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I-TASSER results for job id Rv0900

[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
10.17 49 5e7cH CLA Rep, Mult 7,10,11,14
20.13 37 4xk8g CLA Rep, Mult 4,8
30.08 22 4l6vK CLA Rep, Mult 10,13,14,17,18,20
40.08 23 5sy7A NUC Rep, Mult 2,5,6,9
50.02 5 3v2d2 MG Rep, Mult 15,19
60.01 4 2dr3A ADP Rep, Mult 28,29,30,32,33,37
70.01 3 4il6H CLA Rep, Mult 11,15,18
80.01 4 1jhgA TRP Rep, Mult 8,11,12,40,43,44,47
90.01 2 3rszB GLC Rep, Mult 16,17
100.01 2 3wmoP BCL Rep, Mult 20,21
110.01 4 5hhjB GLY Rep, Mult 38,41
120.01 2 1nm0A SO4 Rep, Mult 33,35,39
130.00 1 2nr9A PA6 Rep, Mult 23,27
140.00 1 1cgpA NUC Rep, Mult 2,4,47

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
10.0602veaA0.5502.720.1630.8402.7.13.3NA
20.0602acxA0.5503.780.0420.9402.7.11.1630
30.0601u22A0.5692.900.0610.9602.1.1.14NA
40.0601szqA0.5762.120.0710.8404.2.1.79NA
50.0601bqbA0.5602.140.0470.7803.4.21.19,3.4.24.29NA
60.0602nq5A0.5702.310.0420.8402.1.1.14NA
70.0602gq3A0.5522.530.0650.9202.3.3.9NA
80.0603hdlA0.5732.480.0220.9001.11.1.-NA
90.0601espA0.4903.620.0850.9003.4.24.288
100.0602gblA0.5482.950.0640.8802.7.11.143
110.0601eb6A0.5612.280.0700.8603.4.24.39NA
120.0603dojA0.5732.640.0850.9201.1.1.79NA
130.0601mj9A0.5492.340.0950.8402.3.1.486,35
140.0601fj3A0.4123.750.1020.8003.4.24.27NA
150.0602gq1A0.4492.450.0480.6803.1.3.11NA
160.0601trlB0.3963.850.1090.9003.4.24.2712,45
170.0603c6gB0.6571.620.0410.8601.14.13.15NA
180.0603l24A0.5662.700.0630.9403.1.8.2,3.4.13.9,3.1.8.1NA
190.0601q57A0.6212.750.0850.9203.6.4.12NA

(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
00.240.4253.310.060.803kw4A GO:0004497 GO:0005506 GO:0005783 GO:0005789 GO:0016020 GO:0016491 GO:0016705 GO:0016712 GO:0020037 GO:0031090 GO:0043231 GO:0046872 GO:0055114 GO:0070330
10.100.5123.070.180.883v8dA GO:0004497 GO:0005506 GO:0005783 GO:0005789 GO:0006629 GO:0006699 GO:0006707 GO:0008123 GO:0008202 GO:0008203 GO:0016020 GO:0016125 GO:0016491 GO:0016705 GO:0020037 GO:0031090 GO:0042632 GO:0043231 GO:0046872 GO:0055114 GO:0070857 GO:0071333 GO:0071397
20.090.4953.520.060.981z11A GO:0004497 GO:0005506 GO:0005783 GO:0005789 GO:0005881 GO:0008202 GO:0008389 GO:0008392 GO:0008395 GO:0009804 GO:0016020 GO:0016491 GO:0016705 GO:0016712 GO:0017144 GO:0019373 GO:0019899 GO:0020037 GO:0031090 GO:0042738 GO:0043231 GO:0046226 GO:0046872 GO:0055114
30.080.6571.620.040.863c6gB GO:0004497 GO:0005506 GO:0005783 GO:0005789 GO:0006766 GO:0008395 GO:0010038 GO:0010164 GO:0010212 GO:0016020 GO:0016491 GO:0016705 GO:0020037 GO:0030343 GO:0031090 GO:0036378 GO:0042359 GO:0043231 GO:0046872 GO:0055114
40.070.4343.470.110.903awmA GO:0005506 GO:0016705 GO:0020037 GO:0046872 GO:0055114
50.070.4142.720.070.763juvA GO:0004497 GO:0005506 GO:0005783 GO:0005789 GO:0005886 GO:0006629 GO:0006694 GO:0006695 GO:0008202 GO:0008203 GO:0008398 GO:0016020 GO:0016021 GO:0016125 GO:0016126 GO:0016491 GO:0016705 GO:0020037 GO:0031090 GO:0033488 GO:0043231 GO:0046872 GO:0055114 GO:0070988
60.070.4153.640.050.721izoA GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
70.070.4432.550.090.764uylA GO:0004497 GO:0005506 GO:0008144 GO:0008168 GO:0016020 GO:0016021 GO:0016491 GO:0016705 GO:0020037 GO:0032259 GO:0035690 GO:0046872 GO:0055114
80.070.4492.030.050.624ck8B GO:0004497 GO:0005506 GO:0006629 GO:0006694 GO:0008202 GO:0008398 GO:0016020 GO:0016021 GO:0016126 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114 GO:0070988
90.070.5582.580.020.965hdiA GO:0004497 GO:0005506 GO:0005618 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
100.070.4173.730.040.901uedA GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0033072 GO:0046872 GO:0055114
110.070.5172.850.090.945ikiB GO:0004497 GO:0005506 GO:0005737 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
120.070.5193.480.020.925d3uA GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
130.070.4533.630.090.863eqmA GO:0002677 GO:0004497 GO:0005506 GO:0005783 GO:0005789 GO:0006694 GO:0006703 GO:0008209 GO:0008395 GO:0009055 GO:0010760 GO:0016020 GO:0016125 GO:0016491 GO:0016705 GO:0016712 GO:0019825 GO:0020037 GO:0046872 GO:0055114 GO:0060736 GO:0070330
140.070.4463.140.070.663ejbH GO:0004497 GO:0005506 GO:0009102 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
150.070.4763.330.020.964tpnA GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
160.070.4333.580.100.822x5lA GO:0004497 GO:0005506 GO:0005886 GO:0006707 GO:0008395 GO:0016491 GO:0016705 GO:0020037 GO:0036199 GO:0044117 GO:0046872 GO:0055114
170.070.4612.180.050.623l4dB GO:0004497 GO:0005506 GO:0008168 GO:0008398 GO:0016491 GO:0016705 GO:0020037 GO:0032259 GO:0046872 GO:0055114 GO:0070988
180.070.4333.370.070.764j14A GO:0004497 GO:0005506 GO:0005783 GO:0005789 GO:0006629 GO:0006699 GO:0006707 GO:0006805 GO:0007399 GO:0008202 GO:0008203 GO:0008395 GO:0016020 GO:0016021 GO:0016125 GO:0016491 GO:0016705 GO:0020037 GO:0031090 GO:0033781 GO:0043231 GO:0046872 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0005506 GO:0020037 GO:0016712
GO-Score 0.46 0.46 0.30
Biological Processes GO:0055114 GO:0006629 GO:1901360
GO-Score 0.46 0.36 0.36
Cellular Component GO:0031090 GO:0005789
GO-Score 0.42 0.42

(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.