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I-TASSER results for job id Rv2843

[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
10.08 4 1j30A OXY Rep, Mult 57,60,91
20.06 3 2xquC CVM Rep, Mult 92,95
30.04 2 3pyrY MG Rep, Mult 50,99,100
40.04 2 1xvgC BRJ Rep, Mult 159,162,166
50.04 2 1cl6A NO Rep, Mult 156,157
60.04 2 5bq6L EFB Rep, Mult 84,88,91,92,95
70.04 2 1xvgA BRJ Rep, Mult 93,96,140,143,144
80.02 1 5buoA ZN Rep, Mult 60,87
90.02 1 3zvwC MG Rep, Mult 53,54
100.02 1 2wsc2 CLA Rep, Mult 18,155
110.02 1 1brrC ARC Rep, Mult 140,162,166
120.02 1 2h8pC GOA Rep, Mult 153,154
130.02 1 3d8aG III Rep, Mult 89,92,93,95,158,166,167
140.02 1 1xvfA 3CL Rep, Mult 134,163,166,167
150.02 1 3etdB B1T Rep, Mult 93,151
160.02 1 1r3nG BIB Rep, Mult 85,156,157

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
10.0601mhyB0.5514.300.0850.8181.14.13.2554
20.0602eabA0.5125.520.0850.8623.2.1.63NA
30.0602vn7A0.4985.040.0590.8013.2.1.354
40.0601xjjA0.5035.000.0720.7961.17.4.172
50.0603hf1B0.5034.820.0550.7961.17.4.1NA
60.0602cvtA0.4965.250.0900.8121.17.4.1NA
70.0601uzrB0.5224.570.0490.8011.17.4.1NA
80.0601jk0A0.4984.700.0680.7791.17.4.1NA
90.0602bq1I0.5264.380.0680.7901.17.4.1NA
100.0603b8eA0.3905.510.0230.6573.6.3.9NA
110.0601mo7A0.2735.970.0340.5143.6.3.9111
120.0601y7910.5044.550.0560.7733.4.15.5NA
130.0603ee4A0.5014.550.0450.7791.17.4.1NA
140.0601fziA0.5334.690.0650.8561.14.13.25NA
150.0601ayxA0.4844.900.0450.8073.2.1.3NA
160.0603b8eC0.3895.520.0230.6523.6.3.960,64
170.0603evhA0.4944.500.1460.7404.2.2.3NA
180.0602vn4A0.4945.150.0650.8073.2.1.3NA
190.0601gaiA0.5015.110.0650.8123.2.1.3NA

(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
00.170.5284.450.030.801oquC GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
10.100.5254.580.050.804dr0B GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
20.080.5474.200.090.804m1fA GO:0004748 GO:0005506 GO:0005737 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0030145 GO:0046872 GO:0055114
30.070.5224.570.050.801uzrB GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0040007 GO:0046872 GO:0055114
40.070.5084.540.060.784djnA GO:0001822 GO:0003014 GO:0004748 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005971 GO:0006260 GO:0006264 GO:0006281 GO:0006974 GO:0006979 GO:0009186 GO:0009200 GO:0009263 GO:0014075 GO:0015949 GO:0016491 GO:0046872 GO:0055114 GO:0070062 GO:1902254
50.070.5014.860.050.832incA GO:0004497 GO:0006725 GO:0016491 GO:0046872 GO:0055114
60.070.5264.380.070.792bq1I GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
70.070.4984.700.070.781jk0A GO:0004748 GO:0005634 GO:0005737 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
80.070.5394.250.080.781h0nA GO:0004748 GO:0005634 GO:0005737 GO:0005971 GO:0006260 GO:0009186 GO:0009262 GO:0009263 GO:0016491 GO:0046872 GO:0051259 GO:0051290 GO:0055114
90.070.5364.040.080.784n83A GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
100.070.4884.610.100.762jcdA GO:0046872
110.070.5613.700.090.774m1hB GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
120.070.5104.760.060.782rccA GO:0004748 GO:0006260 GO:0009186 GO:0016491 GO:0046872 GO:0055114
130.060.5144.290.090.772inpD GO:0006725 GO:0016491 GO:0016709 GO:0055114
140.060.5014.710.060.831fyzC GO:0004497 GO:0006725 GO:0006730 GO:0015049 GO:0015050 GO:0015947 GO:0016491 GO:0016709 GO:0055114
150.060.5204.540.040.794bmqA GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016020 GO:0016021 GO:0016491 GO:0046872 GO:0055114
160.060.5094.780.050.795cnvH GO:0004748 GO:0005506 GO:0005737 GO:0005829 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0015949 GO:0016491 GO:0042802 GO:0046872 GO:0055114
170.060.3864.830.090.601o7dA GO:0003824 GO:0004553 GO:0004559 GO:0005764 GO:0005975 GO:0006013 GO:0006517 GO:0007611 GO:0008152 GO:0008270 GO:0015923 GO:0016787 GO:0016798 GO:0030246 GO:0046872
180.060.4864.860.040.762o1zA GO:0009186 GO:0016491 GO:0046872 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0046872 GO:0004748
GO-Score 0.40 0.40
Biological Processes GO:0009186 GO:0006260 GO:0009263 GO:0055114
GO-Score 0.40 0.40 0.40 0.40
Cellular Component GO:0005971
GO-Score 0.40

(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.