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I-TASSER results for job id Rv1610

[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 5 3rl3A MN Rep, Mult 220,222
20.08 4 5fnyB O Rep, Mult 29,71,75,149,153
30.07 3 2jstB HLT Rep, Mult 71,74,101
40.04 2 3ty8A TAR Rep, Mult 207,211,224
50.04 2 3ag4A CDL Rep, Mult 71,74,77,90,94,97,101,104
60.04 2 5arnA CU1 Rep, Mult 76,98,102,153
70.02 1 1ebeA O Rep, Mult 37,40
80.02 1 1xmeC HAS Rep, Mult 141,145
90.02 1 3dtuC DMU Rep, Mult 71,74,75,78
100.02 1 1izlL CLA Rep, Mult 25,75,79
110.02 1 1rwtB CHL Rep, Mult 62,64
120.02 1 2bhwA CLA Rep, Mult 65,74
130.02 1 1e86A CMO Rep, Mult 69,72,110
140.02 1 4xxjA MPG Rep, Mult 64,101,104

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
10.0601fftA0.5374.850.0470.8261.10.3.-NA
20.0601frvB0.5014.590.0850.7061.12.2.1NA
30.0601vdkA0.4795.380.0680.7494.2.1.2NA
40.0601i0aA0.4535.170.0570.6854.3.2.1NA
50.0602occN0.5494.620.0850.8261.9.3.1NA
60.0603crlB0.4964.900.0360.7232.7.11.2104,105,107
70.0601yfeA0.4785.330.0920.7364.2.1.2NA
80.0601xmeA0.5445.030.0800.8381.9.3.1NA
90.0603no9A0.4775.180.0640.7284.2.1.233
100.0603gtdA0.4755.100.0550.7234.2.1.2NA
110.0601b8fA0.4665.500.0700.7284.3.1.3NA
120.0602hvgA0.4675.230.0660.7234.3.2.2NA
130.0601jswB0.4735.430.0600.7404.3.1.1NA
140.0601y8pA0.4874.510.0580.6942.7.11.2NA
150.0603gzhA0.4725.170.0330.7194.3.2.2NA
160.0601m56A0.5564.550.0800.8211.9.3.1NA
170.0602zdxA0.4694.500.0450.6552.7.11.2NA
180.0601jtnA0.2385.680.0120.3963.2.1.17NA
190.0602pfdB0.4893.900.1200.6302.1.2.5,4.3.1.4NA

