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I-TASSER results for job id Rv3434c

[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
10.10 5 5f5bA III Rep, Mult 53,79,82,86,121,142,143,144,145,146,147,190,191,192
20.06 3 4h1dA DFP Rep, Mult 82,86,144,145,146,147,148,151,178,196
30.06 3 2nrf0 III Rep, Mult 58,71,72,105,107,111,112,115,116,119,123,124,206,215
40.04 2 2agvA PTY Rep, Mult 155,203,207,211,212
50.04 2 3zmhA L62 Rep, Mult 81,82,85,86,89,147,150,151,154,178,189,196
60.04 2 2xtvA MC3 Rep, Mult 116,120,198,202,205
70.02 1 2xtvA MC3 Rep, Mult 39,42
80.02 1 2xtvA MC3 Rep, Mult 36,39
90.02 1 2xtvA MC3 Rep, Mult 65,71
100.02 1 2xtvA MC3 Rep, Mult 86,89,90,93,174
110.02 1 2xtvA MC3 Rep, Mult 58,68,71,115,122
120.02 1 2voyK III Rep, Mult 197,201,204,205,212
130.02 1 2nr9A PA6 Rep, Mult 53,73
140.02 1 2xtvA MC3 Rep, Mult 28,31,84,85,87,88,91
150.02 1 2xtvA MC3 Rep, Mult 72,103,107,111
160.02 1 2xtvA MC3 Rep, Mult 28,32

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
10.2633b45A0.6811.820.1370.7383.4.21.10535,89
20.0602ouyA0.4245.580.0700.7053.1.4.17NA
30.0601occA0.4375.020.0240.6461.9.3.1149
40.0601syyA0.4265.510.0610.7091.17.4.1NA
50.0601lgfA0.4354.700.0520.6161.14.-.-NA
60.0601hm7B0.4235.180.0450.6544.2.3.7,4.6.1.5NA
70.0602uw1B0.4155.860.0780.7221.14.99.6NA
80.0603b8cB0.4825.550.0680.7723.6.3.626
90.0603b8eA0.5415.090.0860.8143.6.3.9NA
100.0602j2fA0.4205.820.0670.7341.14.19.2,1.14.99.6NA
110.0601hm7A0.3944.920.0820.5874.2.3.7,4.6.1.5NA
120.0602r8qA0.4295.630.1060.7133.1.4.17204
130.0601vncA0.4915.070.0660.7641.11.1.1087
140.0601q5eA0.4204.780.0470.6081.14.-.-NA
150.0603ixzA0.5435.080.0590.8193.6.3.10NA
160.0602vuxB0.3805.110.0860.5911.17.4.186
170.0602nr9A0.6952.290.1180.7893.4.21.10535,76
180.0602vdcF0.4735.690.0380.7851.4.1.13NA
190.0601mhyD0.4275.230.0300.6711.14.13.25NA
200.0601mhsA0.4955.340.0750.7683.6.3.6NA

