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I-TASSER results for job id Rv0064

[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
10.04 2 4xk8g CLA Rep, Mult 269,273
20.02 1 1jb0K CLA Rep, Mult 36,41
30.02 1 2y69O HEA Rep, Mult 692,727
40.02 1 2l1lB III Rep, Mult 148,152,166,167,170,171,174,178
50.02 1 2hbvB ZN Rep, Mult 434,439,778
60.02 1 3dc1B AKG Rep, Mult 494,645
70.02 1 2byoA LNL Rep, Mult 320,327
80.02 1 2vglA IHP Rep, Mult 104,136,140,151,155
90.02 1 1w9c0 III Rep, Mult 125,126,129,132,133,136,140,151,154
100.02 1 2bptA III Rep, Mult 135,136,163,165,166,168,169,170,218,219
110.02 1 2b0qA MG Rep, Mult 587,604
120.02 1 1nd4A MG Rep, Mult 642,661
130.02 1 3cknA MN Rep, Mult 604,710
140.02 1 2hykA CA Rep, Mult 417,467,649
150.02 1 3bz1H CLA Rep, Mult 275,278
160.02 1 2vc7D CO Rep, Mult 645,691,710
170.02 1 4gqtA ZN Rep, Mult 693,697
180.02 1 1oekA ZN Rep, Mult 691,710
190.02 1 2z66A UUU Rep, Mult 157,159,187
200.02 1 2xgfA FE2 Rep, Mult 434,439

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
10.0603lxuX0.2749.550.0290.4483.4.14.10123
20.0603h09B0.2828.610.0420.4293.4.21.72NA
30.0602q1fA0.2868.430.0460.4314.2.2.21NA
40.0602zxqA0.2898.750.0610.4473.2.1.97150
50.0601slyA0.2847.070.0410.3894.2.2.-NA
60.0602pffA0.2838.890.0310.4402.3.1.41,2.3.1.86NA
70.0603ffzA0.3249.220.0380.5243.4.24.69NA
80.0602uv8G0.2799.590.0520.4622.3.1.86NA
90.0603ebgA0.2967.890.0370.4243.4.11.-NA
100.0602gtqA0.3007.980.0450.4363.4.11.2NA
110.0602vdcA0.3198.670.0270.4911.4.1.13NA
120.0602ckjA0.2849.200.0460.4551.17.1.4,1.17.3.2NA
130.0602vdcF0.3178.830.0450.4921.4.1.13NA
140.0601bxrA0.2949.470.0550.4796.3.5.5NA
150.0603b9jJ0.1306.280.0170.1681.17.1.4,1.17.3.2NA
160.0601ofdA0.3039.180.0490.4921.4.7.1NA
170.0603b9jI0.0875.590.0290.1071.17.1.4,1.17.3.2NA
180.0603eqlD0.2669.410.0390.4362.7.7.6NA
190.0602r7oA0.2678.630.0330.4062.7.7.48NA

