO:0015299 GO:0072349 GO:0008519 GO:0015651 GO:0042626 GO:0005524
GO-Score 0.59 0.59 0.59 0.59 0.59 0.32 0.32
Biological Processes GO:0033554 GO:0015838 GO:0015696 GO:0009628 GO:0071466 GO:0015893 GO:0072337 GO:0055085 GO:0044237
GO-Score 0.59 0.59 0.59 0.59 0.59 0.59 0.59 0.52 0.50
Cellular Component GO:0031226 GO:0016021
GO-Score 0.59 0.52

(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.