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I-TASSER results for job id Rv2473

[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
10.08 4 5dwkA 78N Rep, Mult 139,167,170,171,174,179
20.06 3 4zttF O Rep, Mult 135,138,166,169
30.05 2 2voyK III Rep, Mult 191,195,198,199,206
40.04 2 2agvA PTY Rep, Mult 201,205,208,209
50.04 2 1vfpA CA Rep, Mult 165,166,169,203,204,227
60.02 1 4hfcA BRJ Rep, Mult 191,233,236
70.02 1 3rl3A MN Rep, Mult 174,176
80.02 1 4o6nB MPG Rep, Mult 161,220,224
90.02 1 4fzpB IUM Rep, Mult 165,168,227,231,234
100.02 1 1c8nA CA Rep, Mult 119,166
110.02 1 3divA 5AX Rep, Mult 164,166
120.02 1 2wsc1 CLA Rep, Mult 39,166
130.02 1 2o011 CLA Rep, Mult 155,156
140.02 1 4il9E UNL Rep, Mult 203,210
150.02 1 5e1jA CA Rep, Mult 126,131,176
160.02 1 2eulB ZN Rep, Mult 176,180
170.02 1 1v6cA CA Rep, Mult 205,206,207,208,212,213,215
180.02 1 1cviC UUU Rep, Mult 144,146

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
10.0601fftA0.4735.110.0740.7351.10.3.-NA
20.0601eulA0.4785.940.0580.8323.6.3.8NA
30.0603b8cA0.4245.450.0500.6853.6.3.6NA
40.0602hc8A0.1764.400.0920.2483.6.3.-145
50.0602ix6A0.4345.030.0490.6131.3.3.6NA
60.0601mhsA0.4855.660.0460.8113.6.3.6NA
70.0601t09A0.4325.410.0440.6851.1.1.42NA
80.0601lwdA0.4305.380.0380.6811.1.1.42NA
90.0601xmeA0.4794.960.0860.7271.9.3.1223
100.0603a1cB0.2745.930.0260.4663.6.3.-98
110.0602z1qB0.4345.170.0360.6301.3.99.3NA
120.0603b8eC0.5145.660.0530.8663.6.3.987,147
130.0603czoB0.4026.010.0360.6854.3.1.3NA
140.0601occA0.4765.120.0350.7401.9.3.1NA
150.0602dkiA0.4365.180.0540.6681.14.13.23NA
160.0603ixzA0.4745.550.0640.7733.6.3.10NA
170.0601qd1B0.2836.060.0410.4792.1.2.5,4.3.1.4NA
180.0601fbvA0.4575.500.0150.7236.3.2.19NA
190.0602nyfA0.4314.320.0260.5804.3.1.5206

(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
00.070.5115.310.080.783ayfA GO:0004129 GO:0005506 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0020037 GO:0046872 GO:0055114 GO:1902600
10.070.5014.600.050.744xydA GO:0004129 GO:0005506 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0016491 GO:0016966 GO:0020037 GO:0055114 GO:0070469 GO:1902600
20.070.4905.470.070.783o0rB GO:0004129 GO:0005506 GO:0005886 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0016491 GO:0016966 GO:0019333 GO:0020037 GO:0046872 GO:0055114 GO:0070469 GO:1902600
30.070.4675.550.070.765djqA GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0005887 GO:0006119 GO:0009055 GO:0009060 GO:0015078 GO:0015990 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0016705 GO:0019411 GO:0019646 GO:0019825 GO:0020037 GO:0045154 GO:0045278 GO:0046872 GO:0055114 GO:0070069 GO:0070469 GO:0070470 GO:1902600
40.060.3055.800.050.524ekzA GO:0000302 GO:0003756 GO:0004656 GO:0005178 GO:0005576 GO:0005783 GO:0005788 GO:0005793 GO:0005886 GO:0005925 GO:0006457 GO:0009897 GO:0016020 GO:0016222 GO:0016853 GO:0018401 GO:0019899 GO:0031012 GO:0034663 GO:0034976 GO:0042158 GO:0042470 GO:0044822 GO:0045454 GO:0046598 GO:0046982 GO:0070062 GO:0071456 GO:1902175
50.060.2986.670.050.585cuvA GO:0000287 GO:0004427 GO:0005737 GO:0006796
60.060.3025.700.030.492vcvA GO:0004364 GO:0005737 GO:0005829 GO:0006749 GO:0008152 GO:0016740 GO:0070062 GO:1901687
70.060.2886.420.040.512p5oB GO:0000166 GO:0003676 GO:0003677 GO:0003887 GO:0004518 GO:0004527 GO:0006260 GO:0008408 GO:0016740 GO:0016779 GO:0016787 GO:0039693 GO:0071897 GO:0090305
80.060.2795.810.050.471kgsA GO:0000160 GO:0003677 GO:0005622 GO:0006351 GO:0006355 GO:0046872
90.060.2845.920.020.485ekqD GO:0009279 GO:0016020 GO:0043165 GO:0051205 GO:1990063
100.060.2984.840.030.444q5rA GO:0004364 GO:0016740
110.060.2796.840.020.543e49A GO:0003824 GO:0016740 GO:0019475 GO:0046872
120.060.2893.520.030.364iwbA GO:0044780
130.060.2676.020.060.483gdeA GO:0000166 GO:0003677 GO:0003909 GO:0003910 GO:0005524 GO:0006260 GO:0006281 GO:0006310 GO:0006974 GO:0007049 GO:0016874 GO:0046872 GO:0051103 GO:0051301 GO:0071897
140.060.2245.100.000.343ieyA GO:0000213 GO:0003676 GO:0004518 GO:0006388 GO:0008033 GO:0016829 GO:0090305 GO:0090501 GO:0090502
150.060.2375.390.050.362wgbB GO:0003677 GO:0006351 GO:0006355
160.060.2215.840.070.393ox5A GO:0000139 GO:0004857 GO:0005509 GO:0005615 GO:0005737 GO:0005794 GO:0005856 GO:0005886 GO:0005938 GO:0008139 GO:0014069 GO:0016020 GO:0030054 GO:0042308 GO:0043086 GO:0045202 GO:0045211 GO:0046872 GO:0048306 GO:0048471
170.060.1945.010.010.292o5aA GO:0005737 GO:0006417 GO:0017148 GO:0042256 GO:0090071
180.060.1941.540.040.212w2uA GO:0005524


Consensus prediction of GO terms
 
Molecular Function GO:0046906 GO:0015078 GO:0016676 GO:0046914 GO:0015002
GO-Score 0.47 0.47 0.47 0.47 0.47
Biological Processes GO:0098662 GO:0015992 GO:0045333
GO-Score 0.47 0.47 0.47
Cellular Component GO:0031224 GO:0071944
GO-Score 0.38 0.36

(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.