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I-TASSER results for job id Rv3129

[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
10.24 3 2hq9A FAD Rep, Mult 38,40,41,42,84,85,86
20.18 3 2i02A FMN Rep, Mult 10,11,15,16,17,67,68
30.06 1 3hy8A PO4 Rep, Mult 3,4,6,8,56
40.06 1 3in6B FMN Rep, Mult 42,46,81
50.06 1 1nrgA PO4 Rep, Mult 10,11,67,68

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
10.0601x31B0.4674.870.1510.7911.5.3.141
20.0601ddtA0.4264.830.1190.7642.4.2.36NA
30.0603hxxA0.4304.430.0280.7186.1.1.7NA
40.0601yiqA0.4334.050.0850.6911.1.99.-NA
50.0602zzgA0.4645.060.0560.8466.1.1.7NA
60.0601j5wB0.4554.980.0750.8556.1.1.14NA
70.0602jbvB0.4404.350.0540.7821.1.3.17NA
80.0601l0wB0.4623.520.0910.7186.1.1.12NA
90.0602a2jA0.5932.680.0850.7641.4.3.5NA
100.0601qtfA0.4303.970.0560.6543.4.21.-NA
110.0601si8A0.4384.380.0640.7361.11.1.6NA
120.0602g5fA0.4524.100.0570.7005.4.4.2NA
130.0602xalA0.4325.150.0850.8642.7.1.158NA
140.0601eqrA0.4473.770.0340.7096.1.1.12NA
150.0602nz2A0.4304.170.0110.7186.3.4.5NA
160.0602gewA0.4314.320.0340.7641.1.3.6NA
170.0601tuuA0.4283.850.0800.6732.7.2.1NA
180.0603c7cB0.4433.960.0740.7461.5.1.11NA
190.0601bdaA0.3205.350.0330.6643.4.21.68NA

(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
00.340.7871.410.410.853fkhD GO:0010181 GO:0016491 GO:0055114
10.170.6602.000.360.763cp3A GO:0010181 GO:0016491 GO:0055114
20.140.6433.060.120.861rfeA GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
30.080.6502.290.100.784zkyA GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
40.080.6622.170.100.792fg9A GO:0000166 GO:0010181 GO:0016491 GO:0055114
50.070.6372.230.140.772htiA GO:0000166 GO:0010181 GO:0016491 GO:0055114
60.070.6222.600.050.805bncA GO:0010181 GO:0016491 GO:0055114
70.070.6382.030.170.733u5wA GO:0010181 GO:0016491 GO:0055114
80.070.6422.680.100.822furA GO:0010181 GO:0016491 GO:0055114
90.070.6242.860.060.803tgvA GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
100.070.6432.520.080.814ybnA GO:0010181 GO:0016491 GO:0055114
110.070.6252.760.110.772x1kA GO:0010181 GO:0016491 GO:0055114
120.070.6042.530.150.752asfA GO:0004733 GO:0005576 GO:0005618 GO:0010181 GO:0016491 GO:0042823 GO:0055114
130.070.6012.680.080.755escA GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
140.070.5932.790.080.773dnhA GO:0010181 GO:0016491 GO:0055114
150.070.5772.770.130.712ou5A GO:0000166 GO:0010181 GO:0016491 GO:0055114
160.070.6082.320.090.753ec6A GO:0000166 GO:0003677 GO:0010181 GO:0016491 GO:0055114
170.070.5162.720.150.653r5lA GO:0005618 GO:0005886 GO:0010181 GO:0016020 GO:0016491 GO:0055114 GO:0070967
180.070.5513.470.170.743f7eA GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
190.060.3064.260.020.524k0vA GO:0000165 GO:0000166 GO:0001525 GO:0001666 GO:0001725 GO:0001934 GO:0001935 GO:0001938 GO:0001958 GO:0002040 GO:0004672 GO:0004713 GO:0004714 GO:0004872 GO:0005088 GO:0005524 GO:0005576 GO:0005737 GO:0005856 GO:0005884 GO:0005886 GO:0005887 GO:0005902 GO:0005911 GO:0005925 GO:0006468 GO:0007165 GO:0007169 GO:0007267 GO:0007507 GO:0009925 GO:0009986 GO:0010033 GO:0010595 GO:0014068 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016323 GO:0016324 GO:0016525 GO:0016740 GO:0018108 GO:0019838 GO:0030054 GO:0031100 GO:0032878 GO:0034446 GO:0035556 GO:0043066 GO:0043114 GO:0043434 GO:0043547 GO:0043552 GO:0043627 GO:0045121 GO:0045766 GO:0046777 GO:0048014 GO:0050728 GO:0050900 GO:0051259 GO:0051591 GO:0051894 GO:0051897 GO:0060216 GO:0060347 GO:0070374 GO:1902533 GO:2000251 GO:2000351 GO:2000352
200.060.2733.360.020.373h0gK GO:0001055 GO:0003677 GO:0003899 GO:0005634 GO:0005665 GO:0005829 GO:0006351 GO:0006366 GO:0016591 GO:0046983


Consensus prediction of GO terms
 
Molecular Function GO:0010181 GO:0016641
GO-Score 0.60 0.41
Biological Processes GO:0055114 GO:0009108 GO:0042822 GO:1901576
GO-Score 0.60 0.41 0.41 0.41
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.