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I-TASSER results for job id Rv0028

[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
10.14 7 4wmrA 865 Rep, Mult 7,10,11,16,40,43,44,47,48,56,59,60,63,64,88
20.08 4 3wixC LC3 Rep, Mult 7,10,11,16,44,47,56,59,60,63,64,88
30.06 3 3islB PLP Rep, Mult 72,73
40.05 2 5jreD ADE Rep, Mult 45,90
50.04 2 3fdmC III Rep, Mult 66,68,69,71
60.04 2 1ysgA 4FC Rep, Mult 27,28,50,55,56,59
70.04 2 4ej7B CA Rep, Mult 9,17
80.02 1 3q80A CDM Rep, Mult 9,10,23
90.02 1 3retB PYR Rep, Mult 52,58,95
100.02 1 2id3A CA Rep, Mult 9,66
110.02 1 3bvcA CA Rep, Mult 40,42

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
10.0602vuaA0.3644.850.0340.7033.4.24.6926,65
20.0602zoxA0.5323.970.0860.8713.2.1.2150
30.0602e9lA0.5323.860.0750.8713.2.1.21NA
40.0601qoxM0.5394.320.0730.9313.2.1.2189
50.0601p33B0.5114.150.1180.8911.5.1.33,1.1.1.253NA
60.0603b9jJ0.4603.390.0270.7231.17.1.4,1.17.3.254,65,67
70.0601vjiA0.5274.050.0850.8711.3.1.42NA
80.0601hkiA0.5314.100.0850.8813.2.1.14NA
90.0602q3rA0.5193.670.0760.8221.3.1.42NA
100.0603ii9C0.5433.570.0570.8221.3.99.7NA
110.0601icpA0.5294.020.1060.8711.3.1.4216
120.0602np0A0.5093.170.0310.7333.4.24.69NA
130.0601tr1D0.5334.450.0930.9413.2.1.2169
140.0603gnoA0.5364.390.0810.9413.2.1.21NA
150.0601z0hB0.3544.540.0260.6533.4.24.6962,84
160.0602e3zA0.5454.210.0910.9313.2.1.21NA
170.0602fhbA0.5553.820.0580.8523.2.1.41NA
180.0602hv7A0.5444.000.0500.8815.2.1.824
190.0603btaA0.5613.900.0850.9013.4.24.69NA

(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
00.070.5753.490.040.873vuoA GO:0004222 GO:0005576 GO:0006508 GO:0009405 GO:0050827 GO:0051609
10.070.5773.650.110.934k0eB GO:0005215 GO:0006810 GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655
20.070.5604.080.060.915bqnA GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806
30.070.5093.170.030.732np0A GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806
40.070.4804.140.040.814ni5B GO:0016491 GO:0055114
50.070.3963.980.110.684l0jA GO:0000746 GO:0003677 GO:0003678 GO:0004386 GO:0005524 GO:0016818 GO:0032508
60.060.6083.580.060.924mt1A GO:0005215 GO:0006810 GO:0016020 GO:0016021
70.060.4984.260.070.893d9bA GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
80.060.5204.330.060.933w9iF GO:0005215 GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0016020 GO:0016021 GO:0046677
90.060.5563.500.100.884k0eC GO:0005215 GO:0006810 GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655
100.060.5624.220.060.953nogA GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
110.060.3763.950.040.615en5C GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
120.060.3574.610.020.651texD GO:0016740
130.060.4113.970.060.694i0wD GO:0004252 GO:0006508 GO:0008233 GO:0008236 GO:0016787
140.060.4093.770.040.684r86B GO:0005215 GO:0006810 GO:0016020 GO:0016021
150.060.5464.260.090.974k0eA GO:0005215 GO:0006810 GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655
160.060.4963.610.080.803v0aB GO:0004222 GO:0005576 GO:0006508 GO:0009405 GO:0050827 GO:0051609
170.060.4184.210.060.693ge6A GO:0000166 GO:0016491 GO:0055114
180.060.4193.860.070.672v50D GO:0005215 GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0016020 GO:0016021 GO:0046677


Consensus prediction of GO terms
 
Molecular Function GO:0004175 GO:0008237 GO:0005102
GO-Score 0.37 0.37 0.37
Biological Processes GO:0051581 GO:0051704 GO:0019538
GO-Score 0.37 0.37 0.37
Cellular Component GO:0005576 GO:0016021 GO:0044164 GO:0044156 GO:0044231
GO-Score 0.18 0.18 0.13 0.13 0.13

(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.