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I-TASSER results for job id Rv0093c

[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
10.20 10 3oj6A ZN Rep, Mult 49,79,82
20.04 2 2qtsC MAL Rep, Mult 136,140
30.04 2 2dysO CDL Rep, Mult 131,135,138,139,142
40.02 1 1izlC CLA Rep, Mult 226,230
50.02 1 3dtuC DXC Rep, Mult 89,92,93,96,167,170
60.02 1 3mk7D CA Rep, Mult 57,65,69
70.02 1 3i9dW MG Rep, Mult 97,101
80.02 1 4jbeB CA Rep, Mult 74,78
90.02 1 2h6bA 3C4 Rep, Mult 142,145
100.02 1 3om3A CA Rep, Mult 55,58,62,64
110.02 1 3dtuC DMU Rep, Mult 86,89,90,93
120.02 1 1qprA PPC Rep, Mult 53,128
130.02 1 1s5lT CLA Rep, Mult 145,148
140.02 1 3luhB 5GP Rep, Mult 116,120

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
10.0603ciaA0.4365.900.0610.7093.4.11.-50
20.0601vncA0.4505.920.0460.7311.11.1.1019,21
30.0602dqbA0.4305.100.0490.6143.1.5.1120,138,177
40.0603gvdI0.3965.320.0960.6032.3.1.30NA
50.0601fgjA0.4086.080.0430.6841.7.3.4NA
60.0601m56A0.4406.180.0450.7381.9.3.1NA
70.0602occN0.4016.870.0560.7381.9.3.1201
80.0601gw6A0.4285.950.0430.7023.3.2.6NA
90.0603b9jJ0.3346.310.0450.5601.17.1.4,1.17.3.289,91,94
100.0603i4lA0.4195.740.0870.6773.6.3.1453,135
110.0601ssqD0.3885.330.0710.5922.3.1.3063
120.0603cskA0.4036.030.0490.6703.4.14.4NA
130.0603b8eC0.4036.210.0570.7023.6.3.984,180
140.0603b9jC0.3126.300.0440.5351.17.3.2,1.17.1.4NA
150.0601fo4A0.3686.800.0270.6701.17.1.4NA
160.0603ixzA0.4285.870.0620.7063.6.3.10NA
170.0601pn0C0.3986.010.0400.6631.14.13.7124
180.0601eulA0.4075.810.0470.6493.6.3.8NA
190.0601dgjA0.4016.460.0530.7131.2.-.-NA

(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
00.290.4156.150.040.711occA GO:0004129 GO:0005506 GO:0005739 GO:0005743 GO:0006119 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0045277 GO:0046872 GO:0055114 GO:0070469 GO:1902600
10.220.4406.180.040.741m56A GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0006119 GO:0006810 GO:0006811 GO:0009055 GO:0009060 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0022900 GO:0046872 GO:0055114 GO:0070469 GO:1902600
20.070.4515.790.050.721iduA GO:0004601 GO:0005576 GO:0016491 GO:0016691 GO:0046872 GO:0055114 GO:0098869
30.070.4266.240.040.731qleA GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0006119 GO:0006810 GO:0006811 GO:0009055 GO:0009060 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0022900 GO:0046872 GO:0055114 GO:0070469 GO:1902600
40.060.3946.900.040.731fftA GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0005887 GO:0006811 GO:0009055 GO:0009060 GO:0009319 GO:0009486 GO:0015078 GO:0015453 GO:0015990 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0016682 GO:0019646 GO:0020037 GO:0046872 GO:0048039 GO:0055114 GO:0070469
50.060.4416.130.050.744he8F GO:0005886 GO:0008137 GO:0016020 GO:0016021 GO:0016491 GO:0042773 GO:0048038 GO:0055114
60.060.3886.310.060.683eh3A GO:0004129 GO:0005506 GO:0005886 GO:0006119 GO:0006811 GO:0009055 GO:0009060 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0046872 GO:0055114 GO:0070469 GO:1902600
70.060.3836.370.060.683w36B GO:0004601 GO:0055114 GO:0098869
80.060.3756.560.040.662yevA GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0006119 GO:0006810 GO:0006811 GO:0009055 GO:0009060 GO:0015002 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0022900 GO:0022904 GO:0046872 GO:0055114 GO:0070469 GO:1902600
90.060.3566.220.090.584he8I GO:0005886 GO:0006810 GO:0008137 GO:0016020 GO:0016021 GO:0016491 GO:0042773 GO:0048038 GO:0050136 GO:0055114
100.060.3606.600.040.654djaA GO:0000166 GO:0000719 GO:0003677 GO:0003914 GO:0006281 GO:0006974 GO:0016829 GO:0018298 GO:0046872 GO:0051536 GO:0051539 GO:0071949
110.060.2775.470.040.441tj7A GO:0003824 GO:0004056 GO:0005737 GO:0005829 GO:0006526 GO:0008652 GO:0016829 GO:0042450 GO:0051262
120.060.3286.190.040.542p5oB GO:0000166 GO:0003676 GO:0003677 GO:0003887 GO:0004518 GO:0004527 GO:0006260 GO:0008408 GO:0016740 GO:0016779 GO:0016787 GO:0039693 GO:0071897 GO:0090305
130.060.2646.080.040.433pgxA GO:0016491 GO:0055114
140.060.3247.060.040.603gdeA GO:0000166 GO:0003677 GO:0003909 GO:0003910 GO:0005524 GO:0006260 GO:0006281 GO:0006310 GO:0006974 GO:0007049 GO:0016874 GO:0046872 GO:0051103 GO:0051301 GO:0071897
150.060.2674.780.020.384iwbA GO:0044780
160.060.2545.340.080.382wgbB GO:0003677 GO:0006351 GO:0006355
170.060.2746.400.090.485ekqD GO:0009279 GO:0016020 GO:0043165 GO:0051205 GO:1990063
180.060.2306.100.050.393tswB GO:0001825 GO:0005516 GO:0005634 GO:0005737 GO:0005829 GO:0005886 GO:0005911 GO:0005912 GO:0005913 GO:0005921 GO:0005923 GO:0007043 GO:0007605 GO:0014704 GO:0016020 GO:0016323 GO:0016324 GO:0016327 GO:0019904 GO:0030054 GO:0035329 GO:0043296 GO:0045177 GO:0046581 GO:0090557 GO:0098609 GO:0098641 GO:1901350


Consensus prediction of GO terms
 
Molecular Function GO:0004129 GO:0005506 GO:0020037 GO:0005507
GO-Score 0.52 0.52 0.52 0.32
Biological Processes GO:0009060 GO:1902600 GO:0006119
GO-Score 0.52 0.48 0.48
Cellular Component GO:0019866 GO:0098803 GO:0031966 GO:0070069 GO:0016021 GO:0005886
GO-Score 0.58 0.58 0.58 0.58 0.52 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.