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I-TASSER results for job id Rv2367c

[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
10.77 18 1slmA ZN Rep, Mult 123,127,133
20.02 1 4khoA CA Rep, Mult 138,141
30.02 1 3ftwA ACT Rep, Mult 68,70,123,124,127

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
10.0603ffzA0.5674.730.0760.8573.4.24.69NA
20.0602etfB0.5264.760.0810.8303.4.24.69NA
30.0603ewjB0.4874.800.0850.7473.4.24.86116,123,127,133
40.0601y7910.5044.260.0690.7423.4.15.5NA
50.0601omjA0.5004.470.0460.7473.4.24.40NA
60.0601aklA0.5014.350.0590.7423.4.24.40116,135
70.0601lmlA0.5294.090.0990.7533.4.24.36NA
80.0601eakD0.4734.350.1050.6813.4.24.2471,127,133
90.0608tlnE0.5014.300.0700.7313.4.24.27116
100.0602imcB0.5294.560.0770.7973.4.24.69NA
110.0601j7mA0.1423.690.0230.1923.4.24.2468
120.0601bqbA0.5113.870.0750.7093.4.21.19,3.4.24.29123
130.0601e1hD0.2365.860.0430.4293.4.24.69NA
140.0601h19A0.5323.670.1130.7423.3.2.6NA
150.0601e1hC0.4084.590.0810.6103.4.24.6923,99,118
160.0601zkxB0.5694.700.0820.8573.4.24.69NA
170.0601t3cA0.5664.780.0820.8633.4.24.69NA
180.0603ebgA0.5394.130.0810.7753.4.11.-NA
190.0601gw6A0.5333.800.1140.7313.3.2.6NA

(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
00.550.7721.420.300.811xm5A GO:0000478 GO:0004222 GO:0004518 GO:0004519 GO:0004521 GO:0005737 GO:0006364 GO:0006412 GO:0006508 GO:0008270 GO:0009408 GO:0016151 GO:0016787 GO:0016892 GO:0030490 GO:0031564 GO:0042254 GO:0042274 GO:0046872
10.440.6942.050.310.771oz9A GO:0004222 GO:0004518 GO:0004519 GO:0004521 GO:0005737 GO:0006364 GO:0006508 GO:0008270 GO:0016787 GO:0042254 GO:0046872 GO:0090305 GO:0090502
20.390.5664.800.110.861yvgA GO:0004222 GO:0005576 GO:0005829 GO:0005886 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016787 GO:0030666 GO:0030669 GO:0046872 GO:0046929 GO:0050827 GO:0051609 GO:0071806
30.340.5604.650.120.851zb7A GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016787 GO:0046872 GO:0050827 GO:0051609 GO:0071806
40.330.5214.650.060.793debA GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033619 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0045955 GO:0046872 GO:0050827 GO:0051609
50.250.5823.570.240.791tviA GO:0004222 GO:0004518 GO:0004519 GO:0004521 GO:0005737 GO:0006364 GO:0006508 GO:0008270 GO:0016787 GO:0042254 GO:0046872 GO:0090305 GO:0090502
60.240.5164.850.080.822np0A 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
70.100.4873.980.210.681xaxA GO:0004222 GO:0004518 GO:0004519 GO:0004521 GO:0005737 GO:0006364 GO:0006508 GO:0008270 GO:0016787 GO:0042254 GO:0046872 GO:0090305 GO:0090502
80.070.3376.000.040.653r4sA GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033619 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0045955 GO:0046872 GO:0050827 GO:0051609
90.070.5694.700.080.861zkxB 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
100.070.5294.560.080.802imcB 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
110.070.5074.670.070.783v0aB GO:0004222 GO:0005576 GO:0006508 GO:0009405 GO:0050827 GO:0051609
120.070.5164.860.070.823v0aA 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
130.070.5154.450.060.763vuoA GO:0004222 GO:0005576 GO:0006508 GO:0009405 GO:0050827 GO:0051609
140.060.5674.730.080.863ffzA 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
150.060.4175.280.050.715bqnA 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
160.060.3525.450.040.634bjpA GO:0008658 GO:0008955 GO:0016020 GO:0016021 GO:0016740 GO:0016757
170.060.3415.630.060.625dfaA GO:0004565 GO:0005975 GO:0006012 GO:0008152 GO:0009341 GO:0016787 GO:0016798 GO:0046872
180.060.3465.830.070.641mjfA GO:0003824 GO:0004766 GO:0005737 GO:0006596 GO:0008295 GO:0010487 GO:0016740 GO:0043918 GO:0043919 GO:0050314


Consensus prediction of GO terms
 
Molecular Function GO:0008270 GO:0004222 GO:0050827 GO:0008320 GO:0016892 GO:0016151
GO-Score 0.93 0.93 0.73 0.60 0.55 0.55
Biological Processes GO:0051609 GO:0009405 GO:0071806 GO:0000478 GO:0031564 GO:0006412 GO:0030490 GO:0009408 GO:0046929 GO:0033619 GO:0045955
GO-Score 0.73 0.73 0.60 0.55 0.55 0.55 0.55 0.55 0.39 0.33 0.33
Cellular Component GO:0005576 GO:0005829 GO:0005886 GO:0030669 GO:0044164 GO:0044231 GO:0044156 GO:0016021
GO-Score 0.73 0.39 0.39 0.39 0.33 0.33 0.33 0.33

(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.