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I-TASSER results for job id Rv3401

[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 8 4ktpA BGC Rep, Mult 347,355,360,361,362,488,590,591,625,627
20.19 4 1h54B PO4 Rep, Mult 355,625,626,669
30.03 1 1agmA MAN Rep, Mult 329,330,333,672,673
40.03 1 1dogA NOJ Rep, Mult 34,35,39
50.03 1 4ktrA GOL Rep, Mult 79,181,354,355,356
60.03 1 3c67B GLC Rep, Mult 405,457,460,461,464
70.03 1 3eqaA TRS Rep, Mult 361,362,486
80.03 1 4ktrA GOL Rep, Mult 12,117,302,306
90.03 1 1dogA MAN Rep, Mult 143,297,298,299,300,301

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
10.5531h54B0.9360.920.2800.9442.4.1.8488
20.1032eabA0.7404.610.0900.8743.2.1.63NA
30.0601fo2A0.3175.320.0700.4003.2.1.11358,410
40.0602vdcA0.3288.860.0390.5441.4.1.13NA
50.0601l2aE0.3665.080.0860.4483.2.1.428
60.0602sqcA0.3407.840.0630.5185.4.99.17NA
70.0601fp3A0.3265.100.0660.4015.1.3.8NA
80.0601llwA0.3378.720.0420.5481.4.7.1NA
90.0602qnoA0.3505.190.0780.4313.2.1.4NA
100.0602f6dA0.3764.680.0840.4473.2.1.3NA
110.0601gaiA0.3673.840.0830.4193.2.1.346
120.0601lf6A0.5834.380.0770.6813.2.1.3NA
130.0603ebgA0.3268.610.0350.5323.4.11.-NA
140.0602cqsA0.7004.820.1220.8422.4.1.20NA
150.0601nxcA0.3386.050.0610.4433.2.1.113NA
160.0602g49A0.3249.150.0370.5533.4.24.56NA
170.0601bxrA0.3438.410.0530.5436.3.5.5NA
180.0601ea0A0.3398.710.0350.5531.4.1.13639
190.0602ri9B0.3386.180.0370.4483.2.1.113NA
200.0602pdaA0.3308.360.0370.5231.2.7.1NA
210.0602vdcF0.3408.680.0390.5521.4.1.13NA

(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
00.430.9360.920.280.941h54B GO:0003824 GO:0005975 GO:0030246
10.410.8692.470.280.923wirA GO:0003824 GO:0005975 GO:0016740 GO:0016757 GO:0030246 GO:0033831
20.120.7254.190.100.844ufcB GO:0003824 GO:0004560
30.100.6964.780.120.843qdeA GO:0003824 GO:0005975 GO:0016740 GO:0016757 GO:0030246 GO:0047738
40.060.2325.620.060.293ly8A GO:0000160 GO:0003677 GO:0005622 GO:0005886 GO:0006351 GO:0006355 GO:0016020 GO:0016021 GO:0045893
50.060.1757.940.040.271sk8A GO:0003993 GO:0005576 GO:0016158 GO:0016311 GO:0016787 GO:0016791
60.060.1996.590.060.284e2pA GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
70.060.1916.410.050.264c0aB GO:0005085 GO:0005086 GO:0005634 GO:0005737 GO:0008289 GO:0016020 GO:0030036 GO:0032012 GO:0043547
80.060.1906.850.040.273v3wA GO:0000287 GO:0003824 GO:0008152 GO:0008927 GO:0009063 GO:0016052 GO:0016829 GO:0046872
90.060.1676.770.050.234f9vA GO:0005576 GO:0016603 GO:0016740 GO:0016746 GO:0017186 GO:0046872
100.060.1937.200.030.284hzvA GO:0004308 GO:0005975 GO:0008152 GO:0016020 GO:0016021 GO:0016787 GO:0016798 GO:0019012 GO:0020002 GO:0033644 GO:0046872 GO:0052794 GO:0052795 GO:0052796 GO:0055036
110.060.1796.410.060.244mhnA GO:0016603 GO:0016740 GO:0016746 GO:0046872
120.060.1776.320.040.244wy9A GO:0004871 GO:0007165 GO:0016020 GO:0016021
130.060.1437.190.050.212jfnA GO:0006807 GO:0008152 GO:0008360 GO:0008881 GO:0009252 GO:0016853 GO:0016855 GO:0036361 GO:0071555
140.060.1275.250.060.161ynaA GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0031176 GO:0045493
150.060.1245.060.040.151pvxA GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0031176 GO:0045493
160.060.1034.860.040.124g3kA GO:0000166 GO:0003677 GO:0005524 GO:0006351 GO:0006355 GO:0008134 GO:0043565
170.060.1116.060.060.153gydB GO:0000166
180.060.1275.810.030.171z81A GO:0000413 GO:0003755 GO:0006457 GO:0016853


Consensus prediction of GO terms
 
Molecular Function GO:0030246 GO:0033831
GO-Score 0.70 0.41
Biological Processes GO:0005975
GO-Score 0.70
Cellular Component GO:0005886 GO:0005622 GO:0016021
GO-Score 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.