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I-TASSER results for job id Rv2562

[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
10.09 5 3l9xA ESG Rep, Mult 11,17,18,21,37
20.06 3 5sv1F III Rep, Mult 86,89,96
30.06 3 3ta8A FE Rep, Mult 68,87
40.06 3 2q3bA MPD Rep, Mult 20,21,32
50.06 3 1fcjB SO4 Rep, Mult 11,12,14,15,16,17
60.04 2 3i8hE MG Rep, Mult 22,25
70.02 1 3sxqA CO Rep, Mult 5,21
80.02 1 1p8nA MN Rep, Mult 57,71,76
90.02 1 2anuA ZN Rep, Mult 60,68
100.02 1 1u4jA MAN Rep, Mult 18,105
110.02 1 4ag5C MG Rep, Mult 93,97
120.02 1 3egmA FE Rep, Mult 84,89
130.02 1 2buqA CAQ Rep, Mult 29,33
140.02 1 2v8vD URP Rep, Mult 14,26

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
10.0603n2oA0.4664.940.0760.8374.1.1.1935
20.0603dkiB0.4264.770.0080.7362.5.1.6531
30.0602zr8A0.4685.030.0420.8685.1.1.18NA
40.0601trkA0.4864.860.0250.8682.2.1.1NA
50.0601ay0A0.5004.790.0570.8842.2.1.141
60.0601vb3A0.4734.590.0270.8064.2.3.1NA
70.0601uwkA0.4734.490.0430.8144.2.1.49NA
80.0602o1xC0.4194.530.0430.7212.2.1.757
90.0601o58A0.4754.850.0330.8372.5.1.477,116
100.0601p5jA0.4504.960.0490.8454.3.1.17NA
110.0602gn0C0.4584.990.0590.8304.3.1.19NA
120.0602rhgB0.4664.500.0890.7604.2.1.20NA
130.0603dwgA0.4904.380.0360.8062.5.1.477
140.0601pwhA0.4574.950.0490.8534.3.1.17,4.3.1.19NA
150.0601r8lB0.4594.910.0630.8373.2.1.89NA
160.0601hkvA0.4474.680.0940.8144.1.1.20NA
170.0601wkvB0.4884.360.0560.8062.5.1.47116
180.0601v8zB0.4704.850.0340.8534.2.1.20NA
190.0602r8oB0.5004.520.0850.8452.2.1.168

(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
00.070.4034.880.070.731itzA GO:0003824 GO:0004802 GO:0008152 GO:0009507 GO:0009535 GO:0009536 GO:0009579 GO:0016020 GO:0016740 GO:0019253 GO:0046872
10.070.3895.090.030.744c7vA GO:0003824 GO:0004802 GO:0008152 GO:0016740 GO:0046872
20.070.3715.120.070.714kxwA GO:0003824 GO:0004802 GO:0005634 GO:0005654 GO:0005777 GO:0005829 GO:0005999 GO:0006098 GO:0008152 GO:0009052 GO:0016740 GO:0031982 GO:0040008 GO:0042803 GO:0043209 GO:0046166 GO:0046872 GO:0048037 GO:0070062
30.070.4874.730.080.844xeuA GO:0003824 GO:0004802 GO:0008152 GO:0016740 GO:0046872
40.070.5004.790.060.881ay0A GO:0003824 GO:0004802 GO:0005737 GO:0006098 GO:0008152 GO:0016740 GO:0046872
50.070.4724.690.050.843l84A GO:0003824 GO:0004802 GO:0008152 GO:0016740 GO:0046872
60.070.4034.720.040.723uptA GO:0003824 GO:0004802 GO:0008152 GO:0016740 GO:0046872
70.070.4894.890.070.852e6kA GO:0003824 GO:0004802 GO:0008152 GO:0016740 GO:0046872
80.070.5014.460.080.843komA GO:0003824 GO:0004802 GO:0008152 GO:0016740 GO:0046872
90.070.4185.240.040.783uk1A GO:0003824 GO:0004802 GO:0008152 GO:0016740 GO:0046872
100.060.4194.530.040.722o1xC GO:0000287 GO:0003824 GO:0008152 GO:0008299 GO:0008661 GO:0009228 GO:0016114 GO:0016740 GO:0030976 GO:0046872 GO:0052865
110.060.3935.000.050.721r9jB GO:0003824 GO:0004802 GO:0008152 GO:0016740 GO:0046872
120.060.5004.520.090.842r8oB GO:0003824 GO:0004802 GO:0005829 GO:0008152 GO:0009052 GO:0016740 GO:0030145 GO:0030976 GO:0046872
130.060.3974.750.030.713m49A GO:0003824 GO:0004802 GO:0008152 GO:0016740 GO:0046872
140.060.3404.840.060.582ej0B GO:0003824 GO:0004084 GO:0008152 GO:0008483 GO:0009081 GO:0016740
150.060.3214.960.040.572pl2A
160.060.3765.390.070.754ni3B GO:0004560 GO:0005975 GO:0006004
170.060.4044.950.030.733rimA GO:0003824 GO:0004802 GO:0005576 GO:0005618 GO:0005829 GO:0005886 GO:0008152 GO:0016740 GO:0040007 GO:0046872
180.060.2795.020.030.532a2gA GO:0005009 GO:0005215 GO:0005550 GO:0005576 GO:0005615 GO:0005634 GO:0005737 GO:0005829 GO:0006112 GO:0006810 GO:0007610 GO:0008286 GO:0009060 GO:0010628 GO:0010888 GO:0010907 GO:0031649 GO:0036094 GO:0042593 GO:0045475 GO:0045721 GO:0045834 GO:0045892 GO:0051055 GO:0051897 GO:0061179 GO:0070584 GO:0071396


Consensus prediction of GO terms
 
Molecular Function GO:0043169 GO:0016744
GO-Score 0.58 0.58
Biological Processes GO:0040008 GO:0046166 GO:0019253 GO:0009052 GO:0005999
GO-Score 0.07 0.07 0.07 0.07 0.07
Cellular Component GO:0043209 GO:0005777 GO:0009535 GO:0070062 GO:0005829 GO:0005654
GO-Score 0.07 0.07 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.