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I-TASSER results for job id Rv1719

[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
10.63 18 2o9aD PYR Rep, Mult 139,144,145,146,196,204,206,222,224
20.02 1 2xroB NUC Rep, Mult 13,14,15,34,35,36,46,50,69,70,71
30.02 1 2xroA NUC Rep, Mult 15,18,45,47,48,51
40.02 1 2o9a0 III Rep, Mult 129,131,132,133,200,203,204,225,226,228
50.02 1 1s0vC APC Rep, Mult 46,50,51,54,55
60.02 1 2ia20 III Rep, Mult 12,13,15,16,17,19,20,23,24,26,31,51,55,56,58,59,61,73,74,75,76,77,78,79,80,83,84,85,86,87

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
10.0601kzhB0.4116.270.0660.7382.7.1.90NA
20.0601xdpA0.4315.760.0650.6912.7.4.1NA
30.0603c39A0.4116.310.0440.7342.7.2.3NA
40.06013pkA0.4016.380.0520.7102.7.2.3NA
50.0603d64B0.4325.780.0760.7103.3.1.189,101,121,127
60.0603dwbA0.4095.780.0490.6643.4.24.71NA
70.0602zmfB0.3953.830.0410.4943.1.4.17109,250
80.0603eqvA0.4225.390.0400.6373.4.16.4NA
90.0602o9bA0.4264.470.0630.5682.7.13.3152,218
100.0602vpiA0.2176.520.0650.3946.3.5.2NA
110.0602f48B0.4066.610.0730.7642.7.1.90NA
120.0602ywcA0.4116.180.0970.6996.3.5.2NA
130.0601k87A0.4696.170.0560.8031.5.99.8203
140.0603c46B0.3856.030.0680.6602.7.7.6184
150.0602vlcA0.4086.160.0470.7033.2.2.2221,24
160.0603hsiB0.4116.560.0630.7532.7.8.8NA
170.0603fwlA0.4335.690.0480.7102.4.1.129NA
180.0603c2wC0.4124.520.1040.5602.7.13.3115
190.0602vumA0.4086.120.0500.6992.7.7.6NA

(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
00.360.5992.350.230.662xrnB GO:0003677 GO:0006351 GO:0006355
10.310.5312.550.220.593bjnA GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0045892
20.300.5971.870.190.641mkmB GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0045892
30.300.7293.640.190.913mq0B GO:0003677 GO:0006351 GO:0006355
40.280.7693.230.210.943r4kA GO:0003677 GO:0006351 GO:0006355
50.260.5982.020.270.651ysqA GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0045892
60.260.5942.110.210.651tf1A GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0006974 GO:0042802 GO:0045892
70.250.6001.980.260.652o99C GO:0003677 GO:0003700 GO:0005829 GO:0006097 GO:0006351 GO:0006355 GO:0045892
80.230.6754.160.200.882ia2A GO:0003677 GO:0006351 GO:0006355 GO:0045893 GO:0046278
90.210.5502.880.150.632o0yC GO:0003677 GO:0006351 GO:0006355
100.210.5652.060.280.621yspA GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0045892
110.180.5712.390.190.643obfA GO:0003677 GO:0006351 GO:0006355
120.140.5632.920.120.663d3oA GO:0003677 GO:0006351 GO:0006355
130.070.5983.080.170.692g7uA GO:0003677 GO:0006351 GO:0006355 GO:0045893 GO:0046278
140.060.3546.460.080.642i3aD GO:0003942 GO:0005737 GO:0006526 GO:0008652 GO:0016491 GO:0016620 GO:0040007 GO:0046983 GO:0051287 GO:0055114 GO:0070401
150.060.3255.710.070.544b3iD GO:0003824 GO:0005618 GO:0005886 GO:0008152 GO:0016740 GO:0016746 GO:0016747
160.060.3316.120.050.572fp9A GO:0005773 GO:0009058 GO:0009820 GO:0016829 GO:0016844
170.060.2315.700.030.385h9mA GO:0000209 GO:0003714 GO:0004842 GO:0005634 GO:0005654 GO:0005737 GO:0005769 GO:0005829 GO:0006511 GO:0006915 GO:0007049 GO:0007264 GO:0007275 GO:0007411 GO:0008270 GO:0016567 GO:0016874 GO:0031396 GO:0031624 GO:0042787 GO:0043005 GO:0043025 GO:0043066 GO:0043154 GO:0043161 GO:0043231 GO:0044257 GO:0044267 GO:0046872 GO:0061630 GO:0090090 GO:1903507 GO:2001237
180.060.1813.460.040.233cbrB GO:0001523 GO:0005179 GO:0005576 GO:0005615 GO:0005737 GO:0006810 GO:0030198 GO:0042562 GO:0042572 GO:0042802 GO:0043234 GO:0044267 GO:0046982 GO:0070062
190.060.1774.470.040.242r4hC GO:0000166 GO:0005524 GO:0005654 GO:0005737 GO:0005886 GO:0005911 GO:0005912 GO:0005923 GO:0006461 GO:0007155 GO:0007166 GO:0008022 GO:0016020 GO:0030054 GO:0032947 GO:0042995 GO:0051393 GO:0070997
200.060.1764.450.050.241wfvA GO:0002092 GO:0003402 GO:0004871 GO:0005634 GO:0005737 GO:0005768 GO:0005770 GO:0005886 GO:0005923 GO:0007165 GO:0007399 GO:0008285 GO:0010976 GO:0014069 GO:0016020 GO:0019902 GO:0030054 GO:0030159 GO:0030336 GO:0030425 GO:0031697 GO:0032516 GO:0032926 GO:0032947 GO:0036057 GO:0038180 GO:0043005 GO:0043113 GO:0043234 GO:0045202 GO:0046332 GO:0048471 GO:0051291 GO:0051898 GO:0060395 GO:0070699 GO:0071850 GO:0072015 GO:0097118 GO:1990090 GO:2000809


Consensus prediction of GO terms
 
Molecular Function GO:0003677 GO:0003700
GO-Score 0.84 0.52
Biological Processes GO:0045892
GO-Score 0.52
Cellular Component
GO-Score

(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.