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I-TASSER results for job id Rv0368c

[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
10.45 21 1mhpA MN Rep, Mult 235,237,239,302,330
20.04 2 1djnA SF4 Rep, Mult 305,308,338,339,340,344,345,346
30.02 1 1ps9A SF4 Rep, Mult 267,275,276,278,279,288,290
40.02 1 2bptA III Rep, Mult 308,311,312,315,316,347,351
50.02 1 2z7xB UUU Rep, Mult 234,326,329,355

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
10.0603b9jI0.1535.230.0530.2081.17.1.4,1.17.3.2260
20.0602eabA0.4037.210.0320.6903.2.1.63NA
30.0601h54B0.3977.560.0610.7072.4.1.8NA
40.0601fo4A0.4087.190.0520.6971.17.1.4NA
50.0602ewbA0.3976.470.0710.6233.4.11.1,3.4.11.5235,306
60.0603b9jC0.2997.100.0370.5061.17.3.2,1.17.1.4NA
70.0601kc7A0.4276.980.0580.7202.7.9.1NA
80.0602vz8B0.3946.470.0650.6102.3.1.85NA
90.0601j0mA0.3957.320.0520.6904.2.2.12266
100.0601bf2A0.4056.480.0440.6453.2.1.68NA
110.0601b0pA0.4357.030.0490.7221.2.7.1NA
120.0601vbgA0.4056.830.0630.6672.7.9.1NA
130.0602j5wA0.4376.840.0580.7321.16.3.1NA
140.0603f93A0.4235.610.0960.6103.2.1.-297
150.0602ebsB0.4117.250.0450.7103.2.1.150NA
160.0603c5wA0.2925.790.0810.4323.1.3.16NA
170.0603ebgA0.4057.380.0470.7023.4.11.-NA
180.0601ps9A0.4616.730.0820.7301.3.1.34247,289
190.0602gtqA0.3947.130.0640.6773.4.11.2NA

(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
00.540.8183.170.090.941yvpB GO:0003723 GO:0005737 GO:0030030 GO:0030529 GO:0034336 GO:0046872
10.110.7034.320.100.912nvoA GO:0003723 GO:0005737 GO:0030529 GO:0046872
20.070.4826.480.080.751djnA GO:0003824 GO:0010181 GO:0016491 GO:0046872 GO:0050470 GO:0051536 GO:0051539 GO:0055114
30.070.4786.430.070.743k30A GO:0000166 GO:0003824 GO:0010181 GO:0016491 GO:0046872 GO:0051536 GO:0051539 GO:0055114
40.070.4616.730.080.731ps9A GO:0003824 GO:0003959 GO:0005622 GO:0008670 GO:0010181 GO:0016491 GO:0033543 GO:0046872 GO:0051536 GO:0051539 GO:0055114 GO:0071949
50.060.3526.930.050.585d80B GO:0000166 GO:0000221 GO:0000329 GO:0003677 GO:0004518 GO:0004519 GO:0005524 GO:0005773 GO:0005774 GO:0006314 GO:0006810 GO:0006811 GO:0007035 GO:0012505 GO:0015991 GO:0015992 GO:0016020 GO:0016539 GO:0016787 GO:0016820 GO:0030908 GO:0033178 GO:0044267 GO:0046034 GO:0046961 GO:0090305
60.060.3476.280.070.534d7kF GO:0008168 GO:0008171 GO:0016740 GO:0032259
70.060.3287.260.060.571fohC GO:0004497 GO:0005737 GO:0016491 GO:0018662 GO:0019336 GO:0019439 GO:0055114 GO:0071949
80.060.3277.200.080.555er0A GO:0005623 GO:0016491 GO:0045454 GO:0050660 GO:0055114
90.060.3107.270.050.532cduA GO:0000166 GO:0005623 GO:0016491 GO:0045454 GO:0050660 GO:0055114
100.060.3017.310.060.523oc4A GO:0000166 GO:0005623 GO:0016491 GO:0045454 GO:0050660 GO:0055114
110.060.2967.200.050.504rnxA GO:0003824 GO:0003959 GO:0010181 GO:0016491 GO:0018548 GO:0052690 GO:0055114
120.060.3196.260.100.491q1wA GO:0005623 GO:0016491 GO:0019383 GO:0045454 GO:0050660 GO:0055114
130.060.3066.200.050.473atyA GO:0000166 GO:0003824 GO:0010181 GO:0016491 GO:0055114
140.060.2926.270.040.451z41A GO:0003824 GO:0003959 GO:0005622 GO:0009636 GO:0010181 GO:0016491 GO:0018548 GO:0050661 GO:0052690 GO:0055114
150.060.2756.870.060.452q3oB GO:0003824 GO:0003959 GO:0005777 GO:0006629 GO:0006631 GO:0006633 GO:0009620 GO:0009695 GO:0010181 GO:0010193 GO:0016491 GO:0016629 GO:0031408 GO:0055114
160.060.2696.620.050.433l5aA GO:0003824 GO:0010181 GO:0016491 GO:0055114
170.060.2846.390.060.441gwjA GO:0000166 GO:0003824 GO:0010181 GO:0016491 GO:0055114
180.060.2736.520.040.424jicA GO:0000166 GO:0003824 GO:0010181 GO:0016491 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0046872 GO:0034336 GO:0051536 GO:0048037 GO:0032553
GO-Score 0.67 0.54 0.37 0.37 0.37
Biological Processes GO:0030030 GO:0044710
GO-Score 0.54 0.37
Cellular Component GO:0005737 GO:0030529
GO-Score 0.59 0.59

(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.