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I-TASSER results for job id Rv0823c

[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
10.82 48 3atyA FMN Rep, Mult 27,28,29,30,60,89,117,120,162,192,224,225,226,247,248,249,387,388
20.02 2 3b0vD NUC Rep, Mult 30,31,32,60,62,64,72,75,117,120,122,124,127,128,130,199,301,308,312,313,314,316,317,318,321,322,325,326,328
30.01 1 3b0uX NUC Rep, Mult 60,61,62,65,69,70,75,76,117,120,122,124,130,202,203
40.01 1 1eepB SO4 Rep, Mult 29,225,226,248,249
50.01 1 3l5lA BU3 Rep, Mult 238,241,243
60.01 1 1o94B SF4 Rep, Mult 103,105,153,154,155,156,157,158

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
10.1861mzhA0.4663.390.1170.5454.1.2.4162
20.1563f4wA0.4533.290.1410.5274.1.2.-27,225
30.0951n7kA0.4533.380.1280.5304.1.2.4NA
40.0673exrA0.4513.370.1300.5304.1.1.8594
50.0671w0mA0.4503.050.1440.5175.3.1.1NA
60.0661hg3A0.4503.230.1130.5225.3.1.1NA
70.0601gthA0.5583.730.1140.6501.3.1.2120
80.0603kruA0.5663.350.1190.6451.6.99.1NA
90.0602djxA0.5243.620.1230.6221.3.3.1120
100.0601bwlA0.5694.030.1450.6891.6.99.128,225,248
110.0602c8nA0.5294.910.0550.6923.2.1.55NA
120.0602epoA0.5455.390.0470.7693.2.1.52NA
130.0601q45B0.5533.600.1430.6531.3.1.42NA
140.0603bg3A0.5325.100.0740.7176.4.1.1NA
150.0602qf7B0.5235.170.0880.7156.4.1.1NA
160.0602j62A0.5344.840.0330.7023.2.1.52130
170.0603figB0.5375.050.0650.7122.3.3.13133,160
180.0602bs9E0.5485.110.0760.7483.2.1.37NA
190.0602ashA0.5345.070.0730.7282.4.2.29NA
200.0602ashD0.5295.190.0570.7332.4.2.29120,254
210.0601icpA0.5533.570.1540.6501.3.1.42NA
220.0603c61A0.5263.550.1110.6221.3.99.11120
230.0601y5xD0.5084.970.0730.6842.4.2.29NA
240.0602zxqA0.5225.480.0610.7303.2.1.97118,132
250.0601ps9A0.6234.150.1390.7561.3.1.34NA

(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
00.410.6912.760.290.781vhnA GO:0000166 GO:0002943 GO:0003824 GO:0005829 GO:0008033 GO:0016491 GO:0017150 GO:0050660 GO:0055114
10.350.6502.640.240.723w9zA GO:0000049 GO:0002943 GO:0003723 GO:0003824 GO:0005829 GO:0008033 GO:0010181 GO:0016491 GO:0017150 GO:0050660 GO:0055114
20.340.6982.900.260.794bf9A GO:0000049 GO:0002943 GO:0003723 GO:0003824 GO:0005829 GO:0008033 GO:0010181 GO:0016491 GO:0017150 GO:0050660 GO:0055114
30.300.7431.830.270.793b0vC GO:0000049 GO:0000166 GO:0002943 GO:0003723 GO:0003824 GO:0008033 GO:0010181 GO:0016491 GO:0017150 GO:0050660 GO:0055114
40.300.6372.840.190.724xp7A GO:0002943 GO:0003723 GO:0003725 GO:0003824 GO:0004860 GO:0005737 GO:0005739 GO:0005783 GO:0005829 GO:0006469 GO:0008033 GO:0016491 GO:0017150 GO:0050660 GO:0055114 GO:0060548
50.130.4424.260.060.563q45A GO:0000287 GO:0003824 GO:0006518 GO:0008152 GO:0016853 GO:0016854 GO:0046872
60.070.5313.830.150.641ep3A GO:0003824 GO:0004152 GO:0004589 GO:0005737 GO:0006207 GO:0006221 GO:0006222 GO:0016491 GO:0016627 GO:0044205 GO:0055114
70.070.5133.960.120.623oixA GO:0000166 GO:0003824 GO:0004152 GO:0005737 GO:0006207 GO:0006221 GO:0006222 GO:0016491 GO:0016627 GO:0044205 GO:0055114
80.070.4904.590.120.624qj1D GO:0003824 GO:0003938 GO:0005737 GO:0006164 GO:0006177 GO:0016491 GO:0046872 GO:0055114
90.070.4873.640.130.583iivB
100.070.4593.740.110.554tx9A GO:0000105 GO:0000162 GO:0003824 GO:0003949 GO:0004640 GO:0005737 GO:0008152 GO:0008652 GO:0009073 GO:0016853
110.070.4683.690.140.563femA GO:0003824 GO:0004359 GO:0008152 GO:0008615 GO:0009228 GO:0016829 GO:0036381 GO:0042819 GO:0042823 GO:1903600
120.070.4654.420.100.583bo9A GO:0003824 GO:0004318 GO:0016491 GO:0018580 GO:0055114
130.070.4583.630.100.544x9sA GO:0000105 GO:0000162 GO:0003824 GO:0003949 GO:0004640 GO:0005737 GO:0008152 GO:0008652 GO:0009073 GO:0016853
140.070.4673.990.150.572issB GO:0003824 GO:0008152 GO:0016829 GO:0036381 GO:0042819 GO:0042823
150.070.4543.630.100.545dn1A GO:0000105 GO:0000162 GO:0003824 GO:0003949 GO:0004640 GO:0005622 GO:0005737 GO:0008152 GO:0008652 GO:0009073 GO:0016853
160.070.4573.480.120.544axkB GO:0000105 GO:0000162 GO:0003824 GO:0003949 GO:0004640 GO:0005737 GO:0008152 GO:0008652 GO:0016853
170.060.4293.980.120.543vzxB GO:0000287 GO:0002094 GO:0006629 GO:0006650 GO:0008654 GO:0016740 GO:0016765 GO:0046474 GO:0046872
180.060.4293.960.140.524uttA GO:0003824 GO:0005975 GO:0006051 GO:0008152 GO:0016853 GO:0016857 GO:0019262 GO:0047465


Consensus prediction of GO terms
 
Molecular Function GO:0050660 GO:0017150 GO:0010181 GO:0000049 GO:0019210 GO:0019887
GO-Score 0.88 0.88 0.70 0.70 0.59 0.59
Biological Processes GO:0055114 GO:0002943 GO:0010941 GO:0045859 GO:0001933 GO:0033673
GO-Score 0.88 0.88 0.59 0.59 0.59 0.59
Cellular Component GO:0005829 GO:0012505 GO:0043231
GO-Score 0.82 0.59 0.59

(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.