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I-TASSER results for job id Rv2797c

[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
10.04 2 4jbeB CA Rep, Mult 193,197
20.04 2 1ea0A F3S Rep, Mult 283,284,285,286,287,301,304,305
30.04 2 3ev6B RSF Rep, Mult 375,379
40.04 2 1u8eA UUU Rep, Mult 395,401,406,407
50.02 1 4zfzA ZN Rep, Mult 49,52
60.02 1 2vf3A CL Rep, Mult 347,348,505
70.02 1 3tptB MG Rep, Mult 502,524,534
80.02 1 3f9oA ZN Rep, Mult 348,446
90.02 1 4ku8A GLY Rep, Mult 144,148
100.02 1 3zs0C UUU Rep, Mult 422,425
110.02 1 1f8yB 5MD Rep, Mult 422,448
120.02 1 1brrC ARC Rep, Mult 67,89,93
130.02 1 3eufA BAU Rep, Mult 347,348
140.02 1 3cu8B MG Rep, Mult 58,205
150.02 1 5ioeB ZN Rep, Mult 62,66
160.02 1 1swiC BNZ Rep, Mult 19,23
170.02 1 3m9gA ZN Rep, Mult 455,479
180.02 1 2qqwA ZN Rep, Mult 502,504
190.02 1 2bgrA UUU Rep, Mult 266,297,435,439,440
200.02 1 3rcqA ZN Rep, Mult 399,446

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
10.0602nyaA0.3327.640.0390.5411.7.99.4NA
20.0601e5tA0.3467.640.0310.5683.4.21.26NA
30.0602f6dA0.3406.980.0420.5123.2.1.3116,155
40.0602j5wA0.3887.660.0290.6421.16.3.1NA
50.0601bf2A0.3417.660.0430.5503.2.1.68140
60.0602gbcA0.3658.110.0390.6253.4.14.5,3.4.15.5NA
70.0601llwA0.3837.980.0410.6441.4.7.1NA
80.0601h16A0.3627.510.0650.5852.3.1.54NA
90.0601orvA0.3547.810.0650.5893.4.14.5NA
100.0602ecfA0.3367.960.0500.5623.4.14.5NA
110.0603ffzA0.3597.650.0340.5853.4.24.69NA
120.0603ig5A0.3347.960.0360.5526.3.2.2485
130.0601ug9A0.3407.580.0540.5533.2.1.70197
140.0602nyaF0.3367.800.0480.5501.7.99.4426
150.0601dgjA0.3417.470.0510.5411.2.-.-196
160.0603hhsA0.3347.930.0470.5591.14.18.1401
170.0601ayxA0.3416.940.0370.5123.2.1.3NA
180.0602d5lA0.3448.030.0380.5853.4.14.-NA
190.0602cqsA0.3727.250.0410.5752.4.1.20179

(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
00.140.7614.350.060.923eb7A GO:0005102 GO:0006952 GO:0009405 GO:0030435
10.130.7394.420.080.901dlcA GO:0005102 GO:0006952 GO:0009405 GO:0030435
20.120.7265.070.070.932c9kA GO:0005102 GO:0006952 GO:0009405 GO:0030435
30.120.7374.480.050.901ji6A GO:0005102 GO:0006952 GO:0009405 GO:0030435
40.120.7204.610.070.894w8jA GO:0005102 GO:0006952 GO:0009405 GO:0030435
50.120.7244.580.070.901ciyA GO:0005102 GO:0006952 GO:0009405 GO:0030435
60.110.7065.000.070.904moaA GO:0005102 GO:0006952 GO:0009405 GO:0030435
70.090.6655.090.050.861i5pA GO:0005102 GO:0006952 GO:0009405 GO:0030435
80.070.6165.490.060.814d8mA GO:0009405 GO:0030435
90.070.5035.180.070.653x0uA GO:0009405
100.060.2407.140.030.373odpA GO:0005975 GO:0016853 GO:0030246
110.060.2206.480.040.324bvkB GO:0016787
120.060.2117.110.050.334p4oA GO:0003677 GO:0003887 GO:0005634 GO:0006281 GO:0034061 GO:0071897
130.060.1856.160.050.263o38A GO:0004316 GO:0016491 GO:0055114 GO:0102132
140.060.2087.060.050.324k3vB GO:0006810 GO:0007155 GO:0030001 GO:0046872
150.060.2056.780.020.311g6oA GO:0000166 GO:0005524 GO:0005737 GO:0006810 GO:0009405
160.060.1753.450.080.201yo7A GO:0006351 GO:0006355
170.060.1766.530.060.262wacA GO:0003712 GO:0004518 GO:0005811 GO:0005829 GO:0005875 GO:0016442 GO:0016787 GO:0031047 GO:0035194 GO:0090305 GO:1903506
180.060.1735.710.050.241lqsR GO:0004871 GO:0004872 GO:0004920 GO:0005886 GO:0016020 GO:0016021 GO:0019221 GO:0019969 GO:0032496


Consensus prediction of GO terms
 
Molecular Function GO:0005102
GO-Score 0.49
Biological Processes GO:0009405 GO:0006952 GO:0030435
GO-Score 0.49 0.49 0.49
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.