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I-TASSER results for job id Rv0168

[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 2h6bA 3C4 Rep, Mult 230,233
20.06 3 4v1fA BQ1 Rep, Mult 223,226,227,230
30.04 2 3h3fD ACT Rep, Mult 223,226,227
40.04 2 3etgC GWD Rep, Mult 172,176,177,180,234
50.02 1 4z90A 4LE Rep, Mult 228,232
60.02 1 1k9zA ZN Rep, Mult 141,226
70.02 1 3v2d2 MG Rep, Mult 165,169
80.02 1 1r3nF BIB Rep, Mult 169,248
90.02 1 3bz1F PL9 Rep, Mult 136,139
100.02 1 2wieA CVM Rep, Mult 275,279
110.02 1 3qmuA XEG Rep, Mult 96,253,258
120.02 1 3eteD H3P Rep, Mult 43,100,101,103
130.02 1 1zoyC EPH Rep, Mult 186,189
140.02 1 2aj4A MG Rep, Mult 69,161
150.02 1 3attA MG Rep, Mult 152,155
160.02 1 2npjA IMD Rep, Mult 125,126,203,205
170.02 1 1vs0A MG Rep, Mult 150,152
180.02 1 1hwyE NAD Rep, Mult 189,234,235,237,238,245,246

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
10.0601hxgA0.4095.800.0700.6504.2.3.9,4.1.99.7133
20.0603b8cB0.3996.080.0490.6443.6.3.6NA
30.0601eulA0.3875.750.0740.6093.6.3.8NA
40.0601s1mB0.4166.190.0540.6756.3.4.2NA
50.0601gpeA0.4205.830.0500.6851.1.3.4NA
60.0601vncA0.4206.530.0780.7301.11.1.10169,172,192,197
70.0601bgvA0.4794.960.0380.6891.4.1.2NA
80.0602dkiA0.3976.500.0600.6991.14.13.23279
90.0601gtmA0.4075.610.0470.6161.4.1.3218
100.0601euzF0.4135.800.0610.6401.4.1.3218
110.0601iduA0.4216.430.0860.7271.11.1.10NA
120.0602bmaA0.4935.030.0300.7161.4.1.4NA
130.0601k8qA0.4016.000.0740.6613.1.1.3NA
140.0601aupA0.4675.170.0430.6891.4.1.2NA
150.0601hwxA0.4604.850.0790.6541.4.1.3204
160.0603b8cA0.3996.080.0490.6443.6.3.6NA
170.0601bvuA0.4065.560.0510.6131.4.1.3NA
180.0601hlgB0.4085.650.0380.6473.1.1.3183
190.0601u8vA0.4106.150.0310.6825.3.3.3NA

(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
00.130.4415.320.090.673aoeB GO:0006520 GO:0016491 GO:0016639 GO:0055114
10.120.7184.210.100.944rp9A GO:0005886 GO:0006810 GO:0008643 GO:0009401 GO:0015882 GO:0016020 GO:0016021 GO:0034219 GO:0090585
20.070.4935.030.030.722bmaA GO:0006520 GO:0016491 GO:0016639 GO:0055114
30.070.4895.070.030.712yfhE GO:0004352 GO:0004354 GO:0005737 GO:0005829 GO:0006520 GO:0006537 GO:0016491 GO:0016639 GO:0019552 GO:0042802 GO:0055114
40.070.4794.960.040.691bgvA GO:0004352 GO:0006520 GO:0016491 GO:0016639 GO:0019552 GO:0055114
50.070.4245.740.040.653r3jA GO:0004354 GO:0006520 GO:0006537 GO:0016491 GO:0016639 GO:0020011 GO:0055114
60.070.4614.740.070.655ijzK GO:0004354 GO:0005737 GO:0006520 GO:0006537 GO:0016491 GO:0016639 GO:0055114
70.070.4675.170.040.691aupA GO:0004352 GO:0006520 GO:0016491 GO:0016639 GO:0019552 GO:0055114
80.070.4705.460.070.714bhtA GO:0004354 GO:0005737 GO:0005829 GO:0006520 GO:0006537 GO:0016491 GO:0016639 GO:0042802 GO:0055114
90.060.4584.920.070.653etdA GO:0000166 GO:0004352 GO:0004353 GO:0005524 GO:0005525 GO:0005739 GO:0005743 GO:0005759 GO:0006520 GO:0006538 GO:0006541 GO:0016491 GO:0055114 GO:0072350
100.060.4075.610.050.621gtmA GO:0004353 GO:0005737 GO:0006520 GO:0016491 GO:0016639 GO:0055114
110.060.4155.710.040.643k8zA GO:0004352 GO:0006520 GO:0016491 GO:0016639 GO:0055114
120.060.4795.060.060.705ijzA GO:0004354 GO:0005737 GO:0006520 GO:0006537 GO:0016491 GO:0016639 GO:0055114
130.060.3856.210.060.642yfqB GO:0004352 GO:0006520 GO:0016491 GO:0016639 GO:0019552 GO:0055114
140.060.4065.560.050.611bvuA GO:0004353 GO:0005737 GO:0006520 GO:0016491 GO:0016639 GO:0055114
150.060.3175.160.060.473vpxB GO:0006520 GO:0016491 GO:0016639 GO:0055114
160.060.4125.550.050.621v9lA GO:0000166 GO:0006520 GO:0016491 GO:0016639 GO:0055114
170.060.3955.700.060.611lehA GO:0006520 GO:0016491 GO:0016639 GO:0055114
180.060.4115.320.040.603k92A GO:0004352 GO:0006520 GO:0016491 GO:0016639 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0016638
GO-Score 0.58
Biological Processes GO:0019752 GO:1901564 GO:0044238
GO-Score 0.58 0.58 0.50
Cellular Component GO:0005886 GO:0016021 GO:0005829
GO-Score 0.12 0.12 0.07

(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.