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I-TASSER results for job id Rv1767

[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 1 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 2p06A MG Rep, Mult 51,54,70,73
20.06 3 2uxhA QUE Rep, Mult 14,15,32,36,63,67,94,97,101
30.06 3 4nilA 2O8 Rep, Mult 48,49,83,87
40.06 3 1m7r0 III Rep, Mult 62,64,65,66,67,68,69,71,72,81
50.04 2 1h2u0 III Rep, Mult 55,59,62,84
60.04 2 1wnoB MG Rep, Mult 62,67,102
70.04 2 1mz9B VDY Rep, Mult 52,55,59
80.02 1 5c6hA III Rep, Mult 72,116
90.02 1 4atkB NUC Rep, Mult 101,102,105
100.02 1 2fkwA BCL Rep, Mult 96,103
110.02 1 3c3yA CA Rep, Mult 83,86
120.02 1 1n52A MG Rep, Mult 53,88,90,91
130.02 1 2yxhA MG Rep, Mult 51,77

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
10.0603hf1B0.4294.790.0600.8071.17.4.1NA
20.0602qubA0.5523.960.0670.8743.1.1.364
30.0601k7hA0.5144.380.0750.8823.1.3.1105
40.0602x38A0.5254.380.0880.8492.7.1.15388
50.0602fp0B0.4914.100.0680.7983.2.1.143NA
60.0602cqsA0.4814.570.0750.8402.4.1.20NA
70.0603cuzA0.5244.030.0610.8152.3.3.9NA
80.0602fiqC0.5104.120.0740.8402.7.1.14462,68,106
90.0603k1dA0.5364.300.0710.8822.4.1.18NA
100.0602a4aA0.5184.000.0760.7904.1.2.4NA
110.0601zefA0.5154.350.0460.8913.1.3.1NA
120.0601gaiA0.5144.440.0700.8403.2.1.386,112
130.0601dwaM0.5074.340.0370.8993.2.1.147NA
140.0603a47A0.5084.300.0670.8743.2.1.10NA
150.0601gowA0.5403.950.0670.8243.2.1.23NA
160.0602bq1I0.5433.380.0510.7561.17.4.1NA
170.0603ebgA0.5093.940.0190.8243.4.11.-NA
180.0602vuxB0.5403.450.0680.7481.17.4.1NA
190.0602e3zA0.5233.570.0480.7483.2.1.21NA

(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
00.550.9300.460.370.945dikA GO:0004601 GO:0016209 GO:0016491 GO:0051920 GO:0055114 GO:0098869
10.450.6351.260.270.693beyD GO:0051920 GO:0055114 GO:0098869
20.450.8411.660.240.961p8cC GO:0004601 GO:0016209 GO:0016491 GO:0016829 GO:0051920 GO:0055114 GO:0098869
30.380.6882.790.200.872af7D GO:0051920 GO:0055114 GO:0098869
40.310.7592.190.200.902qeuB GO:0051920 GO:0055114 GO:0098869
50.310.6862.080.220.823d7iB GO:0051920 GO:0055114 GO:0098869
60.220.6712.600.140.874g9qA GO:0051920 GO:0055114 GO:0098869
70.220.6231.790.180.712cwqA GO:0051920 GO:0055114 GO:0098869
80.070.6012.030.170.702q0tA GO:0051920 GO:0055114 GO:0098869
90.070.5643.610.170.782prrD GO:0004601 GO:0016209 GO:0016491 GO:0051920 GO:0055114 GO:0098869
100.070.6101.930.190.692ouwB GO:0004601 GO:0016209 GO:0016491 GO:0051920 GO:0055114 GO:0098869
110.070.5413.430.130.713lvyA GO:0004601 GO:0016209 GO:0016491 GO:0051920 GO:0055114 GO:0098869
120.070.5463.420.190.762oyoA GO:0004601 GO:0016209 GO:0016491 GO:0051920 GO:0055114 GO:0098869
130.060.3884.590.060.654b2ta GO:0000166 GO:0005524 GO:0005737 GO:0005815 GO:0005832 GO:0005856 GO:0006457 GO:0051082
140.060.3664.810.050.683iygA GO:0000166 GO:0005524 GO:0005737 GO:0005815 GO:0005832 GO:0005856 GO:0006457 GO:0051082
150.060.3715.500.080.764f7rD GO:0019904
160.060.4114.100.030.621ku1A GO:0000137 GO:0005085 GO:0005086 GO:0005737 GO:0005829 GO:0006888 GO:0006890 GO:0006891 GO:0016020 GO:0016236 GO:0019898 GO:0030036 GO:0032012 GO:0033363 GO:0043547
170.060.3624.900.060.651obgA GO:0000166 GO:0004638 GO:0004639 GO:0005524 GO:0006164 GO:0006189 GO:0016874 GO:0046084
180.060.3365.440.050.743skqA GO:0005739 GO:0005743 GO:0006813 GO:0015992 GO:0016020 GO:0016021 GO:0030007 GO:0043022 GO:0051204 GO:0070131 GO:0097033 GO:0097034


Consensus prediction of GO terms
 
Molecular Function GO:0051920 GO:0004601 GO:0016829
GO-Score 0.94 0.75 0.45
Biological Processes GO:0098869 GO:0055114
GO-Score 0.94 0.94
Cellular Component
GO-Score

(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.