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I-TASSER results for job id Rv2598

[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 10 1froA ZN Rep, Mult 85,140
20.08 4 1f9z0 III Rep, Mult 2,3,4,5,6,7,41,44,77,84,85,86,87,88,89,137,140,142,144
30.04 2 1w8qA CO Rep, Mult 48,51,52
40.02 1 1lkdA BP6 Rep, Mult 80,84,135,136,138
50.02 1 2ehzA MCT Rep, Mult 6,7,8,32,45,46,48
60.02 1 3rpeA FAD Rep, Mult 128,147
70.02 1 3dfmA ZN Rep, Mult 80,94
80.02 1 3rykA TYD Rep, Mult 60,62
90.02 1 2ehzA MCT Rep, Mult 7,52,54,55,83
100.02 1 2vrsA ZN Rep, Mult 145,147
110.02 1 3fd3A CA Rep, Mult 98,116
120.02 1 1kllA MC Rep, Mult 3,32,46,71

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
10.1951fa7B0.5413.010.1400.6834.4.1.56,18,134,136
20.1321npbA0.5263.300.1400.6832.5.1.187,17,19,134
30.0671f9zA0.5533.010.1400.6834.4.1.5NA
40.0662c21A0.5333.460.1180.6894.1.1.-NA
50.0601lqoB0.5323.020.1710.6772.5.1.183,7,16,134,136
60.0603c66A0.4264.510.0920.6162.7.7.19NA
70.0601a5lC0.3315.530.0380.6223.5.1.5NA
80.0601a5kC0.4165.000.0850.6953.5.1.5NA
90.0603kzuA0.4205.400.0650.7742.3.1.41NA
100.0601vj7A0.4134.200.0560.6042.7.6.5,3.1.7.2106
110.0602d3aA0.4285.540.0660.7386.3.1.2NA
120.0601mpyA0.5893.610.1220.7561.13.11.2NA
130.0602fiqC0.4305.290.0940.7622.7.1.144108
140.0601q78A0.4154.050.0470.5852.7.7.19NA
150.0601lqkA0.5333.040.1710.6772.5.1.18NA
160.0601k3iA0.4215.360.0330.7871.1.3.9NA
170.0601kraC0.4185.130.0700.7073.5.1.5NA
180.0601zg7A0.3665.190.0670.6523.4.17.2NA
190.0601cjxA0.5344.190.0970.7871.13.11.27NA
200.0601r3nA0.4204.880.0490.7013.5.1.6NA
210.0601f1uA0.5833.520.1210.7681.13.11.15NA
220.0603lm4D0.5793.570.0780.7501.13.11.243,45
230.0601ie7C0.4205.060.0630.7013.5.1.5NA

(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
00.230.5533.010.140.681f9zA GO:0004462 GO:0005829 GO:0016151 GO:0016829 GO:0019243 GO:0046872
10.210.5692.810.160.703kolA GO:0004462 GO:0046872 GO:0051213 GO:0055114
20.200.5272.640.130.643g12B GO:0016829
30.170.5983.400.110.772ehzA GO:0003824 GO:0006725 GO:0008198 GO:0016491 GO:0016702 GO:0019439 GO:0046872 GO:0051213 GO:0055114 GO:1901170
40.150.5512.950.120.703ct8A GO:0046872
50.140.5203.310.110.683ey7A GO:0003824 GO:0051213 GO:0055114
60.110.5992.670.070.732rbbA GO:0051213 GO:0055114
70.100.5103.260.100.673hnqA GO:0009405
80.100.5213.200.110.684hc5D GO:0051213 GO:0055114
90.070.5662.720.100.704qb5D GO:0051213 GO:0055114
100.070.5953.470.120.772wl9A GO:0003824 GO:0005506 GO:0006725 GO:0008198 GO:0016491 GO:0019439 GO:0042178 GO:0046872 GO:0051213 GO:0055114
110.070.5873.560.090.763hpvA GO:0003824 GO:0006725 GO:0008198 GO:0016491 GO:0018577 GO:0019439 GO:0046872 GO:0051213 GO:0055114
120.070.5853.800.130.782zi8A GO:0003824 GO:0005506 GO:0006629 GO:0006707 GO:0006725 GO:0008198 GO:0008202 GO:0008203 GO:0009405 GO:0016042 GO:0016491 GO:0019439 GO:0046872 GO:0047071 GO:0051213 GO:0055114 GO:0070723
130.070.5893.610.120.761mpyA GO:0003824 GO:0006725 GO:0008198 GO:0016491 GO:0018577 GO:0019439 GO:0042203 GO:0046872 GO:0051213 GO:0055114
140.070.5582.880.100.694z04A GO:0046872 GO:0051213 GO:0055114
150.070.5893.470.120.764ghcC GO:0046872 GO:0051213 GO:0055114
160.070.5853.310.080.741eilA GO:0003824 GO:0005506 GO:0006725 GO:0008198 GO:0016491 GO:0018583 GO:0019439 GO:0042178 GO:0046872 GO:0051213 GO:0055114
170.070.5833.520.120.771f1uA GO:0046872 GO:0051213 GO:0055114
180.070.5843.640.080.761kmyA GO:0003824 GO:0005506 GO:0006725 GO:0008198 GO:0016491 GO:0018583 GO:0019439 GO:0042178 GO:0046872 GO:0051213 GO:0055114
190.070.5533.380.070.732rk0A GO:0051213 GO:0055114
200.070.5783.370.070.753vb0A GO:0003824 GO:0006725 GO:0008198 GO:0016491 GO:0019439 GO:0046872 GO:0051213 GO:0055114
210.070.5903.480.090.763lm4D GO:0016491 GO:0018577 GO:0046872 GO:0051213 GO:0055114
220.070.5833.400.090.763b59A GO:0046872 GO:0051213 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0004462 GO:0051213 GO:0005506 GO:0016701
GO-Score 0.39 0.34 0.33 0.33
Biological Processes GO:0061727 GO:0055114 GO:1901361 GO:0019439 GO:0018931
GO-Score 0.46 0.34 0.33 0.33 0.33
Cellular Component GO:0044444
GO-Score 0.46

(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.