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I-TASSER results for job id Rv0061c

[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 4 1ykpC DHB Rep, Mult 39,41,44
20.06 3 2aiyB IPH Rep, Mult 8,11
30.06 3 2d2cA CLA Rep, Mult 19,55
40.04 2 1wemA ZN Rep, Mult 43,56,68,84
50.04 2 3cezA ZN Rep, Mult 43,56,84,100
60.04 2 2qfwE ICT Rep, Mult 3,69
70.02 1 4n1aA MG Rep, Mult 9,64
80.02 1 3n3qB NIZ Rep, Mult 4,7
90.02 1 3pmvA 557 Rep, Mult 16,36,37,38,40,52,53
100.02 1 3pe7A CA Rep, Mult 57,59
110.02 1 3wmgA DMU Rep, Mult 14,18
120.02 1 3lsfE PZI Rep, Mult 9,13,14,17
130.02 1 4lh4A MG Rep, Mult 83,84
140.02 1 3tdjA 3TJ Rep, Mult 19,20,21,22
150.02 1 3il1B B5D Rep, Mult 72,96,99,106
160.02 1 4brbA 78N Rep, Mult 7,15,70,73

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
10.0602nn3D0.4484.600.0600.8303.4.22.36NA
20.0603mddA0.4484.220.0450.7501.3.99.352
30.0602uxyA0.4524.510.0460.8123.5.1.4NA
40.0601udyA0.4484.180.0540.7501.3.99.3NA
50.0601emsA0.4504.460.0610.8123.6.1.29NA
60.0601llwA0.4715.080.0550.9111.4.7.1NA
70.0602prmA0.4594.460.0100.8481.3.5.210,64
80.0601ng4B0.3514.840.0290.6881.4.3.1958
90.0603dlaD0.4594.660.0640.8486.3.5.1NA
100.0603cmmC0.4495.090.0670.9206.3.2.1912,44
110.0601u7zC0.4684.110.0820.7864.1.1.36,6.3.2.5NA
120.0601jqiA0.4564.180.0540.7411.3.99.2NA
130.0601peuA0.4664.620.0370.8301.17.4.1NA
140.0602a06C0.4054.560.0280.7141.10.2.2NA
150.0602masA0.4564.940.0450.8663.2.2.1NA
160.0601u7uA0.4254.170.0800.7146.3.2.537
170.0601ofdA0.3934.560.0360.7231.4.7.1NA
180.0601bucB0.4544.500.0580.8121.3.99.2NA
190.0601t34A0.4144.720.0610.7594.6.1.252,76

(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
00.070.4434.450.080.785h8jH GO:0006596 GO:0006807 GO:0016787 GO:0016810 GO:0050126
10.060.4184.550.060.793hkxA GO:0004040 GO:0006807 GO:0016810
20.060.5134.180.060.863n05A GO:0000166 GO:0003952 GO:0005524 GO:0006807 GO:0009435 GO:0016810 GO:0016874
30.060.5184.220.060.884f4hB GO:0000166 GO:0003952 GO:0005524 GO:0006807 GO:0008795 GO:0009435 GO:0016810 GO:0016874
40.060.4304.570.030.805h8iC GO:0006596 GO:0006807 GO:0016787 GO:0016810 GO:0050126
50.060.4584.490.070.811erzA GO:0006807 GO:0016787 GO:0016810 GO:0047417
60.060.3885.160.050.805ahmA GO:0000166 GO:0003824 GO:0003938 GO:0005524 GO:0006164 GO:0006177 GO:0016491 GO:0046872 GO:0055114
70.060.3665.090.010.732ohhA GO:0009055 GO:0010181 GO:0016491 GO:0046872 GO:0055114
80.060.4704.520.040.843seqA GO:0000166 GO:0003952 GO:0005524 GO:0005618 GO:0005737 GO:0005886 GO:0006807 GO:0008795 GO:0009435 GO:0016810 GO:0016874 GO:0040007
90.060.4444.500.050.802vhhC GO:0003837 GO:0006207 GO:0006208 GO:0006807 GO:0016787 GO:0016810
100.060.3414.930.090.625f23A GO:0000166 GO:0003952 GO:0005524 GO:0005737 GO:0008795 GO:0009435 GO:0016874
110.060.3165.610.040.702pzbA GO:0000166 GO:0003952 GO:0005524 GO:0006734 GO:0008795 GO:0009435 GO:0016874 GO:0030436
120.060.4354.300.040.773ilvA GO:0000166 GO:0003952 GO:0005524 GO:0006807 GO:0009435 GO:0016810 GO:0016874
130.060.3115.150.040.603dpiA GO:0000166 GO:0003952 GO:0005524 GO:0008795 GO:0009435 GO:0016874
140.060.3014.500.050.523dpiB GO:0000166 GO:0003952 GO:0005524 GO:0008795 GO:0009435 GO:0016874
150.060.4494.400.030.791j31A GO:0006807 GO:0016810
160.060.3455.120.050.672dplA GO:0000166 GO:0003922 GO:0005524 GO:0006164 GO:0006177 GO:0016462 GO:0016874
170.060.3375.010.040.621ih8B GO:0000166 GO:0003952 GO:0005524 GO:0005737 GO:0008795 GO:0009435 GO:0016874 GO:0030435
180.060.3334.950.020.624q16D GO:0000166 GO:0003952 GO:0005524 GO:0005737 GO:0008795 GO:0009435 GO:0016874


Consensus prediction of GO terms
 
Molecular Function GO:0016787
GO-Score 0.57
Biological Processes GO:0008152
GO-Score 0.38
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.