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I-TASSER results for job id Rv1498A

[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 1 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
10.61 54 2cz8D FAD Rep, Mult 4,6,35,36,37,38,39,66
20.45 39 2ux9A COA Rep, Mult 29,33,34,35,36,65,66,67,68
30.40 30 2yj0C 420 Rep, Mult 10,12,43,44,46,58,60
40.40 30 2ux9F COA Rep, Mult 7,9,11,29,30,34,65,67
50.09 6 2yj0E 420 Rep, Mult 8,39,62
60.09 14 2vxaA RBF Rep, Mult 46,48,58
70.03 4 2ux9A COA Rep, Mult 7,67
80.01 2 1mogA RBF Rep, Mult 38,39,40
90.00 1 1mogA MG Rep, Mult 17,54

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
10.0601ofdA0.5563.240.0670.8431.4.7.1NA
20.0601ufyA0.5742.700.0760.8145.4.99.5NA
30.0601xrsB0.5382.080.0710.7435.4.3.33NA
40.0601llwA0.5553.180.0670.8431.4.7.1NA
50.0601go3E0.5603.140.0600.9292.7.7.645
60.0601erkA0.5143.080.0980.8002.7.11.24,2.7.1.-NA
70.0602aujD0.5743.610.0620.9002.7.7.67,67
80.0602wb8A0.5423.090.1690.8572.7.11.1NA
90.0601t3tA0.5812.860.0760.8716.3.5.3NA
100.0601novC0.5453.400.0710.8713.4.23.44NA
110.0602iy5B0.6192.560.1130.8866.1.1.2035,42
120.0602pmpA0.5762.740.0830.8434.6.1.1236
130.0603fd5B0.5403.210.0870.9432.7.9.3NA
140.0603cmqA0.5613.400.0920.9296.1.1.20NA
150.0601fmd20.5243.110.1360.9143.4.22.4613
160.0602z01A0.5262.960.0900.8866.3.3.1NA
170.0602v9yA0.5932.690.0920.9296.3.3.1NA
180.0602vd5A0.5362.870.0490.7862.7.11.117
190.0602vdcA0.5343.280.0500.8571.4.1.13NA

(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
00.870.9061.431.001.003oqtA GO:0000166 GO:0005576
10.610.9001.140.520.972cz8D GO:0000166
20.480.9020.770.500.942vxaA GO:0000166
30.340.7662.090.220.943onrA GO:0005618 GO:0005886 GO:0046872
40.320.8011.840.230.901mogA GO:0000166
50.110.5203.240.090.903h0gG GO:0000291 GO:0000932 GO:0003676 GO:0003697 GO:0003723 GO:0003727 GO:0003899 GO:0005634 GO:0005665 GO:0005829 GO:0006351 GO:0006367 GO:0006396 GO:0010590 GO:0016591 GO:0031369 GO:0045948 GO:0060213 GO:0097394
60.100.6662.460.030.934a2bA GO:0000166 GO:0005524 GO:0005886 GO:0007049 GO:0008360 GO:0009898 GO:0016020 GO:0032153 GO:0042802 GO:0043093 GO:0051301
70.090.5513.100.120.944qjfA GO:0003676 GO:0003677 GO:0003899 GO:0006351
80.090.6472.140.130.864hvzA GO:0042597
90.090.4733.500.060.703wt0D GO:0005886 GO:0007049 GO:0008360 GO:0009898 GO:0016020 GO:0032153 GO:0043093 GO:0051301
100.080.6213.290.080.942c35B GO:0000291 GO:0000398 GO:0000932 GO:0003676 GO:0003697 GO:0003723 GO:0003727 GO:0003899 GO:0005634 GO:0005654 GO:0005665 GO:0006283 GO:0006351 GO:0006366 GO:0006367 GO:0006368 GO:0006370 GO:0006915 GO:0008543 GO:0010467 GO:0031047 GO:0031369 GO:0035019 GO:0042795 GO:0045948 GO:0050434 GO:0060213
110.080.6413.130.080.913wqtB GO:0005886 GO:0007049 GO:0008360 GO:0009898 GO:0016020 GO:0032153 GO:0043093 GO:0051301
120.070.6212.760.080.904a3bG GO:0000291 GO:0000932 GO:0001172 GO:0003676 GO:0003697 GO:0003727 GO:0003899 GO:0003968 GO:0005634 GO:0005665 GO:0005737 GO:0006351 GO:0006366 GO:0006367 GO:0031369 GO:0045948 GO:0060213
130.070.5603.140.060.931go3E GO:0000428 GO:0003676 GO:0003677 GO:0003899 GO:0006351 GO:0016740 GO:0016779
140.070.5712.760.090.935fj8G GO:0001056 GO:0003677 GO:0003899 GO:0005634 GO:0005654 GO:0005666 GO:0006351 GO:0006383 GO:0006384 GO:0006385 GO:0006386 GO:0042797
150.070.5563.020.070.943ayhB GO:0000790 GO:0001023 GO:0001056 GO:0003677 GO:0003899 GO:0005634 GO:0005666 GO:0005737 GO:0005829 GO:0006351 GO:0006384
160.070.4983.390.120.913jc8Md GO:0007049
170.070.5012.840.040.801y14B GO:0000291 GO:0000932 GO:0001172 GO:0003676 GO:0003697 GO:0003727 GO:0003899 GO:0003968 GO:0005634 GO:0005665 GO:0005737 GO:0006351 GO:0006366 GO:0006367 GO:0031369 GO:0045948 GO:0060213
180.070.4823.060.060.763offA GO:0005737 GO:0005783 GO:0005788 GO:0006612 GO:0006888 GO:0012505 GO:0016055 GO:0032799 GO:0045177 GO:0048477 GO:0048728


Consensus prediction of GO terms
 
Molecular Function GO:0000166 GO:0046872
GO-Score 0.98 0.34
Biological Processes
GO-Score
Cellular Component GO:0005576 GO:0005618 GO:0005886
GO-Score 0.87 0.34 0.34

(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.