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I-TASSER results for job id Rv0263c

[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
10.08 3 1ezmA ZN Rep, Mult 35,39,56
20.08 3 3owaA FAD Rep, Mult 42,45,46,53,56,114,115
30.05 2 2axtA UNK Rep, Mult 45,46
40.05 2 3n87G N87 Rep, Mult 269,272,273
50.04 1 3va7A BTI Rep, Mult 231,237,239,245,252,255,256,257
60.03 1 3ir5A SF4 Rep, Mult 21,23,27,29,30,31,135
70.03 1 3azeD MN Rep, Mult 273,274
80.03 1 1wd4A AHR Rep, Mult 238,239,241,242
90.03 1 1i5aA MN Rep, Mult 39,43
100.03 1 1u8vC FAD Rep, Mult 56,118,120
110.03 1 2z1qB FAD Rep, Mult 206,210,246,272,273,274
120.03 1 4qcvX MG Rep, Mult 14,57,113
130.03 1 3qq7A CO Rep, Mult 176,283

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
10.0601u8vA0.4025.820.0460.6405.3.3.339
20.0601is2A0.4236.190.0450.6931.3.3.6NA
30.0601aomB0.3816.140.0970.6271.7.99.1,1.7.2.195
40.0602r0nA0.3806.050.0370.6171.3.99.758
50.0601ivhA0.3866.160.0300.6301.3.99.10169
60.0602z1qB0.4026.080.0410.6471.3.99.3209
70.0601bucA0.3796.010.0330.6101.3.99.2NA
80.0601vcnA0.3776.160.0850.6176.3.4.2NA
90.0601udyA0.3856.030.0250.6231.3.99.3NA
100.0601ahpA0.3806.340.0360.6472.4.1.1NA
110.0602jifA0.3816.080.0320.6171.3.99.-NA
120.0601siqA0.3786.250.0330.6231.3.99.7NA
130.0601qksB0.3816.150.0970.6271.7.2.1106
140.0602yyjA0.4006.080.0580.6431.14.13.343
150.0601vcmA0.3836.030.0760.6176.3.4.2NA
160.0602qllA0.3637.000.0380.6702.4.1.1NA
170.0603gpbA0.3626.880.0540.6472.4.1.1NA
180.0601rx0A0.3786.030.0490.6001.3.99.-19
190.0601q16A0.4286.370.0550.7201.7.99.4NA

(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
00.790.8792.160.800.963mmlE GO:0004039 GO:0016787 GO:0016829
10.430.8272.280.310.913opfB
20.200.8742.480.270.983va7A GO:0000166 GO:0003824 GO:0004039 GO:0004075 GO:0004847 GO:0005524 GO:0005737 GO:0016874 GO:0043419 GO:0046872
30.060.3466.960.070.641bxrA GO:0000050 GO:0000166 GO:0003824 GO:0004087 GO:0004088 GO:0005524 GO:0005829 GO:0005951 GO:0006221 GO:0006526 GO:0006807 GO:0008652 GO:0016597 GO:0016874 GO:0019856 GO:0044205 GO:0046872
40.060.2727.250.060.514rcnB GO:0003824 GO:0004075 GO:0005524 GO:0016874 GO:0046872
50.060.3146.930.050.582qf7B GO:0000166 GO:0003677 GO:0003824 GO:0004075 GO:0004736 GO:0005524 GO:0006090 GO:0006094 GO:0009374 GO:0016874 GO:0046872
60.060.2607.030.040.493u9sA GO:0003824 GO:0004075 GO:0004485 GO:0005524 GO:0008300 GO:0046872 GO:1905202
70.060.3126.850.010.574qshC GO:0000166 GO:0003677 GO:0003824 GO:0004075 GO:0004736 GO:0005524 GO:0006090 GO:0006094 GO:0009374 GO:0016874 GO:0046872
80.060.3136.970.030.583n6rA GO:0003824 GO:0004075 GO:0004658 GO:0005524 GO:0016874 GO:0019541 GO:0046872
90.060.2746.810.020.492vpqB GO:0003824 GO:0004075 GO:0005524 GO:0016874 GO:0046872
100.060.3026.540.050.523n6rG GO:0003824 GO:0004075 GO:0004658 GO:0005524 GO:0016874 GO:0019541 GO:0046872
110.060.2726.730.040.494rcnA GO:0003824 GO:0004075 GO:0005524 GO:0016874 GO:0046872
120.060.2877.360.030.563u9sI GO:0003824 GO:0004075 GO:0004485 GO:0005524 GO:0008300 GO:0046872 GO:1905202
130.060.2737.040.030.523tw6B GO:0000166 GO:0003677 GO:0003824 GO:0004075 GO:0004736 GO:0005524 GO:0006090 GO:0006094 GO:0009374 GO:0016874 GO:0046872
140.060.3283.190.090.392phcB
150.060.2576.820.030.464qslG GO:0000166 GO:0003677 GO:0003824 GO:0004075 GO:0004736 GO:0005524 GO:0006090 GO:0006094 GO:0009374 GO:0016874 GO:0046872
160.060.3127.030.050.572qf7A GO:0000166 GO:0003677 GO:0003824 GO:0004075 GO:0004736 GO:0005524 GO:0006090 GO:0006094 GO:0009374 GO:0016874 GO:0046872
170.060.2776.810.040.501dv2A GO:0000166 GO:0003824 GO:0003989 GO:0004075 GO:0005524 GO:0005737 GO:0005829 GO:0006629 GO:0006631 GO:0006633 GO:0016874 GO:0045717 GO:0046872 GO:2001295
180.060.3027.060.030.573floA GO:0003677 GO:0003887 GO:0005634 GO:0005635 GO:0005658 GO:0006260 GO:0006270 GO:0006273 GO:0016233 GO:0046982 GO:0071897


Consensus prediction of GO terms
 
Molecular Function GO:0004039 GO:0016829 GO:0032559 GO:0032550 GO:0035639 GO:0043169 GO:0016879
GO-Score 0.83 0.79 0.59 0.59 0.59 0.59 0.50
Biological Processes GO:0019627 GO:0043605 GO:0044282 GO:1901565
GO-Score 0.39 0.39 0.39 0.39
Cellular Component GO:0044424
GO-Score 0.39

(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.