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I-TASSER results for job id Rv2525c

[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
10.17 4 4pmrA EPE Rep, Mult 70,79,101,144,175,213,227
20.06 2 2gk1A UUU Rep, Mult 62,64,139
30.03 1 2ddsC CO Rep, Mult 144,194
40.03 1 4ea2A MG Rep, Mult 43,159
50.03 1 3d6aA MG Rep, Mult 148,149
60.03 1 3c9zA UUU Rep, Mult 92,144
70.03 1 2q7dA MN Rep, Mult 144,146
80.03 1 2buqA CAQ Rep, Mult 158,159
90.03 1 2gq9A HBA Rep, Mult 98,137,138,139
100.03 1 3lkvA ZN Rep, Mult 129,136,172
110.03 1 2gk1A NGT Rep, Mult 144,145,175,196,218,227
120.03 1 1tq2B MG Rep, Mult 178,227
130.03 1 2wagA MG Rep, Mult 152,156,157,161,162,187,189
140.03 1 2wwdA UUU Rep, Mult 175,177,178,179,196,197

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
10.0661n7kA0.5214.100.0820.6834.1.2.4NA
20.0601jfxA0.6093.940.1640.7833.2.1.17100,175,198,227
30.0601myrA0.5834.280.0550.7873.2.1.147NA
40.0603f4vA0.5824.070.0800.7713.2.1.21NA
50.0601kbiA0.5794.530.0470.8121.1.2.344,210
60.0602tmdA0.5854.090.0810.7871.5.8.261
70.0601c7sA0.6114.300.0420.8383.2.1.52NA
80.0601fa2A0.5964.280.0690.8123.2.1.2NA
90.0602dgaA0.5854.290.0650.7923.2.1.21146,149
100.0601kfwA0.5944.320.0810.8383.2.1.14NA
110.0601h4pA0.5804.390.0710.7963.2.1.58NA
120.0601hp4A0.5814.220.0820.7923.2.1.52NA
130.0601cz1A0.5824.400.0340.7963.2.1.58NA
140.0601j5sA0.5944.820.0760.8795.3.1.12198,200,206
150.0602oykB0.5844.520.0530.7963.2.1.12364,196
160.0602gjxA0.5894.100.0600.7923.2.1.52NA
170.0601b1yA0.5984.310.0690.8123.2.1.2NA
180.0602whjA0.6044.170.0990.7963.2.1.78NA
190.0601djnA0.5844.090.0810.7871.5.8.2,1.5.99.7140
200.0602jepA0.5804.010.0820.7713.2.1.151NA

(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
00.670.8650.760.970.884pmoA GO:0005576 GO:0005975 GO:0008610 GO:0046677
10.250.6442.830.170.751sfsA GO:0005975
20.180.6143.450.120.774ff5A GO:0003796 GO:0005975 GO:0009253 GO:0016020 GO:0016021 GO:0016998
30.180.5743.870.110.743hmcA GO:0003796 GO:0005975 GO:0009253 GO:0016787 GO:0016998
40.170.5683.730.090.721h09A GO:0003796 GO:0003824 GO:0005975 GO:0008152 GO:0009253 GO:0016787 GO:0016798 GO:0016998 GO:0019835 GO:0042742 GO:0044659
50.170.5923.830.130.752x8rB GO:0003796 GO:0005975 GO:0009253 GO:0016787 GO:0016998
60.140.6133.550.140.765a6sA GO:0003796 GO:0005975 GO:0009253 GO:0016998
70.140.5833.960.120.774jz5A GO:0003796 GO:0005975 GO:0009253 GO:0016998
80.120.6204.270.090.822wagA GO:0003796 GO:0005975 GO:0009253 GO:0016020 GO:0016021 GO:0016787 GO:0016998 GO:0046872
90.100.6184.070.090.804krtA GO:0003796 GO:0005975 GO:0009253 GO:0016998
100.090.6494.100.120.852wwdA GO:0003796 GO:0005975 GO:0008152 GO:0009253 GO:0016787 GO:0016798 GO:0016998
110.070.6234.110.080.831uuqA GO:0005975
120.070.6093.940.160.781jfxA GO:0003796 GO:0005576 GO:0005615 GO:0005975 GO:0008152 GO:0009253 GO:0016787 GO:0016798 GO:0016998
130.070.5004.850.040.721rh9A GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0016985 GO:0046355
140.070.5773.590.120.732nw0A
150.070.6124.010.070.813pznA GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0016985
160.070.5434.860.060.784qp0A GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0016985
170.070.5374.990.050.794aweA GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0016985
180.070.6034.010.070.801qnoA GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030248
190.070.6054.220.030.823wh9A GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0016985 GO:0046355
200.070.6024.270.070.823zizA GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0016985
210.070.5065.020.050.774mupB GO:0016787 GO:0016853
220.070.5584.460.050.753lpfA GO:0004553 GO:0004566 GO:0005829 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0019391 GO:0043231
230.060.4145.570.080.664ls8A GO:0003824 GO:0006629 GO:0006631 GO:0006633 GO:0008152 GO:0016740 GO:0016746 GO:0016747 GO:0033817
240.060.4035.720.050.673o04A GO:0003824 GO:0006633 GO:0008152 GO:0016740 GO:0016746 GO:0016747 GO:0033817


Consensus prediction of GO terms
 
Molecular Function GO:0003796
GO-Score 0.45
Biological Processes GO:0005975 GO:0046677 GO:0008610 GO:0016998 GO:0009253 GO:0019076 GO:0009617 GO:0044661 GO:0098542 GO:0001897 GO:0039633
GO-Score 0.86 0.67 0.67 0.45 0.45 0.35 0.35 0.35 0.35 0.35 0.35
Cellular Component GO:0005576
GO-Score 0.67

(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.