(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
00.200.6135.960.070.783gb8A GO:0000055 GO:0000056 GO:0000122 GO:0000776 GO:0003723 GO:0005215 GO:0005487 GO:0005634 GO:0005635 GO:0005642 GO:0005654 GO:0005730 GO:0005737 GO:0005829 GO:0006611 GO:0006810 GO:0006886 GO:0007062 GO:0008536 GO:0008565 GO:0010824 GO:0015030 GO:0015031 GO:0016020 GO:0016032 GO:0019904 GO:0030529 GO:0031965 GO:0034504 GO:0042176 GO:0042493 GO:0043231 GO:0043488 GO:0046825 GO:0051028 GO:0075733
10.110.6276.230.050.813gjxA GO:0000055 GO:0000056 GO:0000122 GO:0000776 GO:0003723 GO:0005487 GO:0005634 GO:0005642 GO:0005654 GO:0005730 GO:0005737 GO:0006611 GO:0006810 GO:0006886 GO:0008536 GO:0008565 GO:0010824 GO:0015030 GO:0015031 GO:0016020 GO:0019904 GO:0030529 GO:0031965 GO:0034504 GO:0042176 GO:0042493 GO:0043231 GO:0046825 GO:0051028
20.080.6366.150.070.825difC GO:0000055 GO:0000776 GO:0005634 GO:0005737 GO:0005816 GO:0006406 GO:0006611 GO:0006810 GO:0006886 GO:0008536 GO:0008565 GO:0015031 GO:0034501 GO:0048471
30.070.6416.100.070.823wyfC GO:0000055 GO:0000776 GO:0005634 GO:0005737 GO:0005816 GO:0006406 GO:0006611 GO:0006810 GO:0006886 GO:0008536 GO:0008565 GO:0015031 GO:0034501 GO:0048471
40.070.5956.470.060.782x1gF GO:0005737 GO:0006606 GO:0006886 GO:0007270 GO:0008139 GO:0008536 GO:0008565 GO:0031965 GO:0042331 GO:0050804
50.070.5397.160.070.744c0qA GO:0004872 GO:0005634 GO:0005737 GO:0006810 GO:0008139 GO:0008565 GO:0015031 GO:0031965 GO:0035048 GO:0042802 GO:0043231
60.070.5656.090.070.723zjyE GO:0005634 GO:0005737 GO:0006606 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0031965
70.070.5766.100.060.733a6pA GO:0000049 GO:0003723 GO:0003729 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0006611 GO:0006810 GO:0006886 GO:0008536 GO:0008565 GO:0015031 GO:0031047 GO:0035281 GO:0042565 GO:0044822 GO:0070883 GO:0090631 GO:1900370
80.070.5547.090.070.764ol0B GO:0004872 GO:0005634 GO:0005737 GO:0006810 GO:0008139 GO:0008565 GO:0015031 GO:0031965 GO:0035048 GO:0042802 GO:0043231
90.070.5096.610.070.672xwuB GO:0005634 GO:0005737 GO:0006606 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0031965
100.070.5126.550.050.673icqT GO:0000049 GO:0003723 GO:0005525 GO:0005634 GO:0005635 GO:0005643 GO:0005737 GO:0005829 GO:0006409 GO:0006605 GO:0006810 GO:0008033 GO:0008536 GO:0015932 GO:0016363 GO:0071528
110.070.5296.690.060.704bsmA GO:0000055 GO:0000056 GO:0000122 GO:0000776 GO:0003723 GO:0005215 GO:0005487 GO:0005634 GO:0005635 GO:0005642 GO:0005654 GO:0005730 GO:0005737 GO:0005829 GO:0006611 GO:0006810 GO:0006886 GO:0007062 GO:0008536 GO:0008565 GO:0010824 GO:0015030 GO:0015031 GO:0016020 GO:0016032 GO:0019904 GO:0030529 GO:0031965 GO:0034504 GO:0042176 GO:0042493 GO:0043231 GO:0043488 GO:0046825 GO:0051028 GO:0075733
120.070.4656.650.030.611wa5C GO:0005049 GO:0005634 GO:0005635 GO:0005737 GO:0005829 GO:0006606 GO:0006611 GO:0006810 GO:0006886 GO:0007049 GO:0007067 GO:0008536 GO:0015031 GO:0051301
130.070.4337.750.060.611z3hB GO:0005049 GO:0005634 GO:0005635 GO:0005737 GO:0005829 GO:0006606 GO:0006611 GO:0006810 GO:0006886 GO:0007049 GO:0007067 GO:0008536 GO:0015031 GO:0051301
140.060.4196.130.040.531qbkB GO:0000059 GO:0000060 GO:0005634 GO:0005737 GO:0005829 GO:0006607 GO:0006610 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0016032 GO:0031965 GO:0034399 GO:0043488 GO:0044822 GO:0070062 GO:0072372
150.060.3876.670.040.514jlqA GO:0000059 GO:0000060 GO:0005634 GO:0005737 GO:0005829 GO:0006607 GO:0006610 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0016032 GO:0031965 GO:0034399 GO:0043488 GO:0044822 GO:0070062 GO:0072372
160.060.2439.170.040.394qshC GO:0000166 GO:0003677 GO:0003824 GO:0004075 GO:0004736 GO:0005524 GO:0006090 GO:0006094 GO:0009374 GO:0016874 GO:0046872
170.060.2189.850.020.375anbK GO:0000166 GO:0003924 GO:0005525 GO:0005622 GO:0006412 GO:0042254 GO:0042256 GO:0043022
180.060.2128.940.030.334qslA GO:0000166 GO:0003677 GO:0003824 GO:0004075 GO:0004736 GO:0005524 GO:0006090 GO:0006094 GO:0009374 GO:0016874 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0003676 GO:0008565 GO:0008536
GO-Score 0.57 0.42 0.42
Biological Processes GO:0009894 GO:0042221 GO:0030163 GO:0046605 GO:0050658 GO:0033365 GO:0033157 GO:0006357 GO:0051298 GO:0051246 GO:0046822 GO:0045892 GO:1902583 GO:0000819 GO:0046794 GO:0043487 GO:0019058 GO:0006611 GO:0000055
GO-Score 0.57 0.57 0.57 0.57 0.57 0.57 0.57 0.57 0.57 0.57 0.57 0.57 0.39 0.39 0.39 0.39 0.39 0.38 0.38
Cellular Component GO:0042175 GO:1990904 GO:0098589 GO:0016604 GO:0044444 GO:0000776 GO:0031965
GO-Score 0.57 0.57 0.57 0.57 0.39 0.38 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.