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I-TASSER results for job id Rv2120c

[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
10.07 4 1x92B M7P Rep, Mult 63,66
20.06 3 3ar7A PTY Rep, Mult 57,85,89,92
30.06 3 5kc0A RBF Rep, Mult 73,76,77,83,120,124,135,138,139,142,143
40.04 2 3retB PYR Rep, Mult 32,108,150
50.04 2 4xk8L CLA Rep, Mult 59,91
60.04 2 3aqtB RCO Rep, Mult 12,25,28,29,32,58,59,62,90
70.04 2 1bjyB CTC Rep, Mult 141,145,148
80.02 1 3ar2A NA Rep, Mult 12,13,15,16,63
90.02 1 3p5nA RBF Rep, Mult 19,82,84,87,116,120,142,143,146
100.02 1 3e3gD SO4 Rep, Mult 73,75
110.02 1 5d92A 8K6 Rep, Mult 28,143
120.02 1 2h2sA SEK Rep, Mult 30,34,157
130.02 1 2yxhA MG Rep, Mult 117,143
140.02 1 2a1oA OXY Rep, Mult 109,113
150.02 1 3dhdA POP Rep, Mult 20,135
160.02 1 1b5dA DCM Rep, Mult 75,84

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
10.0601rqiA0.5165.220.0450.9122.5.1.10NA
20.0601ffuB0.4924.310.0820.7941.2.99.2NA
30.0601z11A0.4814.980.0540.8121.14.14.1NA
40.0602pywA0.5124.640.0520.8122.7.1.100NA
50.0603b8cB0.5184.530.1030.8383.6.3.662,82,85
60.0602vn0A0.4914.670.0450.8061.14.14.1NA
70.0601n6bA0.4834.660.0450.8001.14.14.1NA
80.0603b8eA0.4974.500.0570.7943.6.3.9NA
90.0603b8eC0.5184.350.0440.8253.6.3.920,82,109
100.0602f89F0.5015.150.0380.8312.5.1.1,2.5.1.10NA
110.0603ixzA0.4964.320.0820.7873.6.3.10NA
120.0601hm7B0.4895.070.0720.8504.2.3.7,4.6.1.5NA
130.0602j1pB0.4775.620.0640.8872.5.1.1,2.5.1.10,2.5.1.29NA
140.0603b8cA0.5184.550.0960.8443.6.3.6NA
150.0607reqB0.5244.260.0750.7565.4.99.2NA
160.0602ve3A0.4914.750.0380.7811.14.-.-NA
170.0602i2xA0.4924.990.0720.8562.1.1.90114,116
180.0603dbmA0.4025.130.0320.7064.2.1.9261,64,79
190.0607reqD0.5244.260.0750.7565.4.99.259

(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
00.340.8131.700.150.904hzuS GO:0016020 GO:0016021
10.290.7172.640.150.904tkrB GO:0005886 GO:0015234 GO:0015888 GO:0016020 GO:0016021 GO:0071934
20.250.7092.730.110.904muuA GO:0005886 GO:0015234 GO:0015888 GO:0016020 GO:0016021 GO:0071934
30.240.6823.020.120.894huqS GO:0005215 GO:0006810 GO:0016020 GO:0016021
40.240.6673.290.150.894z7fB GO:0005215 GO:0006810 GO:0016020 GO:0016021
50.240.6752.970.100.895d3mC GO:0005215 GO:0006810 GO:0016020 GO:0016021
60.230.7372.600.120.904rfsS GO:0005215 GO:0006810 GO:0016020 GO:0016021
70.180.6963.130.100.904dveA GO:0005886 GO:0006810 GO:0015225 GO:0015878 GO:0016020 GO:0016021
80.110.6992.820.140.903p5nA GO:0005215 GO:0005886 GO:0006810 GO:0016020 GO:0016021 GO:0032217 GO:0032218
90.090.6982.970.080.904m58A GO:0000041 GO:0016020 GO:0016021
100.070.5763.510.080.815do7A GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0007584 GO:0007588 GO:0010212 GO:0010949 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:0045177 GO:0045796 GO:0046982 GO:0055085
110.070.6133.410.060.845do7D 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
120.070.5244.230.050.784f4cA 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
130.070.3574.680.060.593qf7A GO:0000166 GO:0005524 GO:0006281 GO:0006974 GO:0016787 GO:0046872
140.070.3755.490.060.694pl0B GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0016887 GO:0030153 GO:0042626 GO:0043213 GO:0055085
150.060.4163.160.080.543b5wA 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
160.060.4254.560.060.645c73A GO:0000166 GO:0005524 GO:0006810 GO:0016021 GO:0016887 GO:0042626 GO:0055085
170.060.3965.820.060.782vbfA GO:0000287 GO:0003824 GO:0009082 GO:0016831 GO:0030976 GO:0046872 GO:0047433
180.060.3675.510.070.683wmgA GO:0000166 GO:0005524 GO:0006810 GO:0016020 GO:0016021 GO:0016887 GO:0042626 GO:0055085


Consensus prediction of GO terms
 
Molecular Function GO:0015234
GO-Score 0.47
Biological Processes GO:0071934
GO-Score 0.47
Cellular Component GO:0016021 GO:0005886
GO-Score 0.80 0.47

(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.