(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
00.290.5564.550.080.821m56A GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0006119 GO:0006810 GO:0006811 GO:0009055 GO:0009060 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0022900 GO:0046872 GO:0055114 GO:0070469 GO:1902600
10.250.5484.680.080.831occA GO:0004129 GO:0005506 GO:0005739 GO:0005743 GO:0006119 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0045277 GO:0046872 GO:0055114 GO:0070469 GO:1902600
20.100.3995.040.040.561occC GO:0004129 GO:0005739 GO:0005743 GO:0008535 GO:0015002 GO:0016020 GO:0016021 GO:0019646 GO:0022904 GO:0045277 GO:1902600
30.090.5114.940.080.773o0rB GO:0004129 GO:0005506 GO:0005886 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0016491 GO:0016966 GO:0019333 GO:0020037 GO:0046872 GO:0055114 GO:0070469 GO:1902600
40.070.5525.680.080.922yevA GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0006119 GO:0006810 GO:0006811 GO:0009055 GO:0009060 GO:0015002 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0022900 GO:0022904 GO:0046872 GO:0055114 GO:0070469 GO:1902600
50.070.5374.850.050.831fftA GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0005887 GO:0006811 GO:0009055 GO:0009060 GO:0009319 GO:0009486 GO:0015078 GO:0015453 GO:0015990 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0016682 GO:0019646 GO:0020037 GO:0046872 GO:0048039 GO:0055114 GO:0070469
60.070.5435.020.080.843eh3A GO:0004129 GO:0005506 GO:0005886 GO:0006119 GO:0006811 GO:0009055 GO:0009060 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0046872 GO:0055114 GO:0070469 GO:1902600
70.070.5524.640.070.831qleA GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0006119 GO:0006810 GO:0006811 GO:0009055 GO:0009060 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0022900 GO:0046872 GO:0055114 GO:0070469 GO:1902600
80.070.5174.510.070.755djqA GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0005887 GO:0006119 GO:0009055 GO:0009060 GO:0015078 GO:0015990 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0016705 GO:0019411 GO:0019646 GO:0019825 GO:0020037 GO:0045154 GO:0045278 GO:0046872 GO:0055114 GO:0070069 GO:0070469 GO:0070470 GO:1902600
90.070.5564.820.070.824av3B GO:0000287 GO:0004427 GO:0005509 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006814 GO:0009678 GO:0015081 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030955 GO:0035725 GO:0042803 GO:0046872
100.070.5144.800.090.774xydA GO:0004129 GO:0005506 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0016491 GO:0016966 GO:0020037 GO:0055114 GO:0070469 GO:1902600
110.070.5295.160.070.804av6A GO:0000287 GO:0004427 GO:0005509 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006814 GO:0009678 GO:0015081 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030955 GO:0035725 GO:0042803 GO:0046872
120.060.4945.470.090.784a01A GO:0004427 GO:0005773 GO:0005774 GO:0006810 GO:0006811 GO:0009678 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0046872 GO:0055085
130.060.4004.330.080.531fftC GO:0004129 GO:0005886 GO:0005887 GO:0008827 GO:0009055 GO:0009060 GO:0009319 GO:0009486 GO:0015002 GO:0015078 GO:0015453 GO:0015990 GO:0016020 GO:0016021 GO:0016491 GO:0019646 GO:0022904 GO:0055114
140.060.4614.700.070.681f88B GO:0000139 GO:0001750 GO:0001917 GO:0004871 GO:0004930 GO:0005085 GO:0005794 GO:0005886 GO:0005887 GO:0005911 GO:0006468 GO:0007165 GO:0007186 GO:0007601 GO:0007602 GO:0007603 GO:0008020 GO:0009416 GO:0009583 GO:0009881 GO:0016020 GO:0016021 GO:0016038 GO:0016056 GO:0018298 GO:0022400 GO:0042622 GO:0043547 GO:0045494 GO:0046872 GO:0050896 GO:0050953 GO:0060041 GO:0060342 GO:0071482 GO:0097381
150.060.3994.730.060.541qleC GO:0004129 GO:0005886 GO:0015002 GO:0016020 GO:0016021 GO:0016491 GO:0019646 GO:0022904 GO:0055114 GO:1902600
160.060.4014.880.070.551m56C GO:0004129 GO:0015002 GO:0016020 GO:0019646 GO:0022904 GO:1902600
170.060.2814.960.040.403l0mA GO:0000166 GO:0003824 GO:0005085 GO:0005524 GO:0005576 GO:0005622 GO:0006612 GO:0008152 GO:0008289 GO:0009405 GO:0016020 GO:0016740 GO:0016779 GO:0017137 GO:0018117 GO:0018260 GO:0033644 GO:0043087 GO:0043547 GO:0044161 GO:0044162 GO:0044600 GO:0070273 GO:0070733
180.060.2924.370.030.423l0iC GO:0000166 GO:0003824 GO:0005085 GO:0005524 GO:0005576 GO:0005622 GO:0006612 GO:0008152 GO:0008289 GO:0009405 GO:0016020 GO:0016740 GO:0016779 GO:0017137 GO:0018117 GO:0018260 GO:0033644 GO:0043087 GO:0043547 GO:0044161 GO:0044162 GO:0044600 GO:0070273 GO:0070733


Consensus prediction of GO terms
 
Molecular Function GO:0004129 GO:0005506 GO:0020037 GO:0005507
GO-Score 0.60 0.55 0.55 0.34
Biological Processes GO:1902600 GO:0009060 GO:0006119 GO:0022900
GO-Score 0.60 0.55 0.51 0.34
Cellular Component GO:0016021 GO:0005886 GO:0005743 GO:0045277
GO-Score 0.60 0.40 0.33 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.