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I-TASSER results for job id Rv1421

[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
10.21 7 1ukyA ADP Rep, Mult 27,28,29,30,31,32,114,118,157,158,159
20.06 2 3r0dA ZN Rep, Mult 196,200
30.06 2 1ko8B 6PG Rep, Mult 26,27,30
40.03 1 1zotA MG Rep, Mult 196,200,295
50.03 1 3qebZ MN Rep, Mult 46,196
60.03 1 1l8tA MG Rep, Mult 26,200
70.03 1 1rc8A CA Rep, Mult 194,196,297
80.03 1 3d1lB MPR Rep, Mult 243,266,267
90.03 1 2bo7J CO Rep, Mult 196,270,271

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
10.0601p7cB0.4624.080.1320.5812.7.1.2127
20.0602ad5B0.4345.430.1050.6446.3.4.232,189,191
30.0602dwoA0.4584.820.0790.6312.7.1.105,3.1.3.46230
40.0601zrhA0.4524.220.0630.5952.8.2.2331,117,138
50.0601g3mA0.4304.640.0430.5882.8.2.4NA
60.0601brwA0.4386.090.0690.7242.4.2.2114
70.0603n2aA0.4305.480.0800.6546.3.2.12,6.3.2.1729,31
80.0602gwhB0.4304.580.0650.5882.8.2.-NA
90.0601djnA0.4295.700.0360.6811.5.8.2,1.5.99.7NA
100.0601m7hC0.4203.390.1500.5082.7.1.2525,29,143
110.0602tmdA0.4315.780.0280.6881.5.8.224,27
120.0601osnA0.4384.120.0880.5512.7.1.21NA
130.0603cklB0.4344.690.0560.5952.8.2.-NA
140.0601z28A0.4354.700.0860.5952.8.2.1NA
150.0601e8cB0.4365.200.0680.6386.3.2.13NA
160.0601bifA0.4544.780.0880.6213.1.3.46,2.7.1.105152
170.0601t8uB0.4574.300.0600.6082.8.2.3031,110
180.0602ad1A0.3894.060.0650.5082.8.2.-NA
190.0602wtzB0.4505.460.0860.6546.3.2.1323

(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
00.190.3962.920.200.462iyvA GO:0000166 GO:0000287 GO:0004765 GO:0005524 GO:0005737 GO:0005829 GO:0008652 GO:0009073 GO:0009423 GO:0016301 GO:0016310 GO:0016740 GO:0019632 GO:0040007 GO:0046872
10.130.4564.000.140.573rdpB GO:0000166 GO:0004797 GO:0005524 GO:0006230 GO:0016301 GO:0016310 GO:0016740 GO:0071897
20.120.4743.880.120.581p6xA GO:0000166 GO:0004797 GO:0005524 GO:0006230 GO:0016301 GO:0016310 GO:0016740 GO:0071897
30.120.4013.540.110.491nksA GO:0000166 GO:0004017 GO:0005524 GO:0005737 GO:0016301 GO:0016310 GO:0016740 GO:0046939
40.120.4384.120.090.551osnA GO:0000166 GO:0004797 GO:0005524 GO:0006230 GO:0016301 GO:0016310 GO:0016740 GO:0071897
50.110.4093.660.130.512a2zB GO:0000166 GO:0004137 GO:0005524 GO:0005634 GO:0005829 GO:0006139 GO:0006220 GO:0008144 GO:0009157 GO:0009165 GO:0016301 GO:0016310 GO:0016740 GO:0019206 GO:0042803 GO:0043097 GO:0043101
60.090.4544.780.090.621bifA GO:0000166 GO:0003824 GO:0003873 GO:0004331 GO:0005524 GO:0006000 GO:0006003 GO:0008152 GO:0016301 GO:0016310 GO:0016311 GO:0016740 GO:0016787 GO:0046835
70.070.4594.120.080.604eecA GO:0008146 GO:0016740 GO:0017000
80.070.4574.810.080.631k6mA GO:0000166 GO:0003824 GO:0003873 GO:0004331 GO:0005524 GO:0005829 GO:0006000 GO:0006003 GO:0006094 GO:0006096 GO:0008152 GO:0016301 GO:0016310 GO:0016311 GO:0016740 GO:0016787 GO:0019900 GO:0031100 GO:0032868 GO:0033133 GO:0033762 GO:0042594 GO:0042802 GO:0043540 GO:0046835 GO:0051384 GO:0051591 GO:0061621 GO:0070095
90.070.4604.740.090.632axnA GO:0000166 GO:0003824 GO:0003873 GO:0004331 GO:0005524 GO:0005654 GO:0005829 GO:0006000 GO:0006003 GO:0007420 GO:0008152 GO:0016301 GO:0016310 GO:0016311 GO:0016740 GO:0016787 GO:0046835 GO:0061621
100.070.4473.950.060.584goxA GO:0003824 GO:0008152 GO:0016740 GO:0031177
110.070.4444.000.060.573nibA GO:0008146
120.060.4594.490.060.614gbmA GO:0003824 GO:0008152 GO:0016740 GO:0031177 GO:0046872
130.060.4404.660.060.603ap2A GO:0000139 GO:0005783 GO:0005794 GO:0006478 GO:0008476 GO:0016020 GO:0016021 GO:0016740 GO:0070062
140.060.4394.350.070.581efhB GO:0004062 GO:0004304 GO:0005737 GO:0005829 GO:0006629 GO:0007586 GO:0008146 GO:0008202 GO:0016042 GO:0016740 GO:0030573 GO:0047704 GO:0050294 GO:0050427 GO:0051923
150.060.4304.690.050.591j99A GO:0004062 GO:0004304 GO:0005737 GO:0005829 GO:0006629 GO:0007586 GO:0008146 GO:0008202 GO:0016042 GO:0016740 GO:0030573 GO:0047704 GO:0050294 GO:0050427 GO:0051923
160.060.4304.580.070.592gwhB GO:0004062 GO:0005737 GO:0005829 GO:0008146 GO:0016740 GO:0050427 GO:0051923
170.060.4174.080.040.543rnlA GO:0016740 GO:0046872
180.060.4063.220.160.493vaaA GO:0000166 GO:0000287 GO:0004765 GO:0005524 GO:0005737 GO:0008652 GO:0009073 GO:0009423 GO:0016301 GO:0016310 GO:0016740 GO:0019632 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0005524 GO:0016773 GO:0046872 GO:0004797
GO-Score 0.52 0.38 0.38 0.33
Biological Processes GO:0016310 GO:0046417 GO:0043650 GO:0009072 GO:0032787 GO:0006520 GO:0071897 GO:0006230
GO-Score 0.52 0.38 0.38 0.38 0.38 0.38 0.33 0.33
Cellular Component GO:0044444
GO-Score 0.38

(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.