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

I-TASSER results for job id Rv1290A

[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
10.07 4 2z8yM XE Rep, Mult 10,63,75,92,93,94
20.05 3 3ch6E 311 Rep, Mult 31,32,67,71,94
30.03 2 3oq1A 3OQ Rep, Mult 23,77,90
40.03 2 5j7iD ADP Rep, Mult 12,13,35,36,37,59,81,90
50.03 2 2b1mA UUU Rep, Mult 85,88,98
60.03 2 3lz6B A0D Rep, Mult 21,34,48
70.03 2 3b5zD UUU Rep, Mult 12,13,14,15,17
80.03 2 1rx6A NAP Rep, Mult 13,14,15,17,35,36,37,39,58,78,79,90
90.02 1 3m0jA MN Rep, Mult 13,47,58,97
100.02 1 2bo6B MN Rep, Mult 37,47
110.02 1 1muuC SUC Rep, Mult 7,68,69,70,71,96,97,99
120.02 1 2irwA NN4 Rep, Mult 23,30,62,63,66,67,71
130.02 1 2p66A PO4 Rep, Mult 14,17,18
140.02 1 1ko7B PO4 Rep, Mult 5,12,16,52
150.02 1 3fcoB IIG Rep, Mult 66,67,70
160.02 1 3bzuC A21 Rep, Mult 60,63,82,83,88
170.02 1 3ojyB BMA Rep, Mult 17,21,50
180.02 1 1gzmA C8E Rep, Mult 64,67

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
10.0661wo8A0.5473.790.0330.8654.2.3.3NA
20.0601iy8A0.6273.670.1580.9131.1.1.-76
30.0602a4kB0.6123.520.1600.8941.1.1.100NA
40.0602vhxE0.6183.370.1170.8941.4.1.126
50.0603gvcB0.6253.650.1880.9231.-.-.-76
60.0602xaaA0.6213.210.1430.8751.1.1.113,16,79
70.0602qq5A0.6153.460.1460.9131.1.-.-NA
80.0603lk7A0.6153.140.1670.8656.3.2.914,15
90.0601pjbA0.6093.400.1170.8941.4.1.1NA
100.0602a4kA0.6183.500.1880.9041.1.1.10045
110.0603ch6B0.6193.550.2370.9231.1.1.14676
120.0601gz6B0.6213.570.1960.9231.1.1.6276
130.0601g6kA0.6193.610.1410.9421.1.1.4776
140.0601xhlA0.6243.480.1370.9041.1.1.23676
150.0602vhwE0.6163.460.1160.9041.4.1.1NA
160.0601npdB0.6133.360.1510.8851.1.1.282NA
170.0601rjwC0.6203.430.1600.9041.1.1.122
180.0601uufA0.6153.220.1740.8851.-.-.-NA
190.0601zbqA0.6233.520.1860.9234.2.1.107,1.1.1.3576
200.0601ahiA0.6163.420.1260.8941.1.1.15976

(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
00.110.6143.640.210.915jy1A GO:0004316 GO:0016491 GO:0055114 GO:0102132
10.110.6063.750.140.921vl8B GO:0000166 GO:0016491 GO:0055114
20.110.6283.520.170.933qljA GO:0016491 GO:0055114
30.110.6253.650.190.923gvcB GO:0016491 GO:0055114
40.110.6183.590.200.912jahC GO:0000166
50.100.6223.590.180.924kzpC GO:0004316 GO:0016491 GO:0055114 GO:0102132
60.100.6173.740.160.924ya6A GO:0016491 GO:0055114
70.100.6113.750.200.934jroA GO:0000166 GO:0004316 GO:0006633 GO:0016491 GO:0051287 GO:0055114
80.100.6143.630.180.914bmnA GO:0000166
90.100.6083.690.210.934mowA GO:0016491 GO:0047936 GO:0055114
100.100.6163.410.130.903uf0A GO:0000166 GO:0008678 GO:0016491 GO:0055114
110.100.6123.660.180.914bmsF GO:0000166
120.100.6133.560.180.902ewmB GO:0000166 GO:0010130 GO:0016491 GO:0016616 GO:0051289 GO:0055114
130.100.6023.730.150.923sx2F GO:0000166 GO:0016491 GO:0055114
140.100.6193.560.240.924ijuB GO:0003845 GO:0005783 GO:0005789 GO:0006629 GO:0006704 GO:0008202 GO:0016020 GO:0016021 GO:0016491 GO:0030324 GO:0055114 GO:0070524
150.090.5973.710.140.922p68A GO:0004316 GO:0006629 GO:0006631 GO:0006633 GO:0016491 GO:0030497 GO:0050661 GO:0051287 GO:0055114 GO:0102132
160.090.6273.670.160.911iy8A GO:0016491 GO:0055114
170.090.6253.540.160.911xkqA GO:0000166 GO:0016491 GO:0055114
180.090.6063.690.130.921ja9A GO:0000166 GO:0016491 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0036094 GO:1901265 GO:0016491
GO-Score 0.41 0.41 0.38
Biological Processes GO:0055114
GO-Score 0.38
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.