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I-TASSER results for job id Rv1192

[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
10.30 7 1r50A SIL Rep, Mult 58,59,61,65,119,120,121,197,202,220,221
20.20 5 1lbtA T80 Rep, Mult 58,120,121,146,150,152,165,196,197,220,274,275
30.07 2 2xmgA UUU Rep, Mult 126,130,133,134,186

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
10.3333cn7A0.5602.470.1260.6293.1.1.159,120,195,220
20.3311i6wB0.5412.200.1990.5933.1.1.3120,220
30.3201auoA0.5652.680.1560.6403.1.1.159,120,195,220
40.2752ocgA0.6083.410.1670.7423.1.-.-56,116,120,122,126,195,198,220
50.1933e3aB0.6382.690.1490.7351.11.1.-58
60.1622h1iA0.5283.200.1060.6333.1.1.164,120,146
70.1613esbA0.4843.190.1260.5753.1.1.74120,220
80.1361vkhA0.6133.440.1030.7533.5.1.958
90.1211va4A0.6272.650.1670.7133.1.1.2120
100.0671fj2A0.5683.180.1100.6733.1.4.3959
110.0671dinA0.5572.900.1240.6543.1.1.45195,220
120.0663dcnA0.4853.150.1360.5713.1.1.74120
130.0663gbsA0.4873.270.1280.5753.1.1.74120,220
140.0601c7jA0.6364.400.0820.8363.1.1.-80
150.0602ecfA0.6194.040.1000.7823.4.14.5195,220
160.0601hlgB0.6443.000.1120.7533.1.1.3NA
170.0601a88A0.6332.730.1140.7241.11.1.10NA
180.0601cleA0.6484.360.0710.8473.1.1.3NA
190.0601a88B0.6342.720.1140.7241.11.1.10NA
200.0601maaD0.6444.210.0860.8363.1.1.7NA
210.0601zoiA0.6332.540.0950.7163.1.1.-120,220
220.0601a7uA0.6412.660.1490.7271.11.1.10120
230.0601eveA0.6464.280.0930.8443.1.1.7NA
240.0601qo9A0.6514.190.0670.8403.1.1.7NA
250.0601b41A0.6404.330.0860.8403.1.1.7NA
260.0601a8sA0.6282.680.1260.7131.11.1.10120,220
270.0601e5tA0.6233.950.1060.7823.4.21.26120
280.0602fj0A0.6544.280.0850.8553.1.1.1NA
290.0601lnsA0.6554.440.1100.8803.4.14.11120,195,220
300.0601k8qA0.6472.830.1130.7493.1.1.356
310.0601k4yA0.6374.320.0870.8363.1.1.1NA
320.0601tccA0.8651.860.1640.9313.1.1.3120

(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
00.360.5563.000.140.653trdA GO:0016787
10.300.8102.050.160.883icwA GO:0004806 GO:0006629 GO:0016042 GO:0016787
20.270.5442.850.130.631uxoA GO:0016787
30.250.5373.230.120.642qs9A GO:0005634 GO:0005730 GO:0005737 GO:0016787 GO:0042127 GO:0070062
40.240.8631.970.160.934k6gB GO:0004806 GO:0006629 GO:0016042 GO:0016787
50.230.5212.690.150.603bdvA GO:0016787 GO:0046872
60.190.5992.610.150.681hqdA GO:0004806 GO:0006629 GO:0016042 GO:0016787 GO:0046872
70.180.6163.130.120.734x00A GO:0016787
80.180.6214.420.100.823i2gA GO:0005737 GO:0006508 GO:0008239 GO:0016787 GO:0050784 GO:0052689
90.180.6224.420.070.833iiiA GO:0006508 GO:0008239 GO:0016787
100.150.5953.180.150.701j1iA GO:0016787
110.140.5852.940.120.693p2mA GO:0052689
120.130.5402.200.200.595ct4B GO:0004806 GO:0005576 GO:0006629 GO:0016042 GO:0016787
130.130.5942.700.160.681tahA GO:0004806 GO:0005576 GO:0006629 GO:0016042 GO:0016787 GO:0046872
140.110.6263.400.110.764opmA GO:0004806 GO:0016787
150.090.6554.440.110.881lnsA GO:0004177 GO:0005737 GO:0006508 GO:0008233 GO:0008236 GO:0008239 GO:0016787
160.090.6734.350.100.913guuA GO:0004806 GO:0005576 GO:0006629 GO:0016042 GO:0016787
170.080.6623.290.110.804bvkB GO:0016787
180.080.6323.410.110.762wtmA
190.070.6153.660.120.764eziA GO:0004806 GO:0016042
200.070.6023.810.150.763h2kA GO:0004177 GO:0004806 GO:0006508 GO:0016042
210.070.6053.500.130.741u2eA GO:0003824 GO:0005737 GO:0016787 GO:0018771 GO:0019380 GO:0019439 GO:0019622 GO:0042803 GO:0052823
220.070.6022.530.160.681ex9A GO:0004806 GO:0005576 GO:0005615 GO:0006629 GO:0009986 GO:0016042 GO:0016298 GO:0016787 GO:0046872
230.070.5992.610.130.684hs9A GO:0004806 GO:0016787 GO:0046872
240.070.4495.580.060.693egdB GO:0000139 GO:0002474 GO:0005737 GO:0005783 GO:0005789 GO:0005794 GO:0005829 GO:0006810 GO:0006886 GO:0006888 GO:0008270 GO:0012507 GO:0015031 GO:0016020 GO:0016192 GO:0019886 GO:0030127 GO:0045714 GO:0048208 GO:0048471 GO:0050714 GO:2000189
250.060.3885.920.070.633raoB GO:0016705 GO:0055114
260.060.3684.700.140.514ptyD GO:0006974 GO:0008752 GO:0009970 GO:0016491 GO:0046306 GO:0051289 GO:0052873 GO:0055114
270.060.3995.610.060.633flmA GO:0000287 GO:0003824 GO:0009234 GO:0016740 GO:0030145 GO:0030976 GO:0046872 GO:0070204
280.060.3636.360.060.643sqzA GO:0003824 GO:0004421 GO:0008152 GO:0008299 GO:0016740 GO:0016746
290.060.3856.220.030.673eb7A GO:0005102 GO:0006952 GO:0009405 GO:0030435
300.060.6204.140.100.793azoA GO:0004177 GO:0006508 GO:0008236


Consensus prediction of GO terms
 
Molecular Function GO:0004806
GO-Score 0.47
Biological Processes GO:0050794 GO:0008283 GO:0016042
GO-Score 0.50 0.50 0.47
Cellular Component GO:0031981 GO:0031988 GO:0043232 GO:1903561
GO-Score 0.50 0.50 0.50 0.50

(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.