(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
00.270.6801.960.140.755f5bA GO:0004175 GO:0004252 GO:0005886 GO:0005887 GO:0006508 GO:0008233 GO:0008236 GO:0016020 GO:0016021 GO:0016485 GO:0016787
10.220.5971.940.140.663odjA GO:0004252 GO:0005886 GO:0006508 GO:0008233 GO:0008236 GO:0016020 GO:0016021 GO:0016485 GO:0016787 GO:0042802
20.210.6952.290.120.792nr9A GO:0004252 GO:0005886 GO:0006508 GO:0008233 GO:0008236 GO:0016020 GO:0016021 GO:0016485 GO:0016787 GO:0042802
30.170.5415.090.090.813b8eA GO:0000166 GO:0002028 GO:0005391 GO:0005524 GO:0005886 GO:0005890 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0006883 GO:0010107 GO:0010248 GO:0015991 GO:0016020 GO:0016021 GO:0016787 GO:0030007 GO:0030955 GO:0031402 GO:0036376 GO:0042383 GO:0043231 GO:0046872 GO:0051117 GO:0086009 GO:0090662 GO:1990573
40.070.5245.040.030.783a3yA GO:0000166 GO:0005391 GO:0005524 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0010248 GO:0016020 GO:0016021 GO:0016787 GO:0046872 GO:0090662
50.070.5435.080.060.823ixzA GO:0000166 GO:0000287 GO:0005391 GO:0005524 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0006883 GO:0008900 GO:0010107 GO:0010248 GO:0015991 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030007 GO:0036376 GO:0043231 GO:0046872
60.070.4955.340.070.771mhsA GO:0000166 GO:0005524 GO:0005886 GO:0005887 GO:0006754 GO:0006810 GO:0006811 GO:0008553 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0043231 GO:0046872 GO:0051453 GO:1902600
70.070.3896.170.090.693j09A GO:0000166 GO:0005507 GO:0005524 GO:0005886 GO:0006810 GO:0006811 GO:0006812 GO:0006825 GO:0016020 GO:0016021 GO:0016787 GO:0019829 GO:0030001 GO:0046872 GO:0098655
80.070.4085.290.070.624bbjA GO:0000166 GO:0005886 GO:0006812 GO:0016020 GO:0016021 GO:0016787 GO:0019829 GO:0046872 GO:0098655
90.060.3665.360.060.574umvA GO:0000166 GO:0005886 GO:0006812 GO:0016020 GO:0016021 GO:0016787 GO:0019829 GO:0030001 GO:0046872 GO:0098655
100.060.5155.300.060.813w5bA GO:0000166 GO:0005388 GO:0005509 GO:0005524 GO:0005783 GO:0005789 GO:0005793 GO:0006810 GO:0006811 GO:0006816 GO:0006942 GO:0016020 GO:0016021 GO:0016529 GO:0016787 GO:0031448 GO:0031673 GO:0031674 GO:0033017 GO:0045988 GO:0046872 GO:0048471 GO:0070588
110.060.4825.550.070.773b8cA GO:0000166 GO:0000287 GO:0005524 GO:0005886 GO:0005887 GO:0006754 GO:0006810 GO:0006811 GO:0008553 GO:0015991 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0046872 GO:0051453
120.060.2995.570.070.492ayxA GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0004871 GO:0005524 GO:0005622 GO:0005886 GO:0005887 GO:0006355 GO:0007165 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0018106 GO:0023014 GO:0044010 GO:0046777 GO:0071470
130.060.3134.250.090.432euiA GO:0004596 GO:0006474 GO:0008080 GO:0016740 GO:0031248
140.060.2945.390.060.471bg5A GO:0004364 GO:0016740
150.060.2936.300.040.541g6hA GO:0000166 GO:0005524 GO:0006810 GO:0006865 GO:0016887
160.060.2815.630.010.464dwoA GO:0005737 GO:0016311 GO:0016787 GO:0016791 GO:0044283 GO:0046872
170.060.2705.640.020.462qyhB GO:0016787
180.060.2815.730.010.462rarA GO:0005737 GO:0016311 GO:0016787 GO:0016791 GO:0044283 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0004252 GO:0032550 GO:0008556 GO:0015081 GO:0035639 GO:0032559 GO:0042802 GO:0019899 GO:0031420
GO-Score 0.55 0.45 0.45 0.45 0.45 0.45 0.38 0.34 0.34
Biological Processes GO:0016485 GO:0010959 GO:0098739 GO:0030004 GO:0055078 GO:0055075 GO:0006875 GO:0071436 GO:0015988 GO:0010107 GO:0042391
GO-Score 0.55 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34
Cellular Component GO:0031226 GO:0090533 GO:0043229 GO:0098797 GO:0043227
GO-Score 0.54 0.34 0.34 0.34 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.