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I-TASSER results for job id Rv1006

[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 6 2osyB GLC Rep, Mult 62,138,140,174,226,317,361,387
20.07 4 1wdqA MAL Rep, Mult 91,93,137,227,286,314,360,361,362,387
30.03 2 1nw1A CA Rep, Mult 212,227,230,232
40.03 2 2cksA ZN Rep, Mult 227,356
50.03 2 5j14A GAL Rep, Mult 62,174,326,387
60.02 1 3ndzA CT3 Rep, Mult 117,118,121
70.02 1 3k7tA GP7 Rep, Mult 240,241
80.02 1 2akfB ZN Rep, Mult 209,212
90.02 1 2oymA MNI Rep, Mult 62,138,140,175,178,226,227,229,290,317,361,387
100.02 1 2o011 CLA Rep, Mult 223,224
110.02 1 2zumA ZN Rep, Mult 54,424
120.02 1 1b3zA XYP Rep, Mult 207,208,213
130.02 1 1j0zB CA Rep, Mult 97,111,112,159,196,199
140.02 1 1b1yA UUU Rep, Mult 92,136,286
150.02 1 3c5iA MG Rep, Mult 303,314
160.02 1 2h8pC GOA Rep, Mult 415,416
170.02 1 2xgbA EPG Rep, Mult 90,92,388
180.02 1 1h5vA CA Rep, Mult 54,381

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
10.2542osxA0.6513.240.1000.7273.2.1.123NA
20.1122oykB0.6453.210.1000.7203.2.1.123NA
30.0601b1yA0.5005.000.0740.6243.2.1.2160
40.0601d7fA0.4705.910.0530.6332.4.1.19NA
50.0601qhoA0.4685.930.0580.6333.2.1.133NA
60.0601m53A0.4836.320.0700.6755.4.99.12218
70.0601izjA0.4736.520.0440.6753.2.1.135,3.2.1.1NA
80.0601cgtA0.4695.880.0510.6332.4.1.19225
90.0601eceB0.4663.780.1080.5363.2.1.4318
100.0601qnoA0.4693.600.0650.5363.2.1.78227,359
110.0603a47A0.4956.300.0480.6903.2.1.10134,215
120.0603icgA0.5194.870.0880.6383.2.1.4285
130.0601rh9A0.4813.680.0880.5503.2.1.78359
140.0601cygA0.4735.860.0510.6372.4.1.19NA
150.0601cdgA0.4725.820.0600.6312.4.1.19NA
160.0601b90A0.5115.580.0890.6683.2.1.2NA
170.0601wdpA0.4955.000.0760.6193.2.1.2NA
180.0602fhbA0.4836.100.0700.6633.2.1.4162,93
190.0601fa2A0.5005.160.0670.6303.2.1.2NA
200.0603k1dA0.4736.680.0680.6822.4.1.18NA
210.0602zidA0.4766.170.0750.6563.2.1.70218

(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
00.220.6513.240.100.732osxA GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0047876
10.130.7411.650.130.775j14A GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
20.110.4654.010.100.543ndyA GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798 GO:0030245 GO:0030246 GO:0030247
30.070.5465.150.110.693u7vA GO:0004553 GO:0004565 GO:0005975 GO:0008152 GO:0009341 GO:0016787 GO:0016798
40.070.4874.140.090.574yheA GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
50.070.4853.790.070.564w8aA GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
60.070.4763.910.090.553ayrA GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
70.070.4713.790.070.541edgA GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798 GO:0030245
80.070.4663.770.110.541eceA GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798 GO:0030245 GO:0030246 GO:0030247
90.070.4723.940.100.554nf7A GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798 GO:0030245 GO:0030246 GO:0030247
100.070.4643.650.080.532jepA GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0033946
110.070.4633.940.080.544x0vC GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
120.070.4643.770.070.545d9nA GO:0004553 GO:0005975 GO:0006080 GO:0016985
130.070.4543.700.080.524tufA GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798 GO:0030245 GO:0030246 GO:0030247
140.070.4603.730.100.534w84A GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0033946
150.070.4563.860.080.534im4A GO:0000272 GO:0003824 GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798 GO:0030245 GO:0030248 GO:0045493 GO:0046555 GO:0046872 GO:2000884
160.070.4533.720.110.524lx4B GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
170.060.4523.480.100.514htyA GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
180.060.4513.260.070.515bywE GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798 GO:0030245


Consensus prediction of GO terms
 
Molecular Function GO:0004553
GO-Score 0.47
Biological Processes GO:0005975
GO-Score 0.47
Cellular Component GO:0009341
GO-Score 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.