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I-TASSER results for job id Rv3395A

[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
10.16 7 2e7iB SO4 Rep, Mult 53,54,55,200,202
20.05 2 4eyeA IOD Rep, Mult 54,198,199,200
30.02 1 3bk0B CNU Rep, Mult 44,46
40.02 1 1yt3A ZN Rep, Mult 121,179
50.02 1 3n12A ZN Rep, Mult 79,129
60.02 1 1y9aC MG Rep, Mult 67,131
70.02 1 2cl5B BIE Rep, Mult 15,16,19,53,86
80.02 1 3fytC XYP Rep, Mult 205,206
90.02 1 3hl2A PLR Rep, Mult 53,54,55,75,79,82,83,175,176,203
100.02 1 2vk6A MG Rep, Mult 139,194
110.02 1 4ej7B CA Rep, Mult 139,140,205
120.02 1 3u7eB MG Rep, Mult 44,152
130.02 1 1yrhC FMN Rep, Mult 147,169
140.02 1 1nuiA MG Rep, Mult 89,193
150.02 1 2xecB CA Rep, Mult 89,115

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
10.0663e05B0.5633.840.1010.7502.1.1.132NA
20.0661f38A0.5553.270.1130.7022.1.1.-NA
30.0661jg3B0.5894.050.1010.8122.1.1.77136,200
40.0661i1nA0.5704.210.1170.7982.1.1.77NA
50.0663hnrA0.5073.800.0610.6972.1.1.-NA
60.0663bwmA0.5624.100.0770.7842.1.1.6NA
70.0661nt2A0.5324.080.0490.7552.1.1.-NA
80.0602et6A0.5514.180.0350.7881.1.1.-NA
90.0603bt7B0.5743.730.0620.7792.1.1.35NA
100.0602w37A0.5624.820.0800.8652.1.3.324
110.0603grzB0.5533.920.0910.7742.1.1.-NA
120.0601duvG0.5584.670.0960.8462.1.3.3NA
130.0601acmA0.5554.630.0620.8372.1.3.211
140.0601at1A0.5624.560.0520.8272.1.3.2NA
150.0601ml4A0.5594.710.0560.8462.1.3.236
160.0602pbfA0.5704.160.0850.7982.1.1.77NA
170.0603duwA0.5514.170.0880.7842.1.1.-132
180.0602yxeA0.5834.090.0970.8032.1.1.77NA
190.0602cl5A0.5634.050.0720.7842.1.1.6NA
200.0602b9eA0.5673.790.0870.7742.1.1.-NA
210.0601r18A0.5654.390.0840.8082.1.1.77NA
220.0601jg1A0.5914.090.1010.8122.1.1.77NA
230.0601u7hA0.5803.930.0750.8034.3.1.12NA
240.0603e05D0.5623.690.1030.7402.1.1.13254
250.0602be7A0.5574.680.0460.8412.1.3.2NA
260.0602vs1A0.5633.480.1020.7452.1.1.-NA

