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I-TASSER results for job id Rv2891

[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
10.56 16 5j1lC ZN Rep, Mult 66,70,147
20.03 1 1qwyA ZN Rep, Mult 5,66,70,147
30.02 1 2e26A UUU Rep, Mult 88,90,91,120
40.02 1 1piiA PO4 Rep, Mult 73,76,78,132,133
50.02 1 5j1lA ZN Rep, Mult 70,113,145,147

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
10.2552b44A0.4512.160.2480.5023.4.24.7590,139
20.0602gprA0.3844.010.0960.4942.7.1.69147,149
30.0602ok5A0.3716.180.0380.6473.4.21.47NA
40.0602q2eB0.3716.250.0380.6715.99.1.375
50.0601piiA0.3896.370.0810.6874.1.1.48,5.3.1.24NA
60.0601rtkA0.3146.500.0400.5863.4.21.47NA
70.0601jxaA0.2946.570.0450.5422.6.1.16NA
80.0603ixzA0.3866.140.0610.6673.6.3.10NA
90.0603lxuX0.4105.960.0810.6993.4.14.1093
100.0602pplA0.3756.260.0430.6753.1.1.3NA
110.0601gytJ0.3775.600.0650.6023.4.11.198,158
120.0602pffA0.3996.480.0750.7432.3.1.41,2.3.1.86NA
130.0602pffD0.4006.480.0300.7392.3.1.8673
140.0601ei1A0.3735.820.0500.6235.99.1.3NA
150.0601rs0A0.3106.010.0180.5343.4.21.47NA
160.0601m7xB0.3696.410.0390.6712.4.1.1870
170.0601glaF0.3794.090.0980.4862.7.1.69NA
180.0601jcmP0.2886.400.0650.5144.1.1.48,5.3.1.24NA
190.0601lf6A0.3855.950.0550.6473.2.1.3NA
200.0601rp1A0.3666.510.0520.6833.1.1.3NA

(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
00.310.7142.680.220.824lxcA GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0016787 GO:0046872 GO:0071555
10.290.5113.270.160.612gu1A GO:0046872
20.260.5341.930.190.582hsiB GO:0046872
30.170.4542.390.220.513tufB GO:0016020 GO:0016021 GO:0030435 GO:0042601
40.160.4353.760.200.553it5A GO:0004175 GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0009405 GO:0016787 GO:0046872
50.110.4452.280.230.494bh5A GO:0000920 GO:0001896 GO:0005886 GO:0007049 GO:0009273 GO:0016787 GO:0030288 GO:0032153 GO:0042493 GO:0042597 GO:0051301 GO:0051345
60.070.5023.030.200.591qwyA GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0009405 GO:0016787 GO:0046872 GO:0071555
70.060.2966.690.030.554bbjA GO:0000166 GO:0005886 GO:0006812 GO:0016020 GO:0016021 GO:0016787 GO:0019829 GO:0046872 GO:0098655
80.060.2816.030.040.494dk0A GO:0016020 GO:0042802 GO:0055085
90.060.2596.590.040.481bzlA GO:0005737 GO:0015036 GO:0015042 GO:0016491 GO:0016668 GO:0045454 GO:0050660 GO:0055114
100.060.2646.020.060.454yaiA GO:0016491 GO:0055114
110.060.4554.280.170.584rnyA GO:0016020 GO:0016021 GO:0046872
120.060.4693.510.130.573nyyA GO:0016020 GO:0016021
130.060.2315.870.040.394h67C GO:0009228 GO:0009229
140.060.2286.620.060.414h65B GO:0009228 GO:0009229
150.060.2405.990.070.413rysA GO:0000034 GO:0006146 GO:0008270 GO:0009117 GO:0016787 GO:0019239 GO:0043103 GO:0046872
160.060.4643.590.170.573sluB GO:0016020 GO:0016021
170.060.2135.900.060.361c41A GO:0000906 GO:0009231 GO:0009349 GO:0016740 GO:1902444
180.060.2453.790.110.322mk5A GO:0008745 GO:0009253 GO:0044659 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0046872 GO:0008237
GO-Score 0.70 0.42
Biological Processes GO:0006508 GO:0043934 GO:0048646 GO:0030154 GO:0071555 GO:0051704
GO-Score 0.42 0.33 0.33 0.33 0.31 0.31
Cellular Component GO:0005576 GO:0042763
GO-Score 0.42 0.33

(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.