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I-TASSER results for job id Rv2303c

[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
10.45 37 2hbvA ZN Rep, Mult 14,16,173,208,266
20.10 7 4kirB MN Rep, Mult 14,141,143,173,208,266
30.06 5 2dvxC 23A Rep, Mult 16,173,266,269

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
10.1942wm1A0.7103.820.1910.8704.1.1.45228,260
20.1042wjfA0.5713.910.1040.7203.1.3.48NA
30.0822v81A0.4813.870.1030.6224.1.2.21NA
40.0801vlwB0.4733.940.1430.6164.1.3.16NA
50.0742fliC0.5013.950.0850.6485.1.3.1NA
60.0673ngfA0.5613.960.0800.7265.3.1.22NA
70.0671dvjA0.5463.990.0790.6974.1.1.23NA
80.0672cz5A0.5073.910.0890.6584.1.1.23NA
90.0671tqjC0.4944.220.1150.6615.1.3.1NA
100.0672czfA0.5024.030.0840.6614.1.1.23146,172
110.0661l6wA0.4893.670.0770.6064.1.2.-NA
120.0663ct7A0.4924.030.0560.6385.1.3.-NA
130.0661vqtA0.4654.030.0740.6034.1.1.23NA
140.0661h1yA0.5024.190.0780.6685.1.3.1NA
150.0661h1yB0.5024.260.0730.6715.1.3.1NA
160.0601zzmA0.6423.260.1070.7593.1.21.-265
170.0602ftwA0.7103.700.1200.8703.5.2.2NA
180.0603dc8A0.7053.700.1090.8603.5.2.2NA
190.0602vr2A0.7143.680.1120.8733.5.2.2265
200.0601onxA0.6743.630.1380.8213.4.19.-NA
210.0602z00A0.6803.570.1450.8313.5.2.3192
220.0603iacA0.6594.530.0840.8965.3.1.12274
230.0602vc7B0.6414.000.1130.8083.1.8.1NA
240.0601gkpA0.7163.610.1050.8703.5.2.2265
250.0603griB0.6663.590.1000.8143.5.2.3126
260.0603d6nA0.6843.600.1180.8313.5.2.3265
270.0602zc1A0.6513.860.0900.8013.1.8.1142
280.0602z26A0.6683.430.1190.8083.5.2.3NA
290.0602uz9A0.6334.310.0860.8343.5.4.3NA
300.0601gkrA0.6893.620.1130.8373.5.2.2NA
310.0601ybqA0.6753.610.1270.8183.4.19.182,84
320.0601k1dA0.7033.730.1040.8663.5.2.-NA
330.0601a4lA0.6444.580.0800.8633.5.4.4208
340.0601m7jA0.6603.870.0910.8213.5.1.81NA

(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
00.300.6822.510.160.773cjpA GO:0016787 GO:0046872
10.290.7353.360.180.884qroA GO:0016787 GO:0046872
20.280.7113.730.180.874ofcA GO:0001760 GO:0005829 GO:0006568 GO:0006569 GO:0008270 GO:0016787 GO:0016829 GO:0016831 GO:0046872 GO:0046874 GO:0051259 GO:0070062 GO:1904984 GO:1905004 GO:1905012
30.280.7164.250.140.934dziC GO:0016787
40.270.7293.970.140.914hjwC GO:0001760 GO:0006568 GO:0016787 GO:0046872 GO:1904984
50.270.7043.770.130.864eraA GO:0001760 GO:0006568 GO:0016787 GO:0046872 GO:1904984
60.250.7243.660.180.884icmA GO:0016787 GO:0046872
70.250.7253.820.170.904hk5D GO:0001760 GO:0006568 GO:0016787 GO:0046872 GO:1904984
80.230.7403.540.170.904qrnA GO:0016787 GO:0046872
90.220.6993.680.140.873ij6A GO:0016787 GO:0046872
100.200.8771.270.240.913irsA GO:0016787
110.130.7343.290.180.872dvtA GO:0016787 GO:0046872
120.130.7313.410.160.872f6kA GO:0016787 GO:0046872
130.110.6773.820.180.832gwgA GO:0016787 GO:0046872
140.100.6943.400.170.833nurA GO:0016787
150.070.6793.430.120.812vunA GO:0016787 GO:0016810 GO:0043792 GO:0046872 GO:0051187
160.070.5254.060.060.682gsjA
170.070.4934.000.070.653ve7A GO:0003824 GO:0004590 GO:0006207 GO:0008152 GO:0016829
180.060.3736.730.060.642vn4A
190.060.3576.490.050.611u2vC GO:0003779 GO:0005200 GO:0005737 GO:0005829 GO:0005856 GO:0005885 GO:0005925 GO:0015629 GO:0030833 GO:0034314 GO:0051015 GO:0070062
200.060.3625.220.080.531e3wD GO:0001540 GO:0003857 GO:0004303 GO:0005496 GO:0005739 GO:0007569 GO:0008033 GO:0016491 GO:0018454 GO:0030283 GO:0030331 GO:0033327 GO:0042802 GO:0047015 GO:0051287 GO:0051289 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0016787 GO:0046914 GO:0001760
GO-Score 0.81 0.56 0.47
Biological Processes GO:1901606 GO:1905003 GO:0090357 GO:0030808 GO:1902688 GO:0006461 GO:0009074 GO:0046218 GO:0034354 GO:1904984
GO-Score 0.56 0.56 0.56 0.56 0.56 0.56 0.56 0.56 0.56 0.47
Cellular Component GO:0031988 GO:1903561 GO:0044444
GO-Score 0.56 0.56 0.56

(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.