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I-TASSER results for job id Rv1215c

[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 3 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
10.24 10 2b4kA PG9 Rep, Mult 81,181,182,207,214,215,229,282,283,308
20.08 3 3i2gA DBC Rep, Mult 81,150,181,182,214,229,283,308,388,389
30.05 2 1u8eB NAG Rep, Mult 55,138,157,160
40.05 2 3idaA DBC Rep, Mult 81,181,182,229
50.05 2 1u8eA UUU Rep, Mult 63,65,130,132,133,134
60.02 1 4bzzA ACT Rep, Mult 124,128,322
70.02 1 4c01A QY9 Rep, Mult 50,164,167,168

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
10.1391l7qA0.7602.380.2570.8133.1.1.1NA
20.0601nx9A0.7553.580.2040.8503.1.1.4352,58
30.0601b41A0.4255.150.1130.5313.1.1.7NA
40.0602b4kA0.7553.580.2060.8503.1.1.43181,182,279
50.0601mpxA0.7393.130.1710.8223.2.1.43NA
60.0601aknA0.4315.290.0980.5453.1.1.13,3.1.1.3NA
70.0602jbwD0.4283.470.1500.4883.7.1.-181
80.0601k8qA0.4084.280.1080.4813.1.1.3NA
90.0602d5lA0.4044.180.1330.4723.4.14.-181,279
100.0601l7aA0.3933.120.1300.4393.1.1.72,3.1.1.41172
110.0602fj0A0.4225.380.0930.5333.1.1.1278
120.0601mx9D0.4165.150.1310.5203.1.1.1NA
130.0603fvrA0.3953.300.1260.4443.1.1.6181,279
140.0601e5tA0.4254.220.1190.4973.4.21.26NA
150.0601hlgA0.4064.460.1050.4873.1.1.3553
160.0602veoB0.4394.600.1250.5353.1.1.3139
170.0603g0bB0.4254.020.1170.4953.4.14.5137
180.0601z68A0.4204.100.1230.4903.4.21.-181,279
190.0601c7jA0.4034.880.1290.4923.1.1.-119
200.0601yr2A0.4204.300.1410.4923.4.21.26181,279

(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
00.230.9331.670.330.963iiiA GO:0006508 GO:0008239 GO:0016787
10.230.7622.400.260.823i2gA GO:0005737 GO:0006508 GO:0008239 GO:0016787 GO:0050784 GO:0052689
20.220.7553.580.210.852b4kA GO:0006508 GO:0008239 GO:0016787 GO:0047658
30.140.7603.150.190.844pf1A GO:0006508 GO:0008239 GO:0016787
40.130.7563.350.180.841mpxA GO:0006508 GO:0008239 GO:0016787 GO:0046872 GO:0047658
50.130.7373.500.140.831lnsA GO:0004177 GO:0005737 GO:0006508 GO:0008233 GO:0008236 GO:0008239 GO:0016787
60.060.3713.660.110.423aikA GO:0008152 GO:0016787 GO:0042802 GO:0052689
70.060.3263.390.140.372i3dB GO:0016787
80.060.2517.080.040.395hdrC GO:0004560 GO:0005975 GO:0006004
90.060.2557.440.050.414peeC GO:0004560 GO:0005975 GO:0006004
100.060.2577.540.030.422panA GO:0000287 GO:0003824 GO:0009028 GO:0009436 GO:0016829 GO:0030976 GO:0042802 GO:0046296 GO:0071949
110.060.2427.400.050.391m7sA GO:0004096 GO:0004601 GO:0006979 GO:0016491 GO:0020037 GO:0042597 GO:0042744 GO:0046872 GO:0055114 GO:0098869
120.060.2106.670.040.313hurA GO:0003824 GO:0006522 GO:0008784 GO:0016853 GO:0030170 GO:0030632
130.060.2076.340.040.301dosA GO:0003824 GO:0004332 GO:0005618 GO:0005829 GO:0005886 GO:0005975 GO:0006094 GO:0006096 GO:0008270 GO:0016829 GO:0016832 GO:0046872
140.060.1906.080.060.274gquA GO:0000105 GO:0004424 GO:0005737 GO:0008652 GO:0016829 GO:0040007
150.060.1995.420.050.264pr3A GO:0003824 GO:0008152 GO:0008782 GO:0008930 GO:0009116 GO:0016787 GO:0016798
160.060.1804.870.050.232gd9A GO:0000455 GO:0005829 GO:0008703 GO:0009231 GO:0009982 GO:0016020 GO:0016021 GO:0019239 GO:0055114
170.060.2006.840.040.301zcwA GO:0016740
180.060.1634.610.040.201ns5B GO:0005737 GO:0006364 GO:0008168 GO:0016740 GO:0031167 GO:0032259 GO:0042803 GO:0043022 GO:0070038 GO:0070475


Consensus prediction of GO terms
 
Molecular Function GO:0008239 GO:0047658
GO-Score 0.65 0.32
Biological Processes GO:0006508 GO:0019439 GO:0042737 GO:0050783 GO:1901361 GO:0046700 GO:0009822
GO-Score 0.65 0.46 0.46 0.46 0.46 0.46 0.46
Cellular Component GO:0044424
GO-Score 0.46

(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.