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I-TASSER results for job id Rv1556

[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 10 2yvhB NUC Rep, Mult 42,43,54,58,62,63,64
20.09 14 2uxiB G50 Rep, Mult 81,92,95,99,135,139,142,166,169,173
30.08 12 3whbA DCC Rep, Mult 69,72,73,76,99,102,110,115,124,127,128,132,133,135,136,159,160,162,163,166,170
40.04 7 1qpiA QNA Rep, Mult 53,55,56,59
50.04 6 5aqcB 5JB Rep, Mult 30,102,103,114,132,135,166,169
60.04 6 3angD DCC Rep, Mult 167,171,175,177,178
70.03 5 2uxhB QUE Rep, Mult 92,95,96,113,117,139,165,166,169,170,173
80.03 4 3anpB DCC Rep, Mult 114,125,128,157,160,167,169,170
90.02 2 2id3A CA Rep, Mult 84,145
100.02 3 3b6aA ZCT Rep, Mult 76,79,82,99,138,166
110.02 4 2uxiA G50 Rep, Mult 83,92,95,135,161
120.01 1 2id3B CA Rep, Mult 45,49
130.01 2 3lsrA QNA Rep, Mult 42,43,44,48,54,55,58
140.01 1 3angB DCC Rep, Mult 175,176,180,181,183,187
150.01 1 3p9tA TCL Rep, Mult 72,76,79,103,113,116
160.01 1 2eh3A MG Rep, Mult 94,97
170.01 1 3lsjB COA Rep, Mult 92,146,190,193,194
180.01 1 1t56A DIO Rep, Mult 99,128,132,169,170,173,174
190.01 1 1vi0B DCC Rep, Mult 160,163,164,167,168,189
200.01 1 3angB DCC Rep, Mult 171,175,187,191

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
10.0603a47A0.4415.280.0410.7233.2.1.10NA
20.0602fhcA0.3956.100.0710.7433.2.1.4163,71
30.0601rsrB0.4415.310.0340.7481.17.4.1111
40.0602pywA0.4665.400.0640.8222.7.1.100NA
50.0602ztgA0.4565.520.0590.7826.1.1.7185
60.0603mosA0.4555.290.1060.7772.2.1.1NA
70.0602e6kA0.4425.280.0890.7522.2.1.1NA
80.0601n1zA0.4554.550.0500.6835.5.1.8NA
90.0601umdB0.4445.590.1040.7771.2.4.431,54,60
100.0602ohhA0.4525.100.0400.7231.-.-.-NA
110.0601m7xB0.4445.120.0460.7032.4.1.1874
120.0601r9jB0.4455.340.0660.7672.2.1.1NA
130.0602r8oB0.4455.430.0780.7772.2.1.1NA
140.0601uyrA0.4445.070.0590.7086.4.1.2,6.3.4.14NA
150.0602g25A0.4695.320.0530.8121.2.4.1NA
160.0603k1dA0.4484.990.0640.7032.4.1.1886
170.0601txzA0.4604.550.0480.6783.1.3.-NA
180.0602o1xC0.4625.300.1120.7922.2.1.7NA
190.0603l4uA0.4555.240.0710.7333.2.1.20,3.2.1.3NA

(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
00.460.9070.660.250.922zb9A GO:0003677 GO:0006351 GO:0006355
10.320.5434.410.100.802q24B GO:0003677 GO:0006351 GO:0006355
20.320.7282.880.210.902fq4A GO:0003677 GO:0006351 GO:0006355
30.300.6613.720.140.913hggA GO:0003677 GO:0006351 GO:0006355
40.300.6923.370.110.912f07A GO:0003677 GO:0006351 GO:0006355
50.290.6743.160.140.873mnlA GO:0000976 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0042803
60.290.6333.680.100.853vuqC GO:0003677 GO:0006351 GO:0006355
70.260.5604.250.100.823ppbA GO:0003677 GO:0006351 GO:0006355
80.260.5663.850.080.783egqA GO:0003677 GO:0006351 GO:0006355
90.260.5923.710.140.803zqfA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677 GO:0046872
100.260.6413.960.110.873qbmA GO:0003677 GO:0003700 GO:0006351 GO:0006355
110.260.6453.430.160.864jl3C GO:0003677 GO:0006351 GO:0006355
120.260.6323.820.100.874cgrA GO:0003677 GO:0006351 GO:0006355
130.250.6004.160.100.853c2bA GO:0003677 GO:0006351 GO:0006355
140.240.6933.090.180.872g3bA GO:0003677 GO:0006351 GO:0006355
150.240.5404.270.120.802qwtA GO:0003677 GO:0006351 GO:0006355
160.230.6024.070.100.863bcgA GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0008144 GO:0042493 GO:0043565 GO:0045892
170.210.6573.270.150.843bjbB GO:0003677 GO:0006351 GO:0006355
180.210.6813.370.120.923angC GO:0003677 GO:0006351 GO:0006355
190.210.6353.810.140.882qibA GO:0003677 GO:0003700 GO:0006351 GO:0006355
200.200.6463.550.070.853whcA GO:0003677 GO:0005737 GO:0006351 GO:0006355 GO:0006629 GO:0006631 GO:0016042
210.200.5624.270.150.822oerB GO:0003677 GO:0006351 GO:0006355
220.190.5814.130.170.865f1jA GO:0003677 GO:0006351 GO:0006355
230.190.5964.020.100.843he0C GO:0003677 GO:0006351 GO:0006355
240.190.6623.510.120.875d1wD GO:0003677 GO:0006351 GO:0006355
250.190.5984.390.120.903g7rB GO:0003677 GO:0003700 GO:0006351 GO:0006355
260.190.6993.220.200.902id3A GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0046872
270.190.4954.050.120.713ljlA GO:0003677
280.180.6043.760.130.824auxA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677 GO:0046872
290.170.6753.230.080.863lwjA GO:0003677 GO:0006351 GO:0006355
300.170.5733.750.150.792qkoB GO:0003677 GO:0006351 GO:0006355
310.150.5554.200.040.804gctC GO:0000976 GO:0003677 GO:0003700 GO:0005737 GO:0005829 GO:0006355 GO:0007049 GO:0009295 GO:0010974 GO:0043565 GO:0043590 GO:0051301 GO:0051302
320.140.5224.450.160.782o7tA GO:0003677 GO:0006351 GO:0006355
330.120.5804.120.130.842oi8A GO:0003677 GO:0006351 GO:0006355
340.110.5424.510.100.804pxiB GO:0003677 GO:0006351 GO:0006355
350.080.6333.720.140.854za6A GO:0003677
360.080.6203.620.110.831sgmA GO:0003677 GO:0006351 GO:0006355
370.080.6413.740.120.862hyjA GO:0003677 GO:0003700 GO:0006351 GO:0006355
380.070.6123.920.140.852uxhA GO:0003677 GO:0006351 GO:0006355
390.070.5964.410.100.874jykA GO:0000976 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0045892 GO:0045893
400.070.5713.950.070.802raeA GO:0003677 GO:0006351 GO:0006355
410.070.5364.180.100.772guhA GO:0003677 GO:0006351 GO:0006355


Consensus prediction of GO terms
 
Molecular Function GO:0003677
GO-Score 0.88
Biological Processes GO:0006355
GO-Score 0.88
Cellular Component
GO-Score

(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.