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I-TASSER results for job id Rv3718c

[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
10.10 22 2flhB ZEA Rep, Mult 23,26,56,61,63,88,90,92,124,127
20.10 23 4n3eB 2AN Rep, Mult 8,10,12,19,23,92,103,105,124,125,128
30.10 28 3negB PYV Rep, Mult 56,58,61,63,77,79,82,85,119,123,124
40.08 22 4n3eY 2AN Rep, Mult 26,30,34,38,79,90,109,116,120,123,124
50.04 9 4a81A 2AN Rep, Mult 8,10,22,77,92,105,107,121,124,125,128,129
60.03 8 4n3eP 2AN Rep, Mult 29,32,33,131,134,135,141,142
70.03 8 2wqlC P4C Rep, Mult 23,38,75,92,105,128,131
80.02 4 1txcA 2AN Rep, Mult 129,132,133,136
90.01 3 1bv10 III Rep, Mult 21,25,27,28,31,32,41,42,43,44,47,48,49,68,70,142,143
100.01 3 3c0vB NA Rep, Mult 112,113,115,121,122
110.01 3 1txcB 2AN Rep, Mult 53,64,80,87
120.01 3 4n3eY 2AN Rep, Mult 17,21,70,73,142
130.01 3 2flhB ZEA Rep, Mult 34,37,56,58,61,63
140.01 3 3njoC PYV Rep, Mult 38,56,58,61,63,86,119,123
150.01 2 3c0vC TBR Rep, Mult 67,69,72,74,91
160.01 2 3c0vC TBR Rep, Mult 39,40,42,57
170.00 1 3ie5B PG4 Rep, Mult 79,84,109,123
180.00 1 2qimA CA Rep, Mult 31,35,36,38
190.00 1 5e4mB HBA Rep, Mult 5,6,7,104,106,107,108
200.00 1 3ie5B PG4 Rep, Mult 80,86,87,110

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
10.1942v8qA0.4872.820.0520.6192.7.11.1NA
20.1782vq5A0.7422.680.1150.9464.2.1.7849,51
30.0601t7nA0.5114.880.0380.8642.3.1.7NA
40.0602ewnA0.4934.040.0780.7356.3.4.15NA
50.0601wnlA0.5133.890.0900.7146.3.4.15NA
60.0602cghB0.5103.840.0440.6946.3.4.15NA
70.0601q23B0.4944.800.0680.8302.3.1.28NA
80.0602pmgB0.3634.600.0420.5785.4.2.247
90.0601eg9A0.6833.570.0510.9251.14.12.12NA
100.0601ffuB0.5324.070.0410.8031.2.99.2NA
110.0601sczA0.5044.610.0540.8232.3.1.61NA
120.0601kfqB0.5083.550.0440.7145.4.2.2NA
130.0603en1A0.6973.250.0730.9251.14.12.1125
140.0601z01A0.7063.440.0640.9391.14.13.6125
150.0601ndoA0.6823.590.0510.9251.14.12.1224,138
160.0603b9jI0.2565.370.0450.4691.17.1.4,1.17.3.258,65,123
170.0601wqlA0.6933.400.0730.9251.14.12.-NA
180.0601ordA0.4935.120.0430.8444.1.1.17NA
190.0601vlbA0.5214.520.0550.8091.2.99.7NA
200.0601jrpB0.5004.480.0480.7821.17.1.4117
210.0601jroB0.4994.460.0490.7691.1.1.204NA

(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
00.380.8471.720.150.951ifvA GO:0006952 GO:0009607 GO:0016787
10.380.8092.110.170.952k7hA GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0006952 GO:0009607 GO:0009738 GO:0010427 GO:0043086 GO:0080163
20.350.8401.710.170.932flhB GO:0006952 GO:0009607
30.340.8511.730.160.954m9bA GO:0006952 GO:0009607
40.340.8561.750.180.971e09A GO:0006952 GO:0009607
50.330.8531.830.170.975i8fA GO:0006952 GO:0009607
60.320.6721.860.100.762q3qA GO:0006952 GO:0009607
70.320.7662.450.230.942wqlA GO:0006952 GO:0009607
80.320.7512.830.140.982qimA GO:0006952 GO:0009607 GO:0046872
90.320.8491.710.150.955c9yA GO:0006952 GO:0009607
100.310.8352.200.150.994a80A GO:0005737 GO:0006952 GO:0009607
110.310.8372.050.180.974c94A GO:0006952 GO:0009607
120.300.8262.100.150.974c9iA GO:0006952 GO:0009607
130.290.8251.720.180.934q0kA GO:0006952 GO:0009607 GO:0009740
140.280.7802.080.110.904n0gC GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
150.260.8152.140.150.975amwA GO:0006952 GO:0009607
160.260.7812.110.150.934rehA GO:0006952 GO:0009607
170.250.7912.010.180.932bk0A GO:0006952 GO:0009607
180.250.8411.970.180.964gy9A GO:0006952 GO:0009607 GO:0009736 GO:0009877
190.210.7782.240.120.934igvA GO:0006952 GO:0009607 GO:0016068
200.200.8251.970.160.951tw0A GO:0006952 GO:0009607
210.180.8012.110.120.934oicA GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0009738 GO:0010427 GO:0043086 GO:0080163
220.170.7472.410.120.932vneA GO:0006952 GO:0009607 GO:0009820 GO:0016829 GO:0050474
230.160.8192.320.140.973kdhA GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163


Consensus prediction of GO terms
 
Molecular Function GO:0016787 GO:0010427 GO:0004864 GO:0004872
GO-Score 0.39 0.38 0.38 0.38
Biological Processes GO:0006952 GO:0009607 GO:0080163 GO:0043086 GO:0009738
GO-Score 0.89 0.89 0.38 0.38 0.38
Cellular Component GO:0005634 GO:0005737
GO-Score 0.38 0.38

(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.