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I-TASSER results for job id Rv2353c

[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
10.10 5 2nzmA ADA Rep, Mult 129,165,189,192,227
20.06 3 5amvA ADA Rep, Mult 127,222,225,289
30.06 3 1af0A CA Rep, Mult 254,255,256,266,267,268,271
40.04 2 2quaA CA Rep, Mult 279,280,281,282,285,297,302,303,306
50.04 2 1af0A CA Rep, Mult 267,268,269,271,277,280,281,284
60.02 1 2z8xA CA Rep, Mult 322,333,335,336
70.02 1 2iq7E UUU Rep, Mult 255,256,257,258,288,289,290
80.02 1 1rmgA MAN Rep, Mult 86,88
90.02 1 5amvA ADA Rep, Mult 159,221,289
100.02 1 2o0vA CA Rep, Mult 133,165,166,169
110.02 1 2o04A ADA Rep, Mult 221,225,289
120.02 1 2nzmA ADA Rep, Mult 76,138,172
130.02 1 3s6lA IOD Rep, Mult 231,232,246
140.02 1 3krgA ADA Rep, Mult 138,172,200
150.02 1 2iq7A UUU Rep, Mult 175,179,208,210,230

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
10.1202qx3A0.7123.180.0910.8194.2.2.2NA
20.1111idjA0.6973.060.1060.7944.2.2.10NA
30.1072pecA0.7073.610.0920.8394.2.2.2NA
40.1051qcxA0.6963.030.0890.7944.2.2.10NA
50.0671xg2A0.5653.580.0500.6783.1.1.11212
60.0661qjvA0.5523.970.0830.6723.1.1.11NA
70.0661nhcA0.5094.450.0750.6583.2.1.15NA
80.0661ib4A0.5254.140.0960.6523.2.1.15NA
90.0661ia5A0.5144.490.0710.6613.2.1.15NA
100.0661rmgA0.5754.050.0510.7263.2.1.-NA
110.0661czfA0.5194.240.1010.6523.2.1.15NA
120.0661hg8A0.5304.420.0800.6813.2.1.15NA
130.0601airA0.7073.620.0920.8394.2.2.2NA
140.0602z8gB0.5434.580.0770.7123.2.1.57NA
150.0601nhcE0.5224.120.1010.6503.2.1.15172,195
160.0601ogoX0.5475.150.0760.7513.2.1.11102,177
170.0601pclA0.9031.850.1000.9634.2.2.2NA
180.0602ntqB0.5464.270.0440.6983.1.1.11192
190.0601kcdA0.5314.400.0600.6783.2.1.15256,288
200.0601k5cA0.5314.460.0560.6813.2.1.15NA
210.0601bn8A0.8622.340.1190.9464.2.2.2NA
220.0601vblA0.8602.420.0920.9494.2.2.2NA
230.0602o1dA0.8602.370.1190.9464.2.2.2150
240.0601ru4A0.6044.210.0650.7774.2.2.2NA
250.0603jurD0.5893.770.0630.7233.2.1.15NA
260.0602iq7A0.5224.180.0970.6523.2.1.15NA
270.0601dboA0.6264.350.1040.7854.2.2.19226
280.0601oocB0.8842.220.0970.9554.2.2.2NA
290.0601ofdA0.4205.060.0830.5881.4.7.1NA
300.0603eqoA0.5764.300.0600.7203.2.1.58NA
310.0601jtaA0.8782.290.0970.9554.2.2.2NA

(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
00.310.8602.420.090.951vblA GO:0000272 GO:0005576 GO:0005975 GO:0016829 GO:0046872
10.250.8602.330.120.945amvA GO:0005576 GO:0016829 GO:0030570 GO:0045490 GO:0046872
20.250.8672.740.100.974hwvA GO:0000272 GO:0005576 GO:0005975 GO:0016829 GO:0046872
30.220.9031.850.100.961pclA GO:0005576 GO:0016829 GO:0030570 GO:0045490 GO:0046872
40.210.6973.060.110.791idjA GO:0000272 GO:0005576 GO:0005975 GO:0016829 GO:0047490 GO:0071555
50.210.8782.290.100.951jtaA GO:0005576 GO:0016829 GO:0030570 GO:0045490 GO:0046872
60.130.7253.100.110.823vmvA GO:0000272 GO:0005576 GO:0005975 GO:0016829
70.120.7273.250.090.843zscA GO:0000272 GO:0005576 GO:0005615 GO:0005975 GO:0016829 GO:0046872 GO:0071555
80.110.7162.810.080.811pxzA GO:0016829 GO:0030570 GO:0045490 GO:0046872
90.110.7123.180.090.822qx3A GO:0000272 GO:0005576 GO:0005975 GO:0016829
100.110.6963.030.090.791qcxA GO:0000272 GO:0005576 GO:0005975 GO:0016829 GO:0047490 GO:0071555
110.110.7073.620.090.841airA GO:0005576 GO:0009405 GO:0016829 GO:0030570 GO:0045490 GO:0046872
120.060.3576.190.070.571cm5A GO:0003824 GO:0005737 GO:0005829 GO:0005975 GO:0006006 GO:0006567 GO:0008152 GO:0008861 GO:0016020 GO:0016740 GO:0016746
130.060.3016.880.030.513hhsA GO:0004497 GO:0004503 GO:0005507 GO:0005576 GO:0006583 GO:0006952 GO:0008152 GO:0016491 GO:0031404 GO:0035008 GO:0042438 GO:0046872 GO:0055114
140.060.2496.020.060.393b7mA GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798
150.060.2446.960.030.421gpjA GO:0006779 GO:0006782 GO:0008883 GO:0016491 GO:0033014 GO:0050661 GO:0055114
160.060.2386.830.040.411xhcA GO:0000166 GO:0005623 GO:0016491 GO:0045454 GO:0050660 GO:0055114
170.060.2366.660.050.403nreA GO:0003824 GO:0005975 GO:0006974 GO:0016853 GO:0030246
180.060.2025.880.020.311iybA GO:0003723 GO:0033897 GO:0090502


Consensus prediction of GO terms
 
Molecular Function GO:0046872 GO:0030570
GO-Score 0.70 0.42
Biological Processes GO:0045229 GO:0071554 GO:0045490
GO-Score 0.43 0.43 0.42
Cellular Component GO:0005576
GO-Score 0.76

(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.