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I-TASSER results for job id Rv0616c

[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
10.08 4 1a4fB OXY Rep, Mult 30,66,70
20.06 3 2vwaF PTY Rep, Mult 8,12,62,66,69,73,74,77
30.05 3 1leiB QNA Rep, Mult 35,42,43,44
40.04 2 2vunA FE Rep, Mult 13,39,60
50.04 2 2jfaB III Rep, Mult 27,31,35,57,60,61,64
60.04 2 2zseA PAU Rep, Mult 26,29,30,33,70
70.04 2 3ce2A ZN Rep, Mult 31,35,57
80.04 2 3svlB CA Rep, Mult 15,16
90.02 1 3opqA PO4 Rep, Mult 21,23,24
100.02 1 1t3tA SO4 Rep, Mult 43,83,84,85,86
110.02 1 3e27A MG Rep, Mult 33,50
120.02 1 2w6dA GDP Rep, Mult 25,26,28,29,67
130.02 1 3jcuX CLA Rep, Mult 65,69
140.02 1 4i7zD OZ2 Rep, Mult 80,82
150.02 1 3zt6A ACX Rep, Mult 4,5
160.02 1 2h88C UNL Rep, Mult 75,79

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
10.0603bllA0.4004.460.0630.7162.4.2.29NA
20.0602f9qA0.5523.570.0110.8641.14.14.1NA
30.0603dsiA0.5323.570.0120.8414.2.1.9215,66
40.0602ibpA0.5253.400.0510.8302.3.3.123
50.0602p2wA0.5623.210.0360.8862.3.3.-31
60.0603b98A0.5273.150.0800.8305.3.99.46,34,36
70.0602ckpB0.4653.550.0530.7952.7.1.32NA
80.0603dpgA0.5363.640.0770.8753.1.21.4NA
90.0603hwkE0.5533.650.0710.8982.3.3.131
100.0602hi4A0.5473.210.0230.8301.14.14.1NA
110.0602ashD0.5423.300.0470.8302.4.2.29NA
120.0602fp0B0.5463.920.0850.8983.2.1.143NA
130.0602ashA0.5473.280.0470.8302.4.2.29NA
140.0603fegA0.4663.880.0470.8182.7.1.82NA
150.0602ve3A0.5323.520.0710.8861.14.-.-NA
160.0603dlaD0.5492.760.0690.7736.3.5.1NA
170.0602geuA0.5472.950.0740.7732.7.1.3373
180.0601q5eA0.5313.350.1280.8411.14.-.-NA
190.0601jawA0.5273.760.0490.8753.4.11.954

(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
00.080.5093.440.090.771xu0A GO:0005886 GO:0016020 GO:0046872 GO:0051260
10.080.5214.200.040.895awwY GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0043952 GO:0065002
20.070.5513.680.050.935eulY GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0043952 GO:0065002
30.070.5993.230.040.862kfoA GO:0001933 GO:0005507 GO:0005521 GO:0005737 GO:0005741 GO:0005783 GO:0005794 GO:0005886 GO:0006139 GO:0006878 GO:0006979 GO:0007611 GO:0008017 GO:0009986 GO:0015631 GO:0016020 GO:0031225 GO:0032689 GO:0032700 GO:0032703 GO:0032880 GO:0035690 GO:0042802 GO:0043008 GO:0043066 GO:0043433 GO:0044325 GO:0045121 GO:0046007 GO:0046686 GO:0046688 GO:0046872 GO:0050860 GO:0051087 GO:0051260 GO:0070062 GO:0070885 GO:0071280 GO:1901379
40.070.6012.900.040.832kflA GO:0001933 GO:0005507 GO:0005783 GO:0005794 GO:0005886 GO:0006979 GO:0008017 GO:0009986 GO:0015631 GO:0016020 GO:0016021 GO:0032689 GO:0032700 GO:0032703 GO:0032880 GO:0035690 GO:0042802 GO:0043066 GO:0043433 GO:0045121 GO:0046007 GO:0046872 GO:0050860 GO:0051260 GO:0070062 GO:0070885 GO:0071280 GO:1901379
50.070.4743.930.080.852wwbA GO:0005783 GO:0005789 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0030176 GO:0045047
60.070.5263.860.100.853mp7A GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0065002
70.070.5203.410.080.884q2gB GO:0004605 GO:0005886 GO:0006629 GO:0006655 GO:0008654 GO:0016020 GO:0016021 GO:0016024 GO:0016740 GO:0016772 GO:0016779
80.070.4564.460.010.783ayfA GO:0004129 GO:0005506 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0020037 GO:0046872 GO:0055114 GO:1902600
90.070.5883.340.080.943dl8G GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0043952 GO:0065002
100.070.4873.350.000.743bo0A GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0065002
110.070.4453.530.060.731u5lA GO:0005886 GO:0016020 GO:0016021 GO:0046872 GO:0051260
120.070.5303.770.030.932yxrA GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0065002
130.070.5443.620.070.935abbA GO:0005622 GO:0005886 GO:0005887 GO:0006605 GO:0006810 GO:0006886 GO:0015031 GO:0016020 GO:0016021 GO:0043952 GO:0065002
140.060.4433.650.060.731i17A GO:0005507 GO:0005886 GO:0006878 GO:0016020 GO:0031225 GO:0051260
150.060.4513.450.090.681u3mA GO:0001933 GO:0001948 GO:0005507 GO:0005605 GO:0005623 GO:0005783 GO:0005794 GO:0005886 GO:0006979 GO:0008017 GO:0009986 GO:0010628 GO:0010870 GO:0015631 GO:0016020 GO:0031225 GO:0032689 GO:0032700 GO:0032703 GO:0032880 GO:0035690 GO:0042802 GO:0043066 GO:0043083 GO:0043433 GO:0045121 GO:0046007 GO:0046872 GO:0050731 GO:0050860 GO:0051260 GO:0070062 GO:0070885 GO:0071280 GO:0098737 GO:1901379
160.060.5473.760.070.903dinC GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0043952 GO:0065002
170.060.4273.480.000.692kunA GO:0001933 GO:0005507 GO:0005521 GO:0005634 GO:0005737 GO:0005783 GO:0005794 GO:0005886 GO:0006878 GO:0006979 GO:0007049 GO:0007050 GO:0007611 GO:0008017 GO:0008152 GO:0009986 GO:0015631 GO:0016020 GO:0019898 GO:0031225 GO:0032689 GO:0032700 GO:0032703 GO:0032880 GO:0035690 GO:0042802 GO:0043008 GO:0043066 GO:0043433 GO:0044325 GO:0045121 GO:0046007 GO:0046686 GO:0046688 GO:0046872 GO:0050860 GO:0051087 GO:0051260 GO:0070062 GO:0070885 GO:0071280 GO:1901379
180.060.4093.980.040.702vcvA GO:0004364 GO:0005737 GO:0005829 GO:0006749 GO:0008152 GO:0016740 GO:0070062 GO:1901687


Consensus prediction of GO terms
 
Molecular Function GO:0043169
GO-Score 0.40
Biological Processes GO:0051259
GO-Score 0.40
Cellular Component GO:0031224 GO:0005886
GO-Score 0.32 0.32

(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.