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I-TASSER results for job id Rv0123

[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
10.12 6 2bsqH NUC Rep, Mult 89,93,98,99,100,104
20.04 2 3bdcA CA Rep, Mult 15,35,37,39
30.04 2 1rm6A NA Rep, Mult 56,57,59
40.04 2 4rkuL CLA Rep, Mult 103,107
50.04 2 3cknA MN Rep, Mult 23,85
60.02 1 1revA MG Rep, Mult 12,15
70.02 1 1tkoB FE Rep, Mult 109,112
80.02 1 1t9rA PO4 Rep, Mult 15,49,113
90.02 1 3jwqA VIA Rep, Mult 11,49,53,56
100.02 1 4h6pC FMN Rep, Mult 30,67
110.02 1 2hzaA 3CM Rep, Mult 91,92,95,97,106
120.02 1 2ch1A LLP Rep, Mult 30,37
130.02 1 3zjoB AZI Rep, Mult 78,106,110
140.02 1 3zq4D CA Rep, Mult 54,117
150.02 1 3jwqB MG Rep, Mult 16,32,48
160.02 1 3e25A MG Rep, Mult 21,23

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
10.0601fo4A0.5063.930.0560.8111.17.1.4NA
20.0602ouyA0.4994.360.0490.8363.1.4.1752,57,104
30.0601rm6A0.5234.230.0550.8851.3.99.20NA
40.0603dysB0.4974.530.0260.8283.1.4.35109
50.0603djlA0.4794.660.0330.8031.3.99.-NA
60.0601fa9A0.4874.110.0780.7702.4.1.135
70.0602pywA0.4814.150.1140.7872.7.1.100NA
80.0601tazA0.5024.650.0650.8613.1.4.1754
90.0602o2dB0.4854.110.0690.7705.3.1.985
100.0602e1qA0.5044.440.0550.8691.17.3.2,1.17.1.4NA
110.0601t3qB0.5024.310.0460.8771.3.99.17NA
120.0603b8cA0.4874.750.0430.8443.6.3.6NA
130.0602pulA0.4764.380.1110.8112.7.1.100NA
140.0601jroB0.5004.040.0650.8281.1.1.204NA
150.0601z1wA0.4794.440.0550.8113.4.11.-18
160.0603b9jJ0.4164.950.0810.7461.17.1.4,1.17.3.257
170.0601zklA0.5094.580.0170.8533.1.4.17106,110
180.0602qykB0.5004.710.0630.8693.1.4.1721
190.0603hfwA0.4854.600.0650.8443.2.2.1914

(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
00.240.5234.230.060.891rm6A GO:0016491 GO:0018525 GO:0055114
10.070.5004.040.070.831jroB GO:0016491 GO:0030151 GO:0046872 GO:0055114
20.070.5214.240.020.891n63B GO:0005507 GO:0016491 GO:0018492 GO:0030151 GO:0046872 GO:0055114
30.070.5104.100.060.861ffuB GO:0005507 GO:0016491 GO:0018492 GO:0030151 GO:0046872 GO:0055114
40.070.5024.310.050.881t3qB GO:0016491 GO:0055114
50.070.4804.360.050.843zyvB GO:0003824 GO:0004031 GO:0004854 GO:0005506 GO:0005737 GO:0005829 GO:0009055 GO:0009115 GO:0016491 GO:0016614 GO:0030151 GO:0046872 GO:0050660 GO:0051287 GO:0051536 GO:0051537 GO:0055114
60.070.5044.440.060.872e1qA GO:0001933 GO:0001937 GO:0003824 GO:0004854 GO:0004855 GO:0005506 GO:0005576 GO:0005615 GO:0005737 GO:0005777 GO:0005829 GO:0006195 GO:0006919 GO:0007595 GO:0009055 GO:0009115 GO:0010629 GO:0016491 GO:0016529 GO:0016614 GO:0016903 GO:0030856 GO:0042803 GO:0043546 GO:0045602 GO:0046872 GO:0050660 GO:0051536 GO:0051537 GO:0051898 GO:0055114 GO:1900745 GO:1900747 GO:2000379 GO:2001213
70.070.4954.120.030.841dgjA GO:0009055 GO:0016491 GO:0046872 GO:0051536 GO:0051537 GO:0055114
80.070.5063.930.060.811fo4A GO:0003824 GO:0004854 GO:0004855 GO:0005506 GO:0005576 GO:0005615 GO:0005737 GO:0005777 GO:0005829 GO:0009055 GO:0009115 GO:0016491 GO:0016614 GO:0016903 GO:0043546 GO:0046872 GO:0050660 GO:0051536 GO:0051537 GO:0055114
90.060.4934.130.080.822ckjA GO:0001933 GO:0001937 GO:0003824 GO:0004854 GO:0004855 GO:0005506 GO:0005576 GO:0005615 GO:0005737 GO:0005777 GO:0005829 GO:0006195 GO:0006919 GO:0007595 GO:0009055 GO:0009115 GO:0010629 GO:0016491 GO:0016529 GO:0016614 GO:0016903 GO:0030856 GO:0042803 GO:0043546 GO:0045602 GO:0046872 GO:0050660 GO:0051536 GO:0051537 GO:0051898 GO:0055114 GO:1900745 GO:1900747 GO:2000379 GO:2001213
100.060.4154.770.070.713hrdA GO:0016491 GO:0046872 GO:0050138 GO:0051187 GO:0055114
110.060.4994.130.040.824uhxA GO:0003824 GO:0004031 GO:0004854 GO:0005506 GO:0005737 GO:0005829 GO:0006954 GO:0009055 GO:0009115 GO:0016491 GO:0016614 GO:0042816 GO:0043546 GO:0046872 GO:0050660 GO:0051287 GO:0051536 GO:0051537 GO:0055114 GO:0070062 GO:0072593
120.060.4974.110.060.814zohA GO:0016491 GO:0055114
130.060.4074.870.090.723fahA GO:0009055 GO:0016491 GO:0033727 GO:0046872 GO:0051536 GO:0051537 GO:0055114
140.060.4084.760.060.773gp5A GO:0003824 GO:0004619 GO:0006094 GO:0006096 GO:0008152 GO:0016853 GO:0016868 GO:0046538
150.060.3825.040.040.695a5bW GO:0000502 GO:0005198 GO:0005634 GO:0005829 GO:0006511 GO:0008540 GO:0031593 GO:0043161 GO:0043248
160.060.3955.350.030.734r0cD GO:0015558 GO:0016020 GO:0016021 GO:1902604
170.060.3214.850.100.601xhnA GO:0003714 GO:0005576 GO:0005615 GO:0005667 GO:0006355 GO:0006357 GO:0007275 GO:0008134 GO:0008283 GO:0010181 GO:0016491 GO:0040008 GO:0055114 GO:0070062 GO:1903507
180.060.4074.770.030.673hrdB GO:0016491 GO:0046872 GO:0050138 GO:0051187 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0016636 GO:0046914
GO-Score 0.47 0.37
Biological Processes GO:0055114
GO-Score 0.42
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.