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I-TASSER results for job id Rv0181c

[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
10.49 12 1j1lA FE2 Rep, Mult 60,62,104,106
20.08 2 2vecA CL Rep, Mult 40,41,166,167
30.07 2 3aclA 3F1 Rep, Mult 45,47,49,57,60,62,69,70,76,88,118,119,121
40.03 1 2vecA CL Rep, Mult 214,215
50.03 1 1yll0 III Rep, Mult 68,93,95,122,168,169,170,171,182,183,184,185,234,236
60.03 1 3o14A NIO Rep, Mult 47,49,118,120

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
10.0661uw8A0.6793.230.1110.8164.1.1.2NA
20.0601ey2A0.5674.800.1000.8071.13.11.5NA
30.0602j63A0.4125.470.0210.6724.2.99.18125,164
40.0603bu7B0.6364.540.0990.8891.13.11.4NA
50.0602vhhC0.4125.280.0520.6433.5.1.6144,206
60.0601ua4A0.4165.660.0590.6802.7.1.14724,227
70.0601jn9D0.2875.270.0830.4633.4.19.5,3.5.1.1149
80.0603kzwA0.4134.980.0370.6313.4.11.1109,140
90.0602h0vA0.6104.150.1220.8111.13.11.24NA
100.0601pmiA0.6374.010.0930.8245.3.1.8NA
110.0601xruB0.6543.560.0570.8365.3.1.1778,105,117,122
120.0601ywkA0.6533.520.0550.8245.3.1.17233,235
130.0601ofdA0.4316.090.0370.7461.4.7.1NA
140.0602vdcA0.4485.960.0440.7661.4.1.13NA
150.0603bpsA0.3615.830.0570.6073.4.21.-169
160.0602dgaA0.4115.770.0360.6843.2.1.2169
170.0601h1iB0.6184.270.0890.8361.13.11.24NA
180.0602a8jB0.4145.240.0510.6603.4.25.-NA
190.0602vdcF0.4475.790.0670.7621.4.1.13NA
200.0601qwrA0.6244.170.1100.8205.3.1.8NA

(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
00.550.7662.910.200.893aclA GO:0003712 GO:0005634 GO:0005737 GO:0006351 GO:0006355 GO:0006366 GO:0008127 GO:0016491 GO:0030099 GO:0030224 GO:0046872 GO:0051213 GO:0055114
10.460.7982.310.320.881tq5A GO:0008127 GO:0016491 GO:0046872 GO:0051213 GO:0055114
20.410.8471.790.240.912vecA GO:0005737
30.370.7693.110.230.892p17A GO:0046872
40.360.6723.370.110.822vqaA GO:0030288 GO:0033609 GO:0045735 GO:0046564 GO:0046872
50.290.6933.490.100.853fz3A GO:0045735 GO:0046872
60.160.6264.050.140.832h0vA GO:0008127 GO:0016491 GO:0046872 GO:0051213 GO:0055114
70.150.6953.470.100.853fz3B GO:0045735 GO:0046872
80.110.6913.510.130.853qacA GO:0045735
90.110.6963.370.090.852d5fB GO:0045735
100.110.6903.490.090.851fxzA GO:0045735
110.100.6843.580.100.853c3vA GO:0045735
120.100.6933.640.110.862e9qA GO:0045735 GO:0046872
130.100.6833.850.070.872ea7A GO:0045735 GO:0046872
140.100.6783.250.110.824metA GO:0005737 GO:0016829 GO:0016831 GO:0030288 GO:0033609 GO:0045735 GO:0046564 GO:0046872
150.100.6793.750.070.863smhA GO:0045735
160.100.6943.480.110.863kscB GO:0045735
170.100.6823.660.120.863kglA GO:0045735
180.090.6743.470.090.831uikA GO:0045735
190.090.6803.750.080.862cv6A GO:0045735
200.080.6533.970.080.821phsA GO:0005773 GO:0033095 GO:0045735
210.080.6513.940.090.851rc6A GO:0005737 GO:0006144 GO:0016787 GO:0030145 GO:0046872 GO:0071522


Consensus prediction of GO terms
 
Molecular Function GO:0046872 GO:0008127 GO:0003712 GO:0046564 GO:0045735
GO-Score 0.90 0.75 0.55 0.36 0.36
Biological Processes GO:0055114 GO:0006355 GO:0006366 GO:0030224 GO:0033609
GO-Score 0.75 0.55 0.55 0.55 0.36
Cellular Component GO:0005737 GO:0005634 GO:0030288
GO-Score 0.73 0.55 0.36

(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.