[Home] [Server] [About] [Statistics] [Annotation]

I-TASSER results for job id Rv2722

[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
10.16 8 3hl2D NUC Rep, Mult 38,42
20.06 3 3pt6A ZN Rep, Mult 3,7,10,76
30.04 2 3nm9A NUC Rep, Mult 34,37,38
40.04 2 2iceA CA Rep, Mult 21,51,52,54
50.04 2 1c8fA CA Rep, Mult 77,80
60.04 2 2rfmA BU2 Rep, Mult 42,45,46
70.04 2 1mj2B NUC Rep, Mult 28,29,34
80.02 1 1pegB ZN Rep, Mult 19,23
90.02 1 2r45A PO4 Rep, Mult 22,25,27
100.02 1 1i95K WO2 Rep, Mult 21,22
110.02 1 2ei0A BP7 Rep, Mult 47,49,65,66,67,68

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
10.0601zwxA0.5073.540.0630.8663.1.4.12NA
20.0601g60A0.5093.540.0750.8662.1.1.7233
30.0601db3A0.4723.420.0250.8054.2.1.4738
40.0601epsA0.5003.650.0910.8422.5.1.19,2.5.1.9NA
50.0602iirA0.4693.840.0640.8662.7.2.1NA
60.0603kx2B0.4664.250.0850.8663.6.4.1336
70.0601dctA0.4713.720.0630.8292.1.1.37NA
80.0601dctB0.4723.650.0500.8292.1.1.37NA
90.0601p33B0.4724.150.0410.8541.5.1.33,1.1.1.253NA
100.0602a3zB0.5133.680.0520.8783.1.21.1NA
110.0602bfpD0.4724.000.0530.8421.5.1.3348
120.0601nw7A0.4993.860.0510.9152.1.1.7237
130.0603ek6A0.4883.730.0270.8052.7.4.22NA
140.0601dusA0.4723.330.0620.7562.1.1.-NA
150.0601p89A0.4263.580.0320.6952.5.1.1934
160.0603l76A0.4693.900.0530.7802.7.2.438
170.0602va1B0.4674.050.0250.8292.7.4.2235
180.0602o3hA0.4853.700.0130.8294.2.99.18NA
190.0601akoA0.4913.700.0130.8543.1.11.210

(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
00.070.4624.150.050.902ddsA GO:0004767 GO:0005576 GO:0008081 GO:0016787 GO:0019835 GO:0044179
10.070.5203.410.060.853i48A GO:0005576 GO:0008081 GO:0046872
20.070.5323.300.060.844ruwA GO:0004519 GO:0004527 GO:0046872 GO:0090305
30.070.5193.510.040.873wcxA GO:0004767 GO:0005576 GO:0008081 GO:0016787
40.070.5073.540.060.871zwxA GO:0004767 GO:0005576 GO:0008081 GO:0009405 GO:0016787 GO:0019835 GO:0044179
50.070.5213.540.060.852fphX GO:0003723
60.070.5053.700.050.894zkfA GO:0004518 GO:0004527 GO:0004535 GO:0005739 GO:0005759 GO:0006397 GO:0016787 GO:0046872 GO:0090305 GO:0090503
70.070.5213.650.010.883ngoA GO:0000288 GO:0000289 GO:0004518 GO:0004527 GO:0004535 GO:0005634 GO:0005737 GO:0005829 GO:0006351 GO:0006355 GO:0006397 GO:0006417 GO:0006977 GO:0008284 GO:0010606 GO:0016787 GO:0030014 GO:0031047 GO:0046872 GO:0061157 GO:0090503
80.070.4903.510.090.882imqX GO:0016787 GO:0046856 GO:0046872
90.070.5183.350.050.851i9yA GO:0004439 GO:0005509 GO:0005737 GO:0005829 GO:0006629 GO:0006810 GO:0006897 GO:0015031 GO:0016787 GO:0030487 GO:0032153 GO:0034485 GO:0036092 GO:0042578 GO:0043813 GO:0046856 GO:0048017 GO:0051286 GO:0052658 GO:0052659 GO:1990640 GO:1990648 GO:1990649 GO:1990650 GO:1990651
100.070.5203.220.080.833mprA GO:0004519 GO:0004527 GO:0090305
110.070.5183.190.030.823g6sA GO:0004519 GO:0004527 GO:0090305
120.070.4843.840.090.875a7iA GO:0001701 GO:0004439 GO:0005096 GO:0005737 GO:0005768 GO:0005793 GO:0005794 GO:0005829 GO:0005886 GO:0007165 GO:0007283 GO:0016020 GO:0016021 GO:0016787 GO:0030317 GO:0030670 GO:0031410 GO:0031901 GO:0043547 GO:0043647 GO:0046856 GO:0046872 GO:0051056 GO:0052658 GO:0052659 GO:0070613
130.070.4873.950.050.894cmnA GO:0001701 GO:0001750 GO:0004439 GO:0005096 GO:0005634 GO:0005737 GO:0005768 GO:0005769 GO:0005794 GO:0005795 GO:0005798 GO:0005802 GO:0005829 GO:0005886 GO:0005905 GO:0005929 GO:0006629 GO:0006661 GO:0007165 GO:0016020 GO:0016023 GO:0016787 GO:0030030 GO:0030136 GO:0030670 GO:0031410 GO:0031901 GO:0042384 GO:0042995 GO:0043087 GO:0043547 GO:0043647 GO:0046856 GO:0048365 GO:0051056 GO:0052658 GO:0052659 GO:0052745 GO:0070062
140.070.4963.770.060.913nr8B GO:0001958 GO:0002376 GO:0003779 GO:0005737 GO:0005794 GO:0005829 GO:0005856 GO:0005886 GO:0006006 GO:0006661 GO:0006897 GO:0007015 GO:0007155 GO:0008285 GO:0009791 GO:0010629 GO:0016020 GO:0016787 GO:0017124 GO:0030027 GO:0030175 GO:0032868 GO:0034485 GO:0042169 GO:0042995 GO:0043647 GO:0044255 GO:0046856 GO:0052659 GO:0097178
150.070.5003.700.060.872xswA GO:0000139 GO:0001726 GO:0004439 GO:0004445 GO:0005737 GO:0005794 GO:0005829 GO:0005856 GO:0005886 GO:0005929 GO:0005930 GO:0006629 GO:0006661 GO:0010976 GO:0016020 GO:0016787 GO:0032580 GO:0042995 GO:0046488 GO:0046855 GO:0046856 GO:0072372
160.070.4084.690.030.874xxhA GO:0003677 GO:0003700 GO:0005991 GO:0006351 GO:0006355 GO:0045892
170.060.4144.330.030.824gfvB GO:0004721 GO:0004725 GO:0004726 GO:0005634 GO:0005737 GO:0006470 GO:0016311 GO:0016787 GO:0016791 GO:0035335
180.060.3514.480.050.713nwuB GO:0001558 GO:0001890 GO:0004252 GO:0005520 GO:0005576 GO:0005615 GO:0005737 GO:0005829 GO:0005886 GO:0006508 GO:0008233 GO:0008236 GO:0016020 GO:0016787 GO:0019838 GO:0022617 GO:0030512 GO:0030514 GO:0031012 GO:0050679 GO:0050687 GO:0060718 GO:0070062 GO:0097187


Consensus prediction of GO terms
 
Molecular Function GO:0042578 GO:0004620
GO-Score 0.49 0.38
Biological Processes GO:0044179 GO:0090305 GO:0009405
GO-Score 0.14 0.07 0.07
Cellular Component GO:0005576
GO-Score 0.25

(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.