[Home] [Server] [About] [Statistics] [Annotation]

I-TASSER results for job id Rv3099c

[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
10.53 6 2nsfA ZN Rep, Mult 56,151,155
20.06 1 3rf3A III Rep, Mult 98,100,106
30.06 1 3cf4A SF4 Rep, Mult 34,35,39,40,41,42,51,54,161

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
10.0601ogyI0.4356.410.0590.7741.7.99.4155
20.0601thgA0.3896.660.0620.7073.1.1.3252
30.0601jqoA0.3906.100.0690.6434.1.1.31NA
40.0601eg7A0.3905.820.0660.6296.3.4.3NA
50.0603ma8A0.3905.930.0500.6362.7.1.40NA
60.0601jqkF0.4405.440.0620.6751.2.99.2NA
70.0601c7sA0.3925.850.0520.6293.2.1.52NA
80.0603l4uA0.3916.800.0420.7213.2.1.20,3.2.1.3NA
90.0602jkpB0.4185.820.0320.6783.2.1.20NA
100.0601aqfE0.3746.480.0530.6642.7.1.40NA
110.0601u2zC0.4146.220.0670.7102.1.1.4329
120.0602nyaA0.4356.080.0450.7241.7.99.4NA
130.0602vrkA0.3896.430.0420.6643.2.1.55174
140.0601kqfA0.4086.250.0430.6891.2.1.2NA
150.0603h6oC0.3596.540.0860.6362.7.1.40NA
160.0602v45A0.3876.380.0380.6851.7.99.4NA
170.0603cskA0.3926.850.0640.7103.4.14.4NA
180.0603ecqB0.4106.260.0640.7003.2.1.97149
190.0602sqcA0.3955.660.0500.6255.4.99.17NA

(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
00.430.7612.310.130.842nsfA GO:0046872
10.070.4805.700.070.744x8bA GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0046872 GO:0052699 GO:0055114
20.070.4126.250.050.705f7sB GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246
30.060.3966.250.070.684kwuA GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246 GO:0046872
40.060.3856.720.060.705djwA GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246
50.060.4546.220.060.774amwA GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0016829 GO:0030246 GO:0047457
60.060.3916.800.040.723l4uA GO:0000023 GO:0003824 GO:0004339 GO:0004553 GO:0004558 GO:0005886 GO:0005975 GO:0005983 GO:0008152 GO:0016020 GO:0016021 GO:0016160 GO:0016324 GO:0016787 GO:0016798 GO:0030246 GO:0032450 GO:0044245 GO:0070062
70.060.4366.440.040.763wemA GO:0000023 GO:0003824 GO:0004553 GO:0004558 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246 GO:0032450
80.060.4276.470.060.745aedA GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246
90.060.3826.510.030.682g3mF GO:0000023 GO:0003824 GO:0004553 GO:0004558 GO:0005737 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246 GO:0032450
100.060.4066.530.020.723nsxA GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246
110.060.3796.920.040.724xpqA GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246
120.060.4406.340.050.762f2hA GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246 GO:0042802 GO:0061634 GO:0080176
130.060.4046.840.060.752xvgA GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246
140.060.4096.490.050.715f7cC GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246
150.060.4116.480.050.715f7cA GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246
160.060.4406.560.060.783tonA GO:0000023 GO:0003824 GO:0004339 GO:0004553 GO:0004558 GO:0005886 GO:0005975 GO:0005983 GO:0008152 GO:0016020 GO:0016021 GO:0016160 GO:0016324 GO:0016787 GO:0016798 GO:0030246 GO:0032450 GO:0044245 GO:0070062
170.060.3766.400.050.664ba0A GO:0003824 GO:0004553 GO:0005975 GO:0016740 GO:0016757 GO:0030246 GO:0033825
180.060.4326.610.060.775dkyA GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246


Consensus prediction of GO terms
 
Molecular Function GO:0046872 GO:0016798
GO-Score 0.50 0.36
Biological Processes GO:0044238
GO-Score 0.31
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.