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I-TASSER results for job id Rv1802

[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 3ar3A PTY Rep, Mult 144,147,151,155
20.04 2 1y66B DIO Rep, Mult 150,153,157
30.04 2 3r6yB CA Rep, Mult 112,135
40.04 2 1vd5A GLY Rep, Mult 116,132
50.04 2 2jstB HLT Rep, Mult 31,34,68
60.04 2 3ar3A PTY Rep, Mult 38,79,83,86,87
70.04 2 5absA ZN Rep, Mult 141,145
80.04 2 2eauA PTY Rep, Mult 40,43,76,80
90.02 1 3bwxA CA Rep, Mult 70,73
100.02 1 3c9iC XE Rep, Mult 109,112
110.02 1 3j000 PEV Rep, Mult 31,32
120.02 1 4zzbA XE Rep, Mult 109,139,142,143
130.02 1 2g381 III Rep, Mult 3,14,15,17,18,19,20,23,24,27,30,31,33,34,37,38,40,41,44,45,48,52,56,64,71,74,82,85,89,96,153,154,157,161,164,165
140.02 1 2x7aI MG Rep, Mult 119,123
150.02 1 2q67A CA Rep, Mult 103,104
160.02 1 1iowA MG Rep, Mult 9,11
170.02 1 3hd7F GGG Rep, Mult 113,116

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
10.0601rm6A0.3418.020.0530.6181.3.99.20NA
20.0601bxrA0.3427.270.0480.5596.3.5.583,163
30.0601xmeA0.3446.720.0580.5291.9.3.1NA
40.0601mo7A0.1716.030.0490.2513.6.3.977
50.0603b8eC0.3336.760.0270.5203.6.3.993,287
60.0603cf4A0.3396.500.0540.5121.2.99.2NA
70.0601is2A0.3347.150.0480.5401.3.3.622
80.0601t3qB0.3477.930.0390.6281.3.99.17NA
90.0601y7910.3457.240.0350.5643.4.15.5NA
100.0602fonB0.3627.270.0580.5831.3.3.6NA
110.0602occN0.3346.490.0440.4971.9.3.1NA
120.0601occA0.3356.530.0470.5011.9.3.1NA
130.0601n63B0.3567.540.0620.6131.2.99.2NA
140.0601h16A0.3447.310.0600.5752.3.1.54NA
150.0603b9jI0.1395.460.0570.1901.17.1.4,1.17.3.2NA
160.0601mhsA0.3525.740.0460.4863.6.3.6NA
170.0601w36B0.3326.760.0560.5203.1.11.522
180.0601jrpB0.3357.880.0500.5981.17.1.4145
190.0601jroB0.3357.770.0530.5941.1.1.204NA

(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
00.060.3637.250.070.581w07B GO:0000062 GO:0001676 GO:0003995 GO:0003997 GO:0005777 GO:0005829 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0009055 GO:0009506 GO:0009611 GO:0009620 GO:0009695 GO:0016491 GO:0016627 GO:0033539 GO:0046686 GO:0050660 GO:0052890 GO:0055088 GO:0055114
10.060.3136.950.060.492z1qB GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
20.060.3106.720.050.482uxwA GO:0000062 GO:0001659 GO:0003995 GO:0004466 GO:0005634 GO:0005730 GO:0005737 GO:0005739 GO:0005743 GO:0005759 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0009055 GO:0015980 GO:0016020 GO:0016491 GO:0016627 GO:0017099 GO:0030855 GO:0033539 GO:0036498 GO:0042645 GO:0042760 GO:0045717 GO:0046322 GO:0050660 GO:0052890 GO:0055088 GO:0055114 GO:0090181
30.060.3115.890.070.445j65A GO:0030435
40.060.3627.270.060.582fonB GO:0000062 GO:0000166 GO:0003995 GO:0003997 GO:0005777 GO:0006631 GO:0006635 GO:0008152 GO:0009055 GO:0016627 GO:0033539 GO:0050660 GO:0052890 GO:0055088 GO:0055114
50.060.2686.540.060.413mpiC GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0019439 GO:0050660 GO:0055114
60.060.3347.150.050.541is2A GO:0000062 GO:0003995 GO:0003997 GO:0005504 GO:0005777 GO:0006091 GO:0006629 GO:0006631 GO:0006635 GO:0006693 GO:0008152 GO:0009055 GO:0016401 GO:0016491 GO:0016627 GO:0019395 GO:0033539 GO:0033540 GO:0050660 GO:0052890 GO:0055088 GO:0055114
70.060.3287.010.040.513owaC GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
80.060.2637.000.070.435jscA GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
90.060.2646.350.060.401ivhA GO:0000062 GO:0003995 GO:0005739 GO:0005759 GO:0006552 GO:0008152 GO:0008470 GO:0009055 GO:0009083 GO:0016491 GO:0016627 GO:0033539 GO:0050660 GO:0052890 GO:0055088 GO:0055114
100.060.2566.510.040.401ukwA GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
110.060.2656.990.050.434hr3A GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
120.060.2576.650.030.403ii9C GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
130.060.2636.960.070.425iduC GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
140.060.2686.610.050.412ix6A GO:0000062 GO:0003995 GO:0003997 GO:0005777 GO:0005829 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0009055 GO:0009514 GO:0009793 GO:0016491 GO:0016627 GO:0033539 GO:0046459 GO:0050660 GO:0052890 GO:0055088 GO:0055114
150.060.2586.680.050.403swoA GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
160.060.2546.710.040.402pg0A GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
170.060.2586.510.060.402ebaA GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
180.060.2566.850.030.413sf6A GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0050662 GO:0000166 GO:0016491 GO:1901681
GO-Score 0.46 0.46 0.46 0.36
Biological Processes GO:0048878 GO:0006635
GO-Score 0.36 0.36
Cellular Component GO:0005777 GO:0009506 GO:0042645 GO:0005730 GO:0005829 GO:0005743
GO-Score 0.12 0.06 0.06 0.06 0.06 0.06

(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.