(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
00.210.5914.090.100.811jg1A GO:0004719 GO:0005737 GO:0006464 GO:0006479 GO:0008168 GO:0016740 GO:0030091 GO:0032259
10.190.5604.180.080.793cjtA GO:0005737 GO:0006479 GO:0008168 GO:0008276 GO:0016740 GO:0032259
20.080.6043.990.090.843g8bB GO:0005737 GO:0006364 GO:0008168 GO:0008649 GO:0016740 GO:0031167 GO:0032259 GO:0070043 GO:0070476
30.080.5233.440.090.684iscA GO:0008168 GO:0008757 GO:0009312 GO:0009877 GO:0016740 GO:0032259
40.070.6224.300.080.914fzvA GO:0003723 GO:0005739 GO:0005762 GO:0006364 GO:0008168 GO:0016740 GO:0019843 GO:0031167 GO:0032259 GO:0042254 GO:0042256 GO:0070131 GO:0070181
50.070.5814.010.070.811xdzA GO:0005737 GO:0006364 GO:0008168 GO:0008649 GO:0016740 GO:0031167 GO:0032259 GO:0070043 GO:0070476
60.070.5734.180.100.804o29A GO:0004719 GO:0005737 GO:0006464 GO:0006479 GO:0008168 GO:0016740 GO:0030091 GO:0032259
70.070.5704.160.090.802pbfA GO:0004719 GO:0006464 GO:0006479 GO:0008168 GO:0016740 GO:0030091 GO:0032259
80.070.5584.390.080.811sqfA GO:0003723 GO:0005737 GO:0005829 GO:0006355 GO:0006364 GO:0008168 GO:0008649 GO:0009383 GO:0016434 GO:0016740 GO:0031167 GO:0032259 GO:0070475
90.070.5694.170.140.793lbfA GO:0004719 GO:0005737 GO:0006464 GO:0006479 GO:0008168 GO:0016740 GO:0030091 GO:0032259
100.070.5834.090.100.802yxeA GO:0004719 GO:0005737 GO:0006464 GO:0006479 GO:0008168 GO:0016740 GO:0030091 GO:0032259
110.070.5704.210.120.801i1nA GO:0004719 GO:0005737 GO:0005783 GO:0005829 GO:0005913 GO:0006464 GO:0006479 GO:0008168 GO:0016740 GO:0030091 GO:0032259 GO:0070062 GO:0098609 GO:0098641 GO:1903561
120.070.5453.990.090.755c1iB GO:0008033 GO:0008168 GO:0016429 GO:0016740 GO:0030488 GO:0031515 GO:0032259
130.070.5584.040.080.784xucA GO:0000287 GO:0005737 GO:0005739 GO:0005829 GO:0005886 GO:0006584 GO:0007565 GO:0007612 GO:0007614 GO:0008168 GO:0008171 GO:0008210 GO:0009712 GO:0014070 GO:0016020 GO:0016021 GO:0016036 GO:0016206 GO:0016740 GO:0030424 GO:0030425 GO:0032259 GO:0032496 GO:0032502 GO:0035814 GO:0042135 GO:0042417 GO:0042420 GO:0042493 GO:0043197 GO:0044297 GO:0045211 GO:0045963 GO:0046872 GO:0048265 GO:0048609 GO:0048662 GO:0050668 GO:0051930 GO:0070062
140.070.5633.840.100.753e05B GO:0006479 GO:0008152 GO:0008168 GO:0008276 GO:0009236 GO:0016740 GO:0032259
150.070.5793.630.100.772bh2A GO:0003723 GO:0005506 GO:0006364 GO:0006396 GO:0008168 GO:0008173 GO:0016740 GO:0031167 GO:0032259 GO:0046872 GO:0051536 GO:0051539 GO:0070041 GO:0070475
160.070.5454.500.110.823m4xA GO:0003723 GO:0005737 GO:0006364 GO:0008168 GO:0008757 GO:0016740 GO:0032259
170.070.5474.290.070.783m6uB GO:0003723 GO:0005737 GO:0006364 GO:0008168 GO:0016740 GO:0032259
180.070.5624.550.070.843a4tA GO:0003723 GO:0005737 GO:0006364 GO:0008033 GO:0008168 GO:0008757 GO:0016428 GO:0016740 GO:0030488 GO:0032259
190.070.5673.790.090.772b9eA GO:0003723 GO:0005634 GO:0005730 GO:0006364 GO:0008168 GO:0016740 GO:0032259 GO:0044822
200.070.5544.520.090.823m6wA GO:0003723 GO:0005737 GO:0006364 GO:0008168 GO:0016740 GO:0032259
210.070.4953.430.080.663i9fB GO:0008152 GO:0008168 GO:0032259 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0051998 GO:0008757
GO-Score 0.41 0.41
Biological Processes GO:0006479
GO-Score 0.36
Cellular Component GO:0005737
GO-Score 0.41

(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.