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I-TASSER results for job id Rv3354

[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
10.08 4 3kziT CLA Rep, Mult 96,100
20.08 4 1vhbA HEM Rep, Mult 39,67,74,75,78,96,100
30.06 3 3qb5K MN Rep, Mult 61,104
40.06 3 1pssL BCL Rep, Mult 89,92,93,96,97
50.06 3 1n38A CH1 Rep, Mult 35,36,61,65,66,67
60.02 1 3leeE MG Rep, Mult 25,104,108
70.02 1 2o01G CLA Rep, Mult 106,107
80.02 1 2h2pA SEK Rep, Mult 28,30
90.02 1 1cb2A MAN Rep, Mult 72,76
100.02 1 3go9A ZN Rep, Mult 36,49
110.02 1 3ozvB ECN Rep, Mult 17,18,21,39,78,81
120.02 1 1lghA BCL Rep, Mult 33,34,37
130.02 1 3eerA ZN Rep, Mult 64,105,106
140.02 1 3ze3B 78N Rep, Mult 23,32

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
10.0603f93A0.4984.550.0590.8533.2.1.-NA
20.0601mhsA0.5323.940.0650.8223.6.3.6NA
30.0602uu7A0.4984.060.0490.7676.3.1.2NA
40.0601hbmA0.4874.010.0580.7362.8.4.1NA
50.0602debA0.4984.340.0820.8142.3.1.21NA
60.0601f1hL0.5064.180.0730.7836.3.1.267,70
70.0603fkyC0.5074.090.0760.7836.3.1.2NA
80.0602fknB0.4953.900.0880.7754.2.1.4937
90.0603g4dA0.5154.510.0810.8454.2.3.13NA
100.0601cqxB0.5373.950.0400.7981.14.12.17NA
110.0601eulA0.4644.320.0760.7673.6.3.8NA
120.0602r7oA0.4964.680.0730.8682.7.7.48NA
130.0601e6yA0.4984.750.0890.8532.8.4.1NA
140.0601n1hA0.5314.220.0650.8842.7.7.48NA
150.0601u6zB0.5053.940.0730.7913.6.1.11NA
160.0601dgjA0.4984.380.1000.8061.2.-.-12
170.0602df4A0.4844.250.0730.7986.3.5.-102
180.0601wchA0.4983.780.0610.7603.1.3.48NA
190.0601uwkA0.4973.900.0880.7754.2.1.4991

(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
00.070.5364.200.050.811cqxA GO:0005344 GO:0005737 GO:0006810 GO:0008941 GO:0009636 GO:0015671 GO:0016491 GO:0019825 GO:0020037 GO:0046872 GO:0051409 GO:0055114 GO:0071949
10.070.5374.050.050.763tm9A GO:0005344 GO:0006810 GO:0015671 GO:0019825 GO:0020037 GO:0046872
20.070.5333.970.040.771gvhA GO:0005344 GO:0005504 GO:0005737 GO:0006810 GO:0008941 GO:0009636 GO:0015671 GO:0016491 GO:0019825 GO:0020037 GO:0032843 GO:0046872 GO:0051409 GO:0055114 GO:0071949
30.070.5204.220.060.814g1bA GO:0000166 GO:0016491 GO:0019825 GO:0020037 GO:0046872 GO:0055114
40.070.5943.750.080.863d9bA GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
50.070.5084.560.080.894mt1A GO:0005215 GO:0006810 GO:0016020 GO:0016021
60.070.4724.350.100.792dc3A GO:0001666 GO:0004096 GO:0004601 GO:0005344 GO:0005506 GO:0005737 GO:0005829 GO:0006810 GO:0006979 GO:0008941 GO:0010764 GO:0015671 GO:0019395 GO:0019825 GO:0020037 GO:0032966 GO:0043005 GO:0043025 GO:0046872 GO:0047888 GO:0050999 GO:0098869 GO:2000490
70.070.4104.820.070.723bcqA GO:0005344 GO:0005506 GO:0005833 GO:0006810 GO:0015671 GO:0019825 GO:0020037 GO:0046872
80.070.4164.720.050.711binA GO:0005344 GO:0006810 GO:0009399 GO:0009877 GO:0015671 GO:0019825 GO:0020037 GO:0046872
90.070.4604.940.060.843nogA GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
100.070.4734.350.080.782olpA GO:0005344 GO:0005737 GO:0006810 GO:0015671 GO:0019825 GO:0020037 GO:0046872
110.070.4564.310.060.713qqqA GO:0019825 GO:0020037 GO:0046872
120.070.4914.050.050.741oj6B GO:0005344 GO:0005737 GO:0005739 GO:0006810 GO:0006915 GO:0015671 GO:0019825 GO:0020037 GO:0043204 GO:0046872
130.070.4184.400.020.691cg5B GO:0005344 GO:0006810 GO:0015671 GO:0019825 GO:0020037 GO:0046872
140.070.4474.720.100.761hlmA GO:0005344 GO:0006810 GO:0015671 GO:0019825 GO:0020037 GO:0046872
150.070.4824.370.030.743vreA GO:0005344 GO:0005506 GO:0005833 GO:0006810 GO:0015671 GO:0019825 GO:0020037 GO:0046872
160.070.4704.100.040.733zhwA GO:0001666 GO:0005344 GO:0005618 GO:0005829 GO:0005886 GO:0009506 GO:0019825 GO:0020037 GO:0046872
170.070.5293.700.040.742wy4A GO:0005344 GO:0006810 GO:0015671 GO:0019825 GO:0020037 GO:0046872
180.070.4304.520.080.741hlbA GO:0005344 GO:0005506 GO:0005576 GO:0005833 GO:0006810 GO:0015671 GO:0019825 GO:0020037 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0046906 GO:0043169 GO:0022892
GO-Score 0.48 0.48 0.37
Biological Processes GO:0015669 GO:0044710
GO-Score 0.37 0.37
Cellular Component GO:0005737 GO:0005887
GO-Score 0.13 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.