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I-TASSER results for job id Rv2813

[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
10.68 249 4ly6S 08T Rep, Mult 23,24,25,54,55,56,57,58,59,60,132,133,165,202,206,233,234,237
20.04 11 3glfC BEF Rep, Mult 54,55,58,59,133,234
30.00 1 2qbyB MG Rep, Mult 59,132,165
40.00 2 3glfB QNA Rep, Mult 83,85,86,90,138,142

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
10.2931ixsB0.6383.290.1420.7853.6.4.12234
20.2701njgA0.6483.240.1460.7892.7.7.757,63,133,135,137,167,234
30.2621in5A0.6543.060.1460.7853.6.4.12234
40.0902c9oC0.6893.660.1150.8593.6.1.-234
50.0673glfG0.6663.710.1470.8372.7.7.7NA
60.0602qf7B0.4056.240.0600.6936.4.1.1NA
70.0601xxiA0.5424.340.0720.7412.7.7.7231,235
80.0602epoA0.4385.620.0770.6933.2.1.52132
90.0602c9oA0.6893.690.1120.8633.6.4.12234
100.0601hv8A0.4895.100.0800.7153.6.4.13NA
110.0603kx2B0.4864.440.0990.6563.6.4.13239,242,256
120.0603kw3B0.4455.960.0840.7335.1.1.1178
130.0602hyiI0.4424.980.0680.6413.6.4.1329,59
140.0601nsfA0.6193.670.0900.7813.6.4.658
150.0603e5pB0.4455.920.0740.7335.1.1.1171
160.0602epoB0.3955.580.0600.6193.2.1.52132
170.0602w00B0.5154.790.0890.7303.1.21.3NA
180.0603b9pA0.6323.740.1100.8113.6.4.357,59,203
190.0601a5tA0.5513.900.1680.7262.7.7.755,239
200.0601pjrA0.4565.160.0740.6703.6.4.12NA
210.0601w36D0.4304.880.1160.6043.1.11.5137,148
220.0602db3A0.4565.160.0980.6703.6.4.13137,167
230.0603cioA0.4385.180.0710.6522.7.10.230
240.0601xtkA0.4884.830.0570.7003.6.4.13NA

(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
00.430.8642.290.150.961fnnA GO:0000166 GO:0005524 GO:0006260 GO:0051301
10.390.8951.570.150.952qbyA GO:0000166 GO:0003677 GO:0005524 GO:0006260
20.380.8672.200.150.962v1uA GO:0000166 GO:0003677 GO:0005524 GO:0006260
30.370.8302.450.180.951w5sB GO:0000166 GO:0003677 GO:0005524 GO:0006260
40.360.6603.220.160.803pvsD
50.340.8222.310.140.932qbyB GO:0000166 GO:0003677 GO:0005524 GO:0006260
60.330.7933.520.120.974xgcD GO:0000808 GO:0003677 GO:0003688 GO:0005634 GO:0005664 GO:0006260 GO:0006270
70.310.6423.790.120.811ofhA GO:0000166 GO:0005524 GO:0005737 GO:0006508 GO:0009376 GO:0016887 GO:0043335 GO:0070011
80.290.7163.640.150.904xgcE GO:0000166 GO:0000808 GO:0003677 GO:0005524 GO:0005634 GO:0005664 GO:0006260 GO:0006261 GO:0006270 GO:0006342 GO:0007052 GO:0007076 GO:0046331
90.270.6493.610.100.821g4aE GO:0000166 GO:0005524 GO:0005737 GO:0005829 GO:0006508 GO:0009376 GO:0009408 GO:0016020 GO:0016887 GO:0042802 GO:0043335 GO:0070011
100.240.6393.800.120.823h4mA GO:0000166 GO:0000502 GO:0003924 GO:0005524 GO:0005737 GO:0008540 GO:0010498 GO:0016787 GO:0016887 GO:0017025 GO:0022623 GO:0030163 GO:0030433 GO:0031595 GO:0031597 GO:0036402 GO:0043273 GO:0043335 GO:0045899 GO:1901800
110.240.6513.590.110.821e94E GO:0000166 GO:0005524 GO:0005737 GO:0005829 GO:0006508 GO:0009376 GO:0009408 GO:0016020 GO:0016887 GO:0042802 GO:0043335 GO:0070011
120.240.6353.590.100.801g3iA GO:0000166 GO:0005524 GO:0005737 GO:0006508 GO:0009376 GO:0016887 GO:0043335 GO:0070011
130.210.6993.270.120.872fnaA GO:0000166 GO:0005524
140.200.6353.690.120.813whkA GO:0000166 GO:0000502 GO:0005524 GO:0005634 GO:0005737 GO:0006511 GO:0008540 GO:0010498 GO:0016787 GO:0016887 GO:0017025 GO:0022623 GO:0030163 GO:0030433 GO:0031595 GO:0031597 GO:0036402 GO:0043335 GO:0045899 GO:0070682 GO:1901800
150.180.6373.860.100.811l8qA GO:0000166 GO:0003677 GO:0003688 GO:0005524 GO:0005737 GO:0006260 GO:0006270 GO:0006275 GO:0043565
160.170.6303.840.100.825a5bI GO:0000166 GO:0000502 GO:0005524 GO:0005634 GO:0005737 GO:0006511 GO:0008540 GO:0016787 GO:0016887 GO:0017025 GO:0030163 GO:0030433 GO:0031503 GO:0031595 GO:0031597 GO:0036402 GO:0043171 GO:0045732 GO:0045899 GO:0070651 GO:0070682 GO:1901800
170.170.6053.480.150.764xgcA GO:0000166 GO:0003677 GO:0003682 GO:0005524 GO:0005634 GO:0005664 GO:0006260 GO:0006261 GO:0006270 GO:0006277 GO:0006342 GO:0008283 GO:0019233 GO:0022008 GO:0042023
180.150.6283.690.120.813jcpH GO:0000166 GO:0000502 GO:0005524 GO:0005634 GO:0005737 GO:0006511 GO:0008540 GO:0016787 GO:0016887 GO:0017025 GO:0030163 GO:0030433 GO:0031595 GO:0031597 GO:0036402 GO:0045732 GO:0045899 GO:0070682 GO:1901800
190.140.6143.980.100.814d80F GO:0005524
200.120.6114.040.120.815a5bL GO:0000166 GO:0000502 GO:0005524 GO:0005634 GO:0005737 GO:0006289 GO:0008540 GO:0016787 GO:0016887 GO:0017025 GO:0019904 GO:0030163 GO:0030433 GO:0031595 GO:0031597 GO:0032968 GO:0036402 GO:0045899 GO:0070682 GO:1901800
210.100.6203.930.140.815a5bM GO:0000166 GO:0000502 GO:0005524 GO:0005634 GO:0005737 GO:0006511 GO:0008540 GO:0016787 GO:0016887 GO:0017025 GO:0030163 GO:0030433 GO:0031595 GO:0031597 GO:0036402 GO:0045899 GO:0070682 GO:1901800


Consensus prediction of GO terms
 
Molecular Function GO:0005524 GO:0003677
GO-Score 0.86 0.76
Biological Processes GO:0006260 GO:0051301
GO-Score 0.86 0.43
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.