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I-TASSER results for job id Rv1776c

[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 4 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
10.15 13 4l62P NUC Rep, Mult 37,38,49,53,58,59
20.09 8 3q0vA LL4 Rep, Mult 78,90,91,94,95,98,131,137,138,141,153,178
30.05 5 3angA DCC Rep, Mult 70,112,121,122,125,130,144,147,150,154,157
40.04 4 2uxhA QUE Rep, Mult 94,95,112,134,138,152,156,160
50.04 4 3zqlC QNA Rep, Mult 48,50,51,54,55
60.03 3 4xk8L CLA Rep, Mult 130,160
70.03 3 3frqB ERY Rep, Mult 28,29,70,74,77,101,102,111,112,115,131,132,153,156,157
80.03 3 3lsrA QNA Rep, Mult 9,37,38,39,43,49,50,53
90.01 1 2np5C NDS Rep, Mult 23,24,26
100.01 1 2np5A NDS Rep, Mult 162,163,164,165
110.01 1 4kgkC GTP Rep, Mult 13,69
120.01 1 3angD DCC Rep, Mult 154,158,161,162,164,165
130.01 1 3anpD DCC Rep, Mult 150,153,154,158,159
140.01 1 3zciA BU9 Rep, Mult 59,62
150.01 1 2xquA CVM Rep, Mult 63,67
160.01 1 3angA DCC Rep, Mult 69,73,74
170.01 1 2id3B CA Rep, Mult 40,44

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
10.0601y8bA0.4634.520.0790.7042.3.3.9NA
20.0601pgjA0.4824.850.0930.7741.1.1.44NA
30.0602d0tB0.4685.070.0710.7691.13.11.52NA
40.0601rsrB0.4824.840.0560.7531.17.4.168
50.0601jk0A0.4704.490.0440.6941.17.4.1NA
60.0601h0nA0.4754.640.0390.7041.17.4.1NA
70.0601d8cA0.4804.190.0980.6992.3.3.934,36
80.0602gq3A0.4894.180.0790.7102.3.3.9NA
90.0602eqdA0.4685.350.0990.8173.2.1.151NA
100.0601izjA0.4614.660.0420.7263.2.1.135,3.2.1.1NA
110.0601j0kA0.4555.170.1060.7583.2.1.13559
120.0602zicA0.4734.930.0580.7693.2.1.70NA
130.0602pbgA0.4674.880.0500.7263.2.1.85NA
140.0602nlxA0.4654.820.0440.7202.7.1.17NA
150.0602pulA0.5444.780.0800.8712.7.1.100NA
160.0602aaaA0.4694.690.0510.7313.2.1.119
170.0602vuxB0.4484.460.0450.6611.17.4.1NA
180.0602zidA0.4734.780.0650.7533.2.1.70110
190.0601bf2A0.4805.200.0400.8123.2.1.68NA

(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
00.370.9021.550.180.975d1wD GO:0003677 GO:0006351 GO:0006355
10.340.6672.940.220.843bniA GO:0003677 GO:0006351 GO:0006355
20.340.7403.000.120.932f07A GO:0003677 GO:0006351 GO:0006355
30.270.5944.150.110.873ppbA GO:0003677 GO:0006351 GO:0006355
40.270.7053.290.120.913bjbB GO:0003677 GO:0006351 GO:0006355
50.260.5844.510.080.893bcgA GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0008144 GO:0042493 GO:0043565 GO:0045892
60.250.7023.450.100.932hytA GO:0003677 GO:0006351 GO:0006355
70.240.5554.320.150.812qwtA GO:0003677 GO:0006351 GO:0006355
80.230.6913.540.130.944cgrA GO:0003677 GO:0006351 GO:0006355
90.230.6373.650.130.873vuqC GO:0003677 GO:0006351 GO:0006355
100.220.5644.620.150.893c2bA GO:0003677 GO:0006351 GO:0006355
110.210.6423.730.150.902g3bA GO:0003677 GO:0006351 GO:0006355
120.210.5944.330.090.903lhqA GO:0003677 GO:0003700 GO:0006351 GO:0006355
130.210.6043.800.140.854auxA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677 GO:0046872
140.200.5964.350.210.863he0C GO:0003677 GO:0006351 GO:0006355
150.190.6113.800.120.864hkuA GO:0003677 GO:0006351 GO:0006355
160.190.6363.660.110.882qibA GO:0003677 GO:0003700 GO:0006351 GO:0006355
170.190.5384.160.120.813egqA GO:0003677 GO:0006351 GO:0006355
180.190.5844.230.100.844nn1A GO:0003677 GO:0003700 GO:0006351 GO:0006355
190.180.6453.970.120.923bhqA GO:0003677 GO:0006351 GO:0006355
200.180.5354.210.110.822q24B GO:0003677 GO:0006351 GO:0006355
210.180.6334.100.100.933hggA GO:0003677 GO:0006351 GO:0006355
220.180.6153.930.090.885f1jA GO:0003677 GO:0006351 GO:0006355
230.170.5614.420.080.852id6A GO:0003677 GO:0006351 GO:0006355
240.160.5554.520.090.823vprA GO:0003677 GO:0006351 GO:0006355 GO:0042802
250.160.5764.510.110.873pasB GO:0003677 GO:0006351 GO:0006355
260.160.6074.180.110.894mk6A GO:0003677 GO:0006351 GO:0006355
270.150.5924.460.090.903qbmA GO:0003677 GO:0003700 GO:0006351 GO:0006355
280.150.5984.060.140.892fq4A GO:0003677 GO:0006351 GO:0006355
290.140.5754.480.080.902rasB GO:0003677 GO:0006351 GO:0006355
300.140.5684.190.100.812o7tA GO:0003677 GO:0006351 GO:0006355
310.130.5834.180.090.874l62A GO:0000976 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355
320.120.5434.850.070.883geuA GO:0003677 GO:0006351 GO:0006355
330.120.5524.560.110.843f1bA GO:0003677 GO:0006351 GO:0006355
340.120.7003.190.140.902zb9A GO:0003677 GO:0006351 GO:0006355
350.100.4964.740.120.763colA GO:0003677 GO:0006351 GO:0006355
360.100.6643.720.140.902zcxA GO:0003677 GO:0006351 GO:0006355
370.100.6483.790.160.913cwrA GO:0003677 GO:0006351 GO:0006355
380.090.6463.840.120.895d18A GO:0003677 GO:0006351 GO:0006355
390.090.6633.670.120.923c07A GO:0003677 GO:0006351 GO:0006355
400.070.5943.970.100.862raeA GO:0003677 GO:0006351 GO:0006355
410.070.5934.210.130.894jl3C GO:0003677 GO:0006351 GO:0006355
420.070.5274.420.140.812rekB GO:0003677 GO:0006351 GO:0006355
430.070.5724.540.100.893dpjA GO:0003677 GO:0006351 GO:0006355
440.070.6004.010.080.882iu5A GO:0003677 GO:0006351 GO:0006355
450.070.5564.870.090.912uxhA GO:0003677 GO:0006351 GO:0006355
460.070.5774.300.120.873npiA GO:0003677 GO:0006351 GO:0006355
470.070.5164.520.100.753kkcA GO:0003677 GO:0006351 GO:0006355
480.070.5064.690.130.812guhA GO:0003677 GO:0006351 GO:0006355


Consensus prediction of GO terms
 
Molecular Function GO:0003677
GO-Score 0.85
Biological Processes GO:0006355
GO-Score 0.85
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.