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I-TASSER results for job id Rv0508

[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
10.26 13 2e7pA GSH Rep, Mult 11,14,16,52,58,59,60,71,72,73
20.08 4 3ug6A ZN Rep, Mult 14,17
30.06 3 2ht9A UUU Rep, Mult 14,15,16,58,59,71,72,73
40.04 2 1aiu0 III Rep, Mult 13,40,41,48,52,55,56,58,59
50.02 1 1qfnA III Rep, Mult 13,14,16,19,23,40,41,45,46,47,48,49,59,60,76,77,80,84
60.02 1 3mszB GSH Rep, Mult 5,7,63,64,65,66
70.02 1 3ic4A MG Rep, Mult 67,68
80.02 1 2g9zA MG Rep, Mult 39,41

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
10.2171qfnA0.5482.800.1820.7631.17.4.15,11,18,26,60,75
20.2061t4yA0.6442.580.1050.8562.7.13.366
30.1191cqgA0.6002.790.1710.8351.8.4.1040
40.1153ctgA0.6042.490.1190.8041.20.4.166
50.0671fo5A0.5242.980.1330.7731.8.1.8NA
60.0671dbyA0.6282.580.1450.8451.8.4.10NA
70.0673c1sA0.6073.000.0950.8251.20.4.1NA
80.0672vm1C0.6353.000.1380.8761.8.1.9NA
90.0671nswA0.6142.740.1690.8451.8.1.9NA
100.0672vlvB0.6152.800.1690.8451.8.1.9NA
110.0671aiuA0.6092.700.1460.8351.8.4.10NA
120.0661uc7A0.5852.940.1310.8561.8.1.8NA
130.0662dj2A0.6192.810.0470.8565.3.4.1NA
140.0661t00A0.6242.760.1310.8561.8.1.8NA
150.0661syrA0.5912.830.1500.8141.8.1.8NA
160.0662hzeA0.5892.700.1410.8141.8.5.156
170.0661wmjA0.5743.370.1460.8561.8.4.8NA
180.0602p31A0.6193.000.1490.8871.11.1.9NA
190.0601uvzA0.6222.560.1930.8451.8.1.8NA
200.0602f8aA0.6262.720.1160.8761.11.1.923,72
210.0602dkiA0.6372.550.0930.8661.14.13.23NA
220.0602pn8A0.6362.830.0420.8971.11.1.1575
230.0602pptA0.6112.750.1330.8561.8.1.8NA
240.0603cmiA0.6302.750.0930.8661.11.1.15NA
250.0602p5rA0.6123.160.0930.8661.11.1.-30
260.0601fohC0.6582.520.1050.8761.14.13.7NA
270.0603a5wB0.6322.940.0830.9071.11.1.1520,61,73,79
280.0601yzxB0.6662.380.0860.8662.5.1.1824
290.0603ed3A0.6143.190.0530.9175.3.4.1NA
300.0601pn0C0.6592.370.1170.8661.14.13.7NA
310.0602rm5A0.6572.610.0800.8971.11.1.972
320.0603idvA0.6083.220.0910.8975.3.4.117,21,39,60
330.0602r37A0.6372.690.0860.8871.11.1.9NA
340.0601v98A0.6462.680.1430.8661.8.1.9NA
350.0602vimA0.6132.720.1830.8351.8.4.8NA
360.0601hyuA0.6082.740.1440.8451.8.1.-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
00.360.7711.690.210.901wjkA GO:0005739 GO:0055114
10.250.6412.850.080.882cq9A GO:0003756 GO:0005634 GO:0005654 GO:0005739 GO:0005759 GO:0006355 GO:0006749 GO:0006915 GO:0007568 GO:0008794 GO:0009055 GO:0009266 GO:0009966 GO:0010033 GO:0015035 GO:0015038 GO:0030154 GO:0030425 GO:0042262 GO:0042542 GO:0043025 GO:0043231 GO:0045454 GO:0046872 GO:0051536 GO:0051537 GO:0051775 GO:0055114 GO:0071451
20.230.6162.570.170.841ti3A GO:0005623 GO:0006662 GO:0015035 GO:0045454 GO:0055114
30.220.5722.440.190.761h75A GO:0005623 GO:0009055 GO:0015035 GO:0045454 GO:0051353 GO:0055114
40.130.7182.460.100.954pwoA GO:0016020 GO:0016021
50.130.6182.620.150.844rqrA GO:0005634 GO:0005737 GO:0005739 GO:0005829 GO:0009055 GO:0015035 GO:0015038 GO:0015949 GO:0045454 GO:0045838 GO:0047485 GO:0055114 GO:0070062 GO:0080058 GO:0097573 GO:2000651
60.120.6822.280.130.904xvwL GO:0005623 GO:0045454
70.110.6712.810.100.934n30A GO:0016853
80.110.6032.750.140.814tr0A GO:0005623 GO:0009055 GO:0015035 GO:0045454 GO:0055114
90.100.6872.480.120.914xvwA GO:0005623 GO:0045454
100.100.7102.400.090.913eu3A GO:0016491 GO:0030420 GO:0055114
110.100.6652.580.110.904gxzA GO:0005623 GO:0015035 GO:0045454 GO:0055114
120.100.6792.620.100.923a3tA GO:0005623 GO:0045454
130.100.6892.620.040.943f4tA GO:0003756 GO:0019153 GO:0055114
140.100.6812.830.130.911a8lA GO:0005623 GO:0009055 GO:0015035 GO:0045454 GO:0055114
150.100.6872.690.110.924k2dA GO:0015035 GO:0042597 GO:0045454 GO:0055114
160.100.6502.810.090.922remC GO:0042597 GO:0045454
170.090.5892.700.140.812hzeA GO:0009055 GO:0015035 GO:0019012 GO:0045454 GO:0055114
180.090.6332.950.120.923h93A GO:0015035 GO:0042597 GO:0045454 GO:0055114
190.090.6702.920.130.911j08A GO:0005623 GO:0009055 GO:0015035 GO:0045454 GO:0055114
200.090.6472.530.140.862h0hB GO:0003756 GO:0015035 GO:0042597 GO:0055114
210.080.6722.440.130.893gykA
220.080.6232.560.090.873gmfA GO:0016020 GO:0016021 GO:0016853


Consensus prediction of GO terms
 
Molecular Function GO:0015035 GO:0016864 GO:0030611 GO:0043169 GO:0051540 GO:0015037 GO:0030614 GO:0009055
GO-Score 0.55 0.50 0.50 0.50 0.50 0.50 0.50 0.42
Biological Processes GO:0055114 GO:0045454 GO:0007165 GO:1903506 GO:0010468 GO:0023051 GO:0044767 GO:0000303 GO:0012501 GO:0006259 GO:0048583 GO:0006790 GO:0006575 GO:0071450 GO:0031668 GO:2000112 GO:0009628 GO:0006351 GO:0006518 GO:0048869 GO:0010646 GO:0018904 GO:0009893 GO:0051341 GO:0043085
GO-Score 0.71 0.55 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.45 0.44 0.44 0.44
Cellular Component GO:0044297 GO:0044429 GO:0043005 GO:0036477 GO:0031981
GO-Score 0.50 0.50 0.50 0.50 0.50

(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.