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I-TASSER results for job id Rv2005c

[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 3 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
10.59 22 3cisA ATP Rep, Mult 13,14,15,17,20,41,43,100,116,117,119,120,121,122,123,127,130,131,132,133
20.54 17 3cisA ATP Rep, Mult 165,166,167,172,193,194,195,198,245,261,262,264,265,267,268,272,275,276,277,278
30.04 2 3cisB MG Rep, Mult 198,277
40.01 1 3dloB UNK Rep, Mult 166,167,194,195,262
50.01 1 2cmjB NAP Rep, Mult 132,136,139
60.01 1 3u0bA NA Rep, Mult 179,183,190

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
10.0602qfwD0.4335.640.0810.6681.1.1.42153
20.0601ct9A0.4455.380.0960.6546.3.5.4NA
30.0601xcoD0.4425.870.0930.6922.3.1.8NA
40.0602d4vA0.4355.770.1080.6981.1.1.42NA
50.0602hi1A0.4216.220.1380.7021.1.1.26213
60.0601m21A0.4255.520.0760.6543.5.1.-276
70.0601yxoA0.4325.920.0780.6881.1.1.262252
80.0601t09B0.3825.390.0650.5861.1.1.42131,141,144
90.0603a2pA0.4275.440.0750.6473.5.2.12278
100.0601a05A0.4285.460.1340.6641.1.1.85NA
110.0601hqsA0.4425.660.1270.6981.1.1.42120
120.0601r6tA0.4234.070.0620.5426.1.1.2NA
130.0601vlcA0.4375.560.1260.6851.1.1.85NA
140.0601zorA0.4335.800.0640.6781.1.1.42240
150.0601t09A0.4385.710.0740.6751.1.1.42260
160.0602d1cA0.4305.470.1270.6641.1.1.42NA
170.0601r8kA0.4305.980.0750.6851.1.1.262NA
180.0603khuB0.4334.630.1210.5971.1.1.2241
190.0603focA0.4234.720.0550.5736.1.1.2NA

(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
00.650.9780.720.550.993cisG GO:0000166 GO:0001666 GO:0005524 GO:0005618 GO:0005829 GO:0005886 GO:0006950 GO:0009405 GO:0040007 GO:0040008 GO:0085014
10.610.8720.780.570.882jaxA GO:0000166 GO:0001666 GO:0005524 GO:0005618 GO:0005829 GO:0005886 GO:0006950 GO:0009405 GO:0040007 GO:0040008 GO:0085014
20.410.7483.230.190.883loqA GO:0000166 GO:0006950
30.400.7682.550.230.863ab8A GO:0000166 GO:0005524 GO:0006950
40.390.7322.080.230.803ab7B GO:0000166 GO:0005524 GO:0006950
50.310.3881.920.220.423dloD GO:0006950
60.280.7433.610.140.914r2kA GO:0005737 GO:0006950
70.270.4072.720.230.452z3vA GO:0000166 GO:0005524 GO:0006950
80.250.7403.690.110.914wy2A GO:0006950
90.250.4282.480.240.473hgmA GO:0000166 GO:0005524 GO:0005737 GO:0006950
100.240.6983.580.140.843mt0A GO:0006950
110.240.3932.930.260.445ahwC GO:0000166 GO:0006950
120.230.3831.920.270.412z08A GO:0000166 GO:0005524 GO:0006950
130.230.4302.170.210.473s3tA GO:0000166 GO:0005524 GO:0005737 GO:0006950
140.230.3782.450.280.415ahwB GO:0000166 GO:0006950
150.210.4062.090.240.444r2lA GO:0006950
160.200.3822.910.130.443idfA GO:0006950
170.200.4152.190.220.451mjhB GO:0000166 GO:0005524 GO:0005737 GO:0006950
180.200.3832.470.240.434wnyA GO:0006950


Consensus prediction of GO terms
 
Molecular Function GO:0005524
GO-Score 0.95
Biological Processes GO:0001666 GO:0085014 GO:0040008 GO:0009405
GO-Score 0.86 0.86 0.86 0.86
Cellular Component GO:0005618 GO:0005829 GO:0005886
GO-Score 0.86 0.86 0.86

(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.