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I-TASSER results for job id Rv1517

[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
10.06 3 3bvdA XE Rep, Mult 158,161,206,207
20.06 3 1brrC ARC Rep, Mult 170,192,196
30.06 3 1xvgA BRJ Rep, Mult 12,13,16,88,91,92
40.04 2 3cz3A NUC Rep, Mult 203,205,206
50.02 1 1vf5S III Rep, Mult 25,26
60.02 1 1ocoB HEA Rep, Mult 198,199
70.02 1 3zuyA PTY Rep, Mult 13,17,20,41,95,98,99,102
80.02 1 4bo3B U98 Rep, Mult 10,83,90,91
90.02 1 1mhy1 III Rep, Mult 6,7,10,11,13,14,15,18,19,140,144
100.02 1 3zvwC MG Rep, Mult 113,114
110.02 1 1vltA ASP Rep, Mult 101,105
120.02 1 3ri5B UND Rep, Mult 28,31
130.02 1 3d9sB PS6 Rep, Mult 6,181
140.02 1 4ub8h CLA Rep, Mult 89,92
150.02 1 2bhwA CLA Rep, Mult 17,19
160.02 1 2wyiA PG0 Rep, Mult 143,209
170.02 1 3k7tA GP7 Rep, Mult 134,135
180.02 1 3asoA DMU Rep, Mult 194,197
190.02 1 3zuxA TCH Rep, Mult 4,8,148,149,150

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
10.0602fonB0.3915.610.0450.6141.3.3.6141
20.0601mhyB0.3885.270.0610.6181.14.13.2535,99
30.0602vycA0.3825.300.0450.5834.1.1.19NA
40.0601hm7B0.4055.070.0560.6024.2.3.7,4.6.1.5NA
50.0601hm7A0.3775.650.0560.5984.2.3.7,4.6.1.5NA
60.0601fziA0.4345.480.0630.7131.14.13.25NA
70.0602yyjA0.3905.870.0520.6421.14.13.3NA
80.0602vuaA0.3076.010.0510.5243.4.24.69188
90.0601js4A0.3875.560.0790.5983.2.1.4NA
100.0602bq1I0.3845.260.1080.6101.17.4.1NA
110.0603dy5A0.3856.060.0230.6651.13.11.40,4.2.1.92NA
120.0601q5nA0.3935.790.0250.6465.5.1.2NA
130.0601w07B0.3975.730.0450.6301.3.3.6NA
140.0601h19A0.3855.820.0440.6533.3.2.6171
150.0601g87B0.3845.910.0560.6303.2.1.4NA
160.0602z1qB0.3835.560.0520.5981.3.99.3141
170.0602p0mB0.3905.770.0430.6421.13.11.33NA
180.0601ks8A0.4005.710.0330.6503.2.1.4NA
190.0601ksdA0.4015.700.0550.6463.2.1.4211

(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
00.090.6422.680.110.754bwzA GO:0006810 GO:0006812 GO:0015299 GO:0016020 GO:0016021 GO:0046872 GO:0055085 GO:1902600
10.070.5673.700.070.723zuxA GO:0016020 GO:0016021
20.070.4345.680.090.722uw1B
30.060.4395.540.080.732xz1A GO:0006629 GO:0006631 GO:0006633 GO:0009507 GO:0009536 GO:0016491 GO:0045300 GO:0046872 GO:0055114
40.060.5833.840.100.764cz8A GO:0006810 GO:0006812 GO:0015299 GO:0016020 GO:0016021 GO:0055085 GO:1902600
50.060.6103.570.100.784czbB GO:0005886 GO:0006810 GO:0006811 GO:0006812 GO:0006814 GO:0015297 GO:0015299 GO:0016020 GO:0016021 GO:0042802 GO:0055085 GO:1902600
60.060.3125.680.050.514rpfA GO:0000166 GO:0004413 GO:0005524 GO:0005737 GO:0006566 GO:0008652 GO:0009088 GO:0016301 GO:0016310 GO:0016740
70.060.5713.530.110.714atvA GO:0005886 GO:0006810 GO:0006811 GO:0006814 GO:0006885 GO:0015081 GO:0015297 GO:0015491 GO:0015992 GO:0016020 GO:0016021 GO:0035725 GO:0055085 GO:0098655
80.060.2625.800.050.433i48A GO:0005576 GO:0008081 GO:0046872
90.060.2775.170.050.411za0A GO:0005618 GO:0005829 GO:0005886 GO:0006629 GO:0006631 GO:0006633 GO:0016491 GO:0040007 GO:0045300 GO:0046872 GO:0055114
100.060.5693.860.100.744n7wA GO:0016020 GO:0016021
110.060.2765.470.060.441u0uA GO:0003824 GO:0005737 GO:0008152 GO:0009058 GO:0016740 GO:0016746 GO:0016747 GO:0050198
120.060.2306.040.030.392w2hA GO:0000307 GO:0003677 GO:0003682 GO:0005634 GO:0005654 GO:0006351 GO:0006355 GO:0006468 GO:0007049 GO:0008024 GO:0016032 GO:0016538 GO:0017069 GO:0044212 GO:0045737 GO:0045944 GO:0051301 GO:0097322 GO:1900364 GO:1901409
130.060.2435.910.050.411pv9B GO:0005737 GO:0006508 GO:0008233 GO:0008237 GO:0016787 GO:0016805 GO:0046872 GO:0102009
140.060.3006.250.040.523ug4C GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0046373 GO:0046556
150.060.2436.200.040.421t6lA GO:0003677 GO:0006260 GO:0019012 GO:0019079 GO:0030337 GO:0039686 GO:0042025
160.060.2146.080.070.372fckA GO:0008080 GO:0016740 GO:0016746
170.060.2505.600.040.403lb9A GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0031176 GO:0045493
180.060.2334.460.060.332m89A GO:0006950


Consensus prediction of GO terms
 
Molecular Function GO:0043169 GO:0015298 GO:0015078
GO-Score 0.30 0.30 0.30
Biological Processes GO:0015992 GO:0098662
GO-Score 0.30 0.30
Cellular Component GO:0031224
GO-Score 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.