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I-TASSER results for job id Rv0313

[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
10.07 3 2y04B 2CV Rep, Mult 87,90,94,97
20.07 3 3q13A CA Rep, Mult 68,93,103
30.05 2 1iujB ZN Rep, Mult 13,16
40.05 2 1hwyA PO4 Rep, Mult 22,112,113
50.05 2 3ginA CA Rep, Mult 65,100,122,126
60.02 1 3py8A MN Rep, Mult 20,23
70.02 1 4q5jB III Rep, Mult 14,17,19,89,92,96
80.02 1 3jskM FE2 Rep, Mult 103,104
90.02 1 3athC AKG Rep, Mult 8,88
100.02 1 4f6xA MG Rep, Mult 70,98
110.02 1 2ct9A CA Rep, Mult 97,101,103,107
120.02 1 5apwB CA Rep, Mult 27,30
130.02 1 1f61A MG Rep, Mult 12,65
140.02 1 4u10A ZN Rep, Mult 99,100
150.02 1 1wrlC TFP Rep, Mult 35,95,98

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
10.0601lufA0.4934.660.0330.8912.7.10.194,96
20.0602jiiB0.4794.670.0780.8442.7.11.165
30.0602f57B0.4784.740.0870.8752.7.11.1,2.7.1.37NA
40.0602f2uA0.4794.780.0680.8592.7.11.1,2.7.1.3793
50.0603hx4A0.4784.810.0510.8672.7.11.1723
60.0603h9fA0.4824.610.0610.8672.7.12.193,97,98
70.0602ogvA0.4904.880.0560.9062.7.10.189
80.0601rjbA0.4875.020.0630.9382.7.10.1NA
90.0602h96A0.4774.500.0440.8362.7.11.24NA
100.0603eqdA0.4934.540.0840.8832.7.12.293,98
110.0601csnA0.4684.710.0260.8592.7.11.1NA
120.0602a1aB0.4774.770.1030.8522.7.11.198
130.0603g0eA0.4865.100.0730.9142.7.10.1NA
140.0602j4zB0.4964.790.0340.9062.7.11.1,NA
150.0601s9iA0.4804.680.0930.8672.7.12.2,2.7.1.3798
160.0602fh9A0.4834.850.0850.9062.7.11.191
170.0603c4wB0.4774.790.0760.8752.7.11.14NA
180.0603a62A0.4834.780.0340.9062.7.11.193,98
190.0601p4oB0.4935.050.0630.9222.7.10.1,2.7.1.11294,96

(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
00.070.5164.120.060.834hdtA GO:0003860 GO:0016787 GO:0046872
10.070.5093.920.070.803ju1A GO:0003860 GO:0005829 GO:0006635 GO:0016787
20.070.5024.550.030.853bptA GO:0003860 GO:0005739 GO:0005759 GO:0006574 GO:0006635 GO:0009083 GO:0016787 GO:0070062
30.070.5054.480.100.844j2uA GO:0003860 GO:0004300 GO:0016829
40.070.3784.670.030.651wdlA GO:0003824 GO:0003857 GO:0004165 GO:0004300 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0008692 GO:0009062 GO:0016042 GO:0016491 GO:0016829 GO:0016853 GO:0036125 GO:0055114
50.070.3604.920.070.653peaC GO:0003824 GO:0008152 GO:0016853
60.060.4334.400.060.703fduA
70.060.3805.190.020.722ogiB GO:0046872
80.060.4064.690.060.703gkbB GO:0003824 GO:0008152
90.060.3724.560.070.623g64A GO:0003824 GO:0008152
100.060.3854.410.060.664jcsA GO:0003824 GO:0004300 GO:0008152 GO:0016829 GO:0016853
110.060.3765.050.070.704i42A GO:0003824 GO:0005829 GO:0008152 GO:0008935 GO:0009234 GO:0016829 GO:0071890
120.060.3674.530.020.624og1A GO:0003824 GO:0008152 GO:0016853
130.060.3624.970.100.652wtbA GO:0003824 GO:0003857 GO:0004165 GO:0004300 GO:0005618 GO:0005730 GO:0005777 GO:0005829 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0008692 GO:0009506 GO:0009514 GO:0016491 GO:0016508 GO:0016829 GO:0016853 GO:0055114
140.060.3455.390.030.665e0nX GO:0003824 GO:0008152 GO:0016853
150.060.3624.800.050.664i4zA GO:0003824 GO:0005829 GO:0008152 GO:0008935 GO:0009234 GO:0016829 GO:0042372
160.060.3765.020.080.694jsbA GO:0003824 GO:0004300 GO:0008152 GO:0016829
170.060.4234.530.070.703p5mB GO:0003824 GO:0008152 GO:0016853
180.060.3794.820.070.663r9tB GO:0003824 GO:0008152


Consensus prediction of GO terms
 
Molecular Function GO:0016289
GO-Score 0.48
Biological Processes GO:0009062 GO:0019395
GO-Score 0.37 0.37
Cellular Component GO:0005759 GO:0005829 GO:0070062 GO:0036125
GO-Score 0.07 0.07 0.07 0.07

(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.