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I-TASSER results for job id Rv0474

[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
10.23 17 4iwrA NUC Rep, Mult 30,36,37,38,48,49,52,56,62
20.07 6 3p4tB FAO Rep, Mult 29,38,68,69,71
30.06 5 3dtuC TRD Rep, Mult 26,66,70,71,74
40.04 3 3s8qB NUC Rep, Mult 45,46,47,48,49,50,59,60,61,62,65
50.02 2 1zzcB TRS Rep, Mult 101,116,133,136,140
60.02 2 1zzcA TRS Rep, Mult 116,133,136,140
70.01 1 1b0nA ZN Rep, Mult 82,85
80.01 1 1y9qA MED Rep, Mult 63,67,102,117,119,130,133,140
90.01 1 2bnoB HG Rep, Mult 103,104,105,117,119
100.01 1 1b0nA ZN Rep, Mult 21,83
110.01 1 1b0nA ZN Rep, Mult 74,107
120.01 1 1b0n0 III Rep, Mult 29,32,74,75,76,79,82,84,85,88,91,92,95,96,97,99,100,105,106,107,109,110,111,113,114,117,118,121
130.01 1 4i8tA NUC Rep, Mult 30,36,37,56

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
10.0603d9dA0.4014.870.0760.6711.7.3.1NA
20.0601ivhA0.5014.800.0660.8431.3.99.10NA
30.0601itzB0.4654.340.0580.7432.2.1.1NA
40.0602nyfA0.4694.770.0550.8294.3.1.551
50.0602pfmA0.4614.790.0720.8074.3.2.2NA
60.0601qleA0.4515.090.0460.7861.9.3.125
70.0601pg3B0.4735.550.0430.9216.2.1.142
80.0601fftA0.4824.930.0450.8501.10.3.-NA
90.0601qw6A0.4734.640.0250.7861.14.13.39NA
100.0602ix6A0.4994.860.0880.8641.3.3.6NA
110.0602rioA0.4664.440.0340.7572.7.11.1NA
120.0602ix6E0.5004.860.0880.8641.3.3.6NA
130.0601itzA0.4644.440.0570.7502.2.1.144
140.0602jifA0.4615.140.0830.8291.3.99.-NA
150.0601t9gC0.4805.060.0860.8361.3.99.378
160.0601d0cA0.4764.550.0850.7861.14.13.39NA
170.0602fenD0.4824.840.0640.8075.5.1.255
180.0601udyA0.4795.140.0860.8501.3.99.3NA
190.0603fbvD0.4614.290.0890.7432.7.11.1,NA

(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
00.330.4731.880.270.523f51A GO:0003677 GO:0043565
10.280.4851.930.250.542b5aA
20.250.5092.950.170.644jqdE GO:0003677 GO:0043565
30.240.4642.440.220.534i6uA GO:0003677 GO:0043565
40.230.5602.090.220.633vk0A GO:0003677 GO:0043565
50.230.6761.360.290.721b0nA GO:0003677 GO:0006351 GO:0006355 GO:0010629 GO:0030435 GO:0043565 GO:0046983
60.220.4631.230.280.491y7yA GO:0003677 GO:0043565
70.180.4733.240.140.643ivpA GO:0003677 GO:0043565
80.180.5163.010.210.664o8bA GO:0003677 GO:0043565
90.140.5203.350.130.695d4z1 GO:0003677 GO:0043565
100.070.5144.860.100.863oibA GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
110.070.5024.790.070.864m9aB GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
120.070.5062.450.170.581y9qA GO:0003677 GO:0003700 GO:0006355 GO:0043565 GO:0046872
130.070.5044.960.060.854w9uB GO:0003995 GO:0004361 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
140.070.5084.650.080.832pg0A GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
150.070.5014.800.070.841ivhA 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
160.070.4954.950.070.863x0yA GO:0003995 GO:0008152 GO:0016627 GO:0050660 GO:0055114
170.070.4805.160.070.863mddA GO:0000062 GO:0001889 GO:0003995 GO:0005739 GO:0005759 GO:0005777 GO:0005978 GO:0006082 GO:0006111 GO:0006629 GO:0006631 GO:0006635 GO:0007507 GO:0008152 GO:0009055 GO:0009409 GO:0009437 GO:0009791 GO:0016491 GO:0016627 GO:0019254 GO:0033539 GO:0042594 GO:0050660 GO:0051791 GO:0052890 GO:0055007 GO:0055088 GO:0055114 GO:0070991
180.070.4524.960.070.793r7kA GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
190.070.4825.160.090.861ukwA GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
200.070.4835.130.070.862d29A GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
210.070.3985.760.050.803pfdC GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0043565
GO-Score 0.70
Biological Processes
GO-Score
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.