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I-TASSER results for job id Rv2307A

[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
10.24 7 1iw7F MG Rep, Mult 57,58,61
20.10 3 5da5A CA Rep, Mult 53,56
30.06 2 4xk8K CLA Rep, Mult 55,62
40.06 2 2zo5A HEC Rep, Mult 17,20,22,26,34,38,39,42,43
50.03 1 3lg1A NA Rep, Mult 40,43,49
60.03 1 2jfsA CAC Rep, Mult 5,6,8,25

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
10.0603e47U0.4913.180.0540.8093.4.25.1NA
20.0601br2A0.4903.320.0540.8253.6.1.32NA
30.0602dknB0.3793.760.0750.7141.1.1.50NA
40.0601uliC0.4913.540.0190.7941.14.12.18NA
50.0602h7fX0.5093.050.0510.8415.99.1.2NA
60.0602dknA0.5013.600.1550.8571.1.1.50NA
70.0602c82B0.4683.470.0500.8411.1.1.26718
80.0601dofA0.5043.960.1190.8894.3.2.2NA
90.0601ezfB0.4952.420.0650.6822.5.1.2154
100.0603focA0.5053.240.0660.8576.1.1.2NA
110.0603bp1D0.5033.430.1300.8411.7.1.1316,18,31
120.0601txoB0.5213.280.1030.8573.1.3.1621
130.0601hqdA0.4193.430.0350.7143.1.1.3NA
140.0603bjxA0.5023.580.0820.9683.8.1.1023
150.0603bvlF0.5062.880.0320.7941.16.3.1NA
160.0602ts1A0.4933.560.0510.7946.1.1.144
170.0603d6nB0.5133.620.0330.9052.1.3.2NA
180.0602lipA0.4153.830.0340.7463.1.1.33,5
190.0601jilA0.4913.400.0850.7946.1.1.1NA

(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
00.070.5432.950.100.873mktA
10.070.5353.120.080.874z3nA GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
20.070.5693.000.080.903vvpA GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
30.070.4403.880.050.865c6nA GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
40.070.4292.960.020.751v4aA GO:0000166 GO:0000287 GO:0000820 GO:0005524 GO:0005829 GO:0008882 GO:0016740 GO:0016779
50.060.5403.180.030.893k7dA GO:0000166 GO:0000287 GO:0000820 GO:0005524 GO:0005829 GO:0008882 GO:0016740 GO:0016779
60.060.3962.670.040.622ejeA GO:0000981 GO:0003677 GO:0003700 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0006351 GO:0006355 GO:0006357 GO:0006366 GO:0006367 GO:0007165 GO:0014886 GO:0016020 GO:0016525 GO:0042995 GO:0043025 GO:0051019 GO:0051481
70.060.3524.360.070.831u3iA GO:0004364 GO:0016740
80.060.4543.580.020.734ffcA GO:0003824 GO:0003867 GO:0008483 GO:0009448 GO:0016740 GO:0030170
90.060.4342.500.040.592i9eB GO:0003824 GO:0004807 GO:0006094 GO:0006096 GO:0006098 GO:0008152 GO:0016853
100.060.4913.160.080.865c6pA GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
110.060.3373.640.040.634wlpB GO:0002020 GO:0003677 GO:0005634 GO:0005654 GO:0006281 GO:0006310 GO:0006351 GO:0006355 GO:0006366 GO:0006954 GO:0006974 GO:0031011
120.060.3104.170.040.712kq2A GO:0003676 GO:0004523 GO:0090502
130.060.5863.030.080.924mlbB GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
140.060.3393.310.040.593a0bE GO:0005506 GO:0009055 GO:0009523 GO:0009539 GO:0009579 GO:0009767 GO:0015979 GO:0016020 GO:0016021 GO:0019684 GO:0020037 GO:0042651 GO:0046872 GO:0055114
150.060.3312.980.020.544x5mB GO:0005886 GO:0006810 GO:0008643 GO:0016020 GO:0016021
160.060.2594.220.100.605a9zAS GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0019843 GO:0030529
170.060.2771.050.030.301h88B GO:0000779 GO:0000790 GO:0000977 GO:0000978 GO:0001077 GO:0001541 GO:0001889 GO:0001892 GO:0002432 GO:0003677 GO:0003682 GO:0003700 GO:0003705 GO:0005634 GO:0005654 GO:0005737 GO:0006351 GO:0006355 GO:0006366 GO:0006953 GO:0006954 GO:0006955 GO:0007613 GO:0008134 GO:0016363 GO:0019900 GO:0030154 GO:0030182 GO:0032496 GO:0032753 GO:0033598 GO:0034976 GO:0035035 GO:0035259 GO:0035711 GO:0036488 GO:0042130 GO:0042742 GO:0042803 GO:0042826 GO:0043524 GO:0043565 GO:0044212 GO:0044389 GO:0045408 GO:0045444 GO:0045600 GO:0045669 GO:0045670 GO:0045892 GO:0045893 GO:0045944 GO:0046982 GO:0050873 GO:0060644 GO:0060850 GO:0070059 GO:0071222 GO:0071230 GO:0071347 GO:0071407 GO:0072574 GO:0097421 GO:1990440
180.060.2703.680.000.514yuuE2 GO:0005506 GO:0009055 GO:0009507 GO:0009523 GO:0009535 GO:0009536 GO:0009539 GO:0009579 GO:0009767 GO:0015979 GO:0016020 GO:0016021 GO:0019684 GO:0020037 GO:0046872 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0090484 GO:0015291
GO-Score 0.37 0.37
Biological Processes GO:0044763 GO:0015893
GO-Score 0.37 0.37
Cellular Component GO:0016021 GO:0005829
GO-Score 0.18 0.07

(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.