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I-TASSER results for job id Rv3075c

[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
10.44 45 4l80B OXL Rep, Mult 84,134,136,159,160,161,162,198,224
20.13 12 1pknA MN Rep, Mult 112,136,162
30.12 10 3r4iA CA Rep, Mult 84,136,162
40.06 8 4l80E 1VU Rep, Mult 30,31,38,39,42,57,58,84,161,198,224,226,228
50.03 4 1sgjA OAA Rep, Mult 84,157,198,224,226
60.02 2 1z6kA OAA Rep, Mult 56,84,136
70.01 1 1sgjB MG Rep, Mult 84,136,157
80.01 1 1u5vA ATP Rep, Mult 177
90.01 1 2g50F NA Rep, Mult 113,114,115,117,118
100.01 1 3oyzA UUU Rep, Mult 26,27,28,39,42,43,54,57,58,136,159,160,161,162,198,202,203,224,226,227,228,260,265,267
110.01 1 3oyxA GLV Rep, Mult 267
120.01 1 3n25B PRO Rep, Mult 148,150,153,154,155

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
10.2091tqxA0.5403.460.1320.6455.1.3.1NA
20.1851rpxA0.5373.840.0710.6615.1.3.154,197
30.1793inpA0.5293.530.0960.6355.1.3.154,197
40.1663exrA0.5203.480.0450.6384.1.1.85119
50.1321xi3B0.5103.050.1370.5962.5.1.3198
60.1221xi3A0.5103.060.1140.6032.5.1.3NA
70.1012yw3E0.5042.940.1150.5934.1.2.14NA
80.0951h1yB0.5353.490.1320.6455.1.3.1197,227
90.0851mxsA0.5173.220.0890.6224.1.2.14NA
100.0751h1yA0.5363.490.1230.6455.1.3.154,197
110.0751xbzB0.5393.370.0650.6514.1.1.85NA
120.0713f4wA0.5323.270.0970.6384.1.2.-198,224
130.0682fliC0.5313.360.0900.6355.1.3.1NA
140.0671tqjC0.5263.520.0850.6355.1.3.154,197
150.0671g69B0.5413.420.0930.6552.5.1.3NA
160.0673ct7A0.5203.620.1010.6325.1.3.-54
170.0671nsjA0.4973.350.1140.5995.3.1.24NA
180.0671v5xA0.4833.860.0850.6095.3.1.24NA
190.0662cz5A0.5063.190.1080.6064.1.1.23NA
200.0602g50D0.6754.080.1050.8372.7.1.40NA
210.0603h6oC0.6754.160.1010.8402.7.1.40NA
220.0601rh9A0.5863.870.0600.7493.2.1.78NA
230.0602oykB0.5954.780.0860.8113.2.1.123NA
240.0601jqoA0.5773.620.0490.7174.1.1.31NA
250.0603cuxA0.6452.750.1250.7262.3.3.954,56,84
260.0602bmbA0.5993.910.0680.7562.5.1.15,2.7.6.3,4.1.2.25NA
270.0602qezF0.5804.120.0900.7464.3.1.7179
280.0601pkyA0.6633.660.1080.7852.7.1.40NA
290.0602x0sA0.5783.570.1260.7002.7.9.1118
300.0601b90A0.5954.190.0650.7783.2.1.238
310.0601aqfE0.6744.010.1050.8342.7.1.40NA
320.0602wqdA0.5823.300.0960.6912.7.3.9NA
330.0602osxA0.5984.650.0920.8053.2.1.123219
340.0603ma8A0.6703.910.0970.8182.7.1.4063
350.0601vr6A0.5793.610.1050.7132.5.1.54NA
360.0601dioA0.5914.130.0660.7754.2.1.28197
370.0601wkyA0.5954.560.0550.7913.2.1.78NA
380.0603lrkA0.6074.400.0630.8013.2.1.22202

(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
00.490.7443.040.170.853r4iA GO:0003824 GO:0008815 GO:0016829 GO:0046872
10.470.8271.680.260.884roqA GO:0003824 GO:0016829 GO:0046872 GO:0050083
20.430.6692.210.160.733oyzA GO:0003824 GO:0004474 GO:0005737 GO:0006097 GO:0006099 GO:0016740 GO:0046872
30.410.7542.150.170.823qqwE GO:0003824 GO:0016829 GO:0046872
40.390.6571.900.300.711sgjA GO:0003824 GO:0016829 GO:0046872
50.380.7682.820.260.874l9yC GO:0003824 GO:0016829 GO:0046872 GO:0047777 GO:0050083
60.380.6481.590.290.683qllA GO:0003824 GO:0016829 GO:0046872
70.370.8452.610.220.944l80B GO:0003824 GO:0015977 GO:0016829 GO:0043427 GO:0046872 GO:0047777 GO:0050083
80.340.6472.190.330.701u5hA GO:0000287 GO:0003824 GO:0006107 GO:0016829 GO:0046872
90.330.5602.930.120.652v5jA GO:0003824 GO:0010124 GO:0016829 GO:0016832 GO:0018802 GO:0019439 GO:0046872
100.300.5612.860.130.652vwsA GO:0000287 GO:0003824 GO:0005737 GO:0005975 GO:0006725 GO:0016151 GO:0016829 GO:0016832 GO:0046872
110.290.5603.130.180.651izcA GO:0003824
120.220.5682.890.170.651dxeA GO:0000287 GO:0003824 GO:0005737 GO:0008672 GO:0016829 GO:0016830 GO:0019394 GO:0042838 GO:0046392 GO:0046872
130.200.5692.770.180.654mf4A GO:0003824 GO:0016829 GO:0046872
140.200.5563.140.140.653qz6A GO:0003824 GO:0046872
150.090.6712.440.150.743pugA GO:0003824 GO:0004474 GO:0005737 GO:0006097 GO:0006099 GO:0016740 GO:0046872
160.070.4904.780.080.692a3cA GO:0000272 GO:0004553 GO:0004568 GO:0005576 GO:0005975 GO:0006032 GO:0008152 GO:0016787 GO:0016798
170.070.5443.990.100.694lv4A GO:0003824 GO:0004332 GO:0005576 GO:0005618 GO:0005829 GO:0005886 GO:0005975 GO:0006094 GO:0006096 GO:0008270 GO:0016829 GO:0016832 GO:0046872
180.060.3386.410.050.564f6lA GO:0003824 GO:0008152
190.060.2825.890.040.461wzcB GO:0005737 GO:0016311 GO:0016787 GO:0046872 GO:0050531 GO:0051479
200.060.2876.740.040.504dsgA GO:0000166 GO:0016491 GO:0055114
210.060.2494.820.050.351c41A GO:0000906 GO:0009231 GO:0009349 GO:0016740 GO:1902444


Consensus prediction of GO terms
 
Molecular Function GO:0046872 GO:0008815 GO:0050083 GO:0004474
GO-Score 0.94 0.49 0.47 0.43
Biological Processes GO:0006099 GO:0006097
GO-Score 0.43 0.43
Cellular Component GO:0005737
GO-Score 0.43

(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.