[Home] [Server] [About] [Statistics] [Annotation]

I-TASSER results for job id Rv2575

[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
10.20 11 3dtiA ZN Rep, Mult 166,167,170,197
20.09 5 4fgmA ZN Rep, Mult 162,166,197
30.06 3 3r2lA FE Rep, Mult 137,167,170
40.04 2 2e84A ZN Rep, Mult 197,201
50.04 2 1fjqA ACN Rep, Mult 92,110,168,172
60.04 2 3c37A ZN Rep, Mult 166,170,197,262
70.02 1 1n38A CH1 Rep, Mult 119,120,130,131,133,134
80.02 1 2a68P MG Rep, Mult 201,204

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
10.0601fohC0.4265.820.0430.6791.14.13.7NA
20.0603ebgA0.3955.800.0500.6143.4.11.-167
30.0601gz3A0.3706.420.0380.6421.1.1.38NA
40.0608tlnE0.4235.860.0950.6623.4.24.27NA
50.0601fj3A0.4225.870.0950.6623.4.24.27167
60.0601ezmA0.4275.630.0660.6623.4.24.26167
70.0601jxaA0.3986.320.0610.6592.6.1.16NA
80.0601w18B0.4025.810.0330.6422.4.1.10NA
90.0602e1pA0.3366.820.0530.6183.4.21.62NA
100.0601thgA0.4126.390.0520.7033.1.1.3NA
110.0602b0tA0.4045.680.0560.6451.1.1.42175,243
120.0601mosA0.3736.230.0590.6082.6.1.16164
130.0601ej6A0.3996.450.0570.6762.7.7.50NA
140.0602vf4X0.3716.110.0550.6142.6.1.16NA
150.0601bxrA0.4166.040.0440.6726.3.5.5109
160.0601espA0.4215.850.0760.6593.4.24.28NA
170.0602o36A0.4255.500.0670.6483.4.24.15207
180.0601i1iP0.4245.550.0620.6593.4.24.16162
190.0601ii2A0.3956.180.0620.6424.1.1.49NA

(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
00.180.4245.550.060.661i1iP GO:0004222 GO:0005737 GO:0005739 GO:0005758 GO:0005829 GO:0006508 GO:0006518 GO:0008233 GO:0008237 GO:0016787 GO:0046872 GO:0070012
10.070.4335.660.070.683ihgA GO:0000166 GO:0016491 GO:0016709 GO:0017000 GO:0055114 GO:0071949 GO:1901771
20.070.4825.720.100.754k90A GO:0004222 GO:0005576 GO:0005615 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0009405 GO:0016787 GO:0046872
30.070.3926.130.030.652dkiA GO:0016491 GO:0018668 GO:0042803 GO:0055114 GO:0071949
40.070.4265.820.040.681fohC GO:0004497 GO:0005737 GO:0016491 GO:0018662 GO:0019336 GO:0019439 GO:0055114 GO:0071949
50.070.4205.900.070.674k5rB GO:0000166 GO:0016491 GO:0055114 GO:0071949
60.070.4295.420.070.661y791 GO:0004180 GO:0004222 GO:0005737 GO:0005829 GO:0006508 GO:0006518 GO:0008233 GO:0008237 GO:0016787 GO:0030288 GO:0046872
70.060.4215.850.080.661espA GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0016787 GO:0046872
80.060.4275.620.050.662qa1A GO:0000166 GO:0016491 GO:0055114 GO:0071949
90.060.4265.710.070.682r0gA GO:0000166 GO:0004497 GO:0008168 GO:0016491 GO:0032259 GO:0055114 GO:0071949
100.060.4255.500.070.652o36A GO:0004222 GO:0005737 GO:0005758 GO:0006508 GO:0006518 GO:0008233 GO:0008237 GO:0016787 GO:0042277 GO:0046872
110.060.4205.760.040.664x4jA GO:0016491 GO:0055114 GO:0071949
120.060.4175.810.070.674k2xB GO:0000166 GO:0016491 GO:0055114 GO:0071949
130.060.4225.830.060.684cy8A GO:0004497 GO:0016491 GO:0055114 GO:0071949
140.060.4205.810.050.684icyA GO:0000166 GO:0016491 GO:0055114 GO:0071949
150.060.4235.820.060.684z2rA GO:0004497 GO:0016491 GO:0055114 GO:0071949
160.060.3535.690.040.552qa2A GO:0000166 GO:0016491 GO:0055114 GO:0071949
170.060.3756.550.030.663efmA GO:0004872 GO:0005506 GO:0006810 GO:0009279 GO:0015891 GO:0016020
180.060.3775.460.050.573nixA GO:0000166 GO:0016491 GO:0055114 GO:0071949


Consensus prediction of GO terms
 
Molecular Function GO:0004175 GO:0008237 GO:0043169 GO:0050660
GO-Score 0.47 0.47 0.47 0.37
Biological Processes GO:0019538 GO:0044710 GO:1901564 GO:0043603
GO-Score 0.47 0.37 0.37 0.37
Cellular Component GO:0031970 GO:0005740
GO-Score 0.37 0.37

(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.