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I-TASSER results for job id Rv0799c

[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
10.88 46 4grcA HEM Rep, Mult 143,145,147,148,149,150,151,152,183,185,202,204,222,223,226,227,228,238,240,255,257,267,270,271,274,286,290,292
20.13 9 4uziA IMD Rep, Mult 149,240,255,257

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
10.0603k92A0.3606.250.0530.5671.4.1.2NA
20.0601llwA0.3845.850.0470.5941.4.7.1NA
30.0601vncA0.3756.480.0520.6241.11.1.1012,159
40.0603ikmD0.3626.110.0490.5702.7.7.7NA
50.0601xjjA0.3715.770.0460.5641.17.4.1242
60.0603cmmC0.3696.040.0420.5886.3.2.19NA
70.0603nn1A0.5493.520.1260.6571.13.11.49134
80.0601peuA0.3815.880.0340.5761.17.4.1226
90.0602pbgA0.3536.360.0540.5823.2.1.85NA
100.0601bxrA0.3576.630.0380.6006.3.5.5NA
110.0601hbmA0.3746.040.0660.5732.8.4.1NA
120.0603d2jA0.3836.210.0510.6211.21.3.3NA
130.0603ig5A0.3516.730.0480.6036.3.2.296,228
140.0603gnoA0.3326.420.0480.5463.2.1.2185,183
150.0602j5nB0.3526.240.0680.5551.5.1.12NA
160.0603gnrA0.3436.540.0620.5583.2.1.21NA
170.0601kwgA0.3556.180.0580.5763.2.1.23NA
180.0601e6vA0.3696.470.0350.5912.8.4.1NA
190.0601t7nA0.3526.500.0320.5912.3.1.777

(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
00.750.8871.450.590.923qnsA GO:0004601 GO:0020037 GO:0046872 GO:0055114 GO:0098869
10.620.9110.790.600.924gu7A GO:0004601 GO:0020037 GO:0046872 GO:0055114 GO:0098869
20.550.8731.550.480.912gvkA GO:0004601 GO:0020037 GO:0055114 GO:0098869
30.520.8621.750.360.912hagA GO:0004601 GO:0006582 GO:0020037 GO:0046872 GO:0055114 GO:0098869
40.490.8471.640.370.895de0B GO:0004601 GO:0006582 GO:0020037 GO:0055114 GO:0098869
50.390.7962.810.210.904gs1B GO:0004601 GO:0020037 GO:0046872 GO:0055114 GO:0098869
60.370.7972.910.220.904gt2A GO:0004601 GO:0005623 GO:0015684 GO:0020037 GO:0033212 GO:0046872 GO:0055114 GO:0098869
70.360.7923.080.210.905fw4A GO:0004096 GO:0004601 GO:0005576 GO:0016491 GO:0020037 GO:0046872 GO:0055114 GO:0098869
80.330.7873.050.200.894grcA GO:0004601 GO:0005623 GO:0015684 GO:0020037 GO:0033212 GO:0046872 GO:0055114 GO:0098869
90.320.7932.960.200.902y4eA GO:0004601 GO:0006974 GO:0015684 GO:0016491 GO:0016675 GO:0020037 GO:0033212 GO:0042597 GO:0046872 GO:0055114 GO:0098869
100.060.2866.950.040.491nfgA GO:0005737 GO:0016787 GO:0016810 GO:0046872
110.060.2936.410.040.492xe1A GO:0006810 GO:0006811 GO:0009279 GO:0015288 GO:0016020 GO:0016021 GO:0046930 GO:0055085
120.060.2896.930.040.514hlnA GO:0004373 GO:0009501 GO:0009507 GO:0016757 GO:0019252
130.060.2956.560.050.493mjmA GO:0004151 GO:0006221 GO:0008270 GO:0016787 GO:0016812 GO:0019856 GO:0044205 GO:0046872
140.060.2756.840.050.485cyyA GO:0005886 GO:0016020 GO:0016021 GO:0016209 GO:0016491 GO:0017004 GO:0055114 GO:0098869
150.060.2476.350.050.414pcgB GO:0005198 GO:0019028
160.060.2505.590.040.381uliD GO:0003824 GO:0006725 GO:0016491 GO:0018687 GO:0019439 GO:0051213 GO:0055114
170.060.2186.650.010.363w2vB GO:0000166 GO:0003723 GO:0005737 GO:0051607
180.060.2205.700.050.344s1oB GO:0000166 GO:0000309 GO:0003824 GO:0004515 GO:0005524 GO:0009058 GO:0009435 GO:0016740 GO:0016779 GO:0019363 GO:0034628 GO:0040007


Consensus prediction of GO terms
 
Molecular Function GO:0020037 GO:0004601 GO:0046872
GO-Score 0.99 0.99 0.95
Biological Processes GO:0055114 GO:0098869 GO:0006582
GO-Score 0.99 0.99 0.75
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.