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I-TASSER results for job id Rv0552

[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 2 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
10.74 94 4dzhA ZN Rep, Mult 67,69,339,435
20.05 6 4c5yA ZN Rep, Mult 67,278,339,371
30.01 3 3be7E ARG Rep, Mult 284,285,339,341,371,393,396,401,418,435,438

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
10.3692gokA0.6113.200.1630.6873.5.2.7435
20.2082qt3A0.6003.320.1570.6803.5.99.461,484
30.1522vunD0.5293.520.1800.6033.5.2.18104
40.1121k6wA0.5863.860.1270.6873.5.4.1NA
50.0822uz9A0.6103.900.1340.7143.5.4.330,33,498
60.0823e0lA0.6083.840.1340.7123.5.4.3NA
70.0691ybqA0.5363.600.1810.6183.4.19.1343
80.0681onxA0.5363.600.1870.6183.4.19.-NA
90.0672p50A0.5093.500.1310.5863.5.1.25NA
100.0673egjA0.5073.360.1170.5793.5.1.25NA
110.0673hm7B0.5404.210.1410.6423.5.2.5NA
120.0673d6nA0.5333.930.1500.6273.5.2.3435
130.0661a4lA0.4654.240.1060.5583.5.4.4371,435
140.0663iarA0.4654.350.1080.5623.5.4.4371,435
150.0603iv8D0.5083.320.1170.5793.5.1.25NA
160.0601a5lC0.5164.370.1980.6123.5.1.5NA
170.0603e74B0.5064.110.1690.6073.5.2.5NA
180.0602g3fA0.6033.610.1660.6953.5.2.7216
190.0602i9uA0.5993.580.1180.6893.5.4.3186
200.0601ra0A0.5833.790.1330.6803.5.4.1398
210.0601gkrA0.5394.210.1890.6393.5.2.2435
220.0601xrtA0.5213.480.1320.5973.5.2.3435
230.0602vhlB0.5043.560.1420.5813.5.1.25197,199
240.0602puzA0.6103.220.1630.6873.5.2.7NA
250.0602icsA0.5013.640.1520.5813.5.4.237
260.0603lggA0.4984.950.0680.6253.5.4.4343,345
270.0603la4A0.5234.350.1390.6223.5.1.5143
280.0602oofA0.5873.370.1590.6673.5.2.7419
290.0601nfgA0.4685.450.1090.6203.5.2.2435
300.0602qt3B0.5983.350.1490.6803.5.99.461,484,487
310.0601ie7C0.5194.480.1380.6273.5.1.5NA
320.0603gipA0.4655.120.1470.5973.5.1.82NA
330.0601p1mA0.5903.330.1450.6703.5.4.28257

(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
00.310.6023.430.180.684whbA GO:0016787 GO:0016810
10.310.8781.040.210.893ighX GO:0006259 GO:0016810 GO:0016888
20.290.6183.460.220.714v1xE GO:0005737 GO:0016787 GO:0016810 GO:0018788 GO:0019381 GO:0046872
30.220.6023.370.150.682oofA GO:0005506 GO:0005737 GO:0006547 GO:0006548 GO:0008270 GO:0016787 GO:0016810 GO:0016812 GO:0019556 GO:0019557 GO:0046872 GO:0050480
40.180.8391.540.240.873icjA GO:0006259 GO:0016810 GO:0016888 GO:0046872
50.160.5314.390.200.623ooqF GO:0016787 GO:0016810 GO:0019239
60.150.5983.380.150.684cqbA GO:0005737 GO:0016787 GO:0016810 GO:0018764 GO:0019381 GO:0046872
70.070.6113.200.160.692gokA GO:0005506 GO:0005737 GO:0006547 GO:0006548 GO:0008270 GO:0016787 GO:0016810 GO:0016812 GO:0019556 GO:0019557 GO:0046872 GO:0050480
80.070.6103.350.180.693hpaA
90.070.5943.320.140.671j6pA GO:0004000 GO:0016787 GO:0016810 GO:0019239 GO:0019700 GO:0046872 GO:0050270 GO:0090614
100.070.5863.300.190.663mkvA GO:0016787 GO:0016810 GO:0046872
110.070.5863.360.210.663mtwA GO:0016787 GO:0016810 GO:0046872
120.070.5853.080.170.653be7A
130.070.5873.240.170.663n2cA
140.070.5363.600.180.621ybqA GO:0005737 GO:0005829 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008798 GO:0016787 GO:0016810 GO:0046872
150.070.5284.240.200.631m7jA GO:0016787 GO:0016810 GO:0016811 GO:0046872 GO:0047420
160.070.5363.740.140.624bjhA GO:0004151 GO:0006221 GO:0008270 GO:0016787 GO:0016810 GO:0016812 GO:0044205 GO:0046872
170.070.5324.130.120.633mpgA GO:0004151 GO:0006221 GO:0008270 GO:0009220 GO:0016787 GO:0016810 GO:0016812 GO:0044205 GO:0046872
180.070.5213.480.130.601xrtA GO:0004151 GO:0006221 GO:0008270 GO:0016787 GO:0016810 GO:0016812 GO:0044205 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0016810 GO:0019120 GO:0046914 GO:0016888
GO-Score 0.78 0.58 0.45 0.43
Biological Processes GO:0018873 GO:0042204 GO:0043606 GO:0006547 GO:0006536 GO:0015942 GO:0009063 GO:0006259
GO-Score 0.58 0.58 0.45 0.45 0.45 0.45 0.45 0.43
Cellular Component GO:0005737
GO-Score 0.45

(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.