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

I-TASSER results for job id Rv2054

[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 4 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
10.23 13 3f98A NTJ Rep, Mult 34,35,111,112,113,135,159,190,191
20.05 3 1u8eA UUU Rep, Mult 17,19,54,56,57,58
30.03 2 3fytE XYP Rep, Mult 188,191,192
40.03 2 2bgrA UUU Rep, Mult 4,13,58,60,61
50.03 2 2h1iA ZN Rep, Mult 133,159,162,190
60.02 1 1tqhA 4PA Rep, Mult 34,35,37,41,112,113,190
70.02 1 4ao7A ZN Rep, Mult 183,216
80.02 1 1x70A UUU Rep, Mult 109,152,153,154
90.02 1 1xfdB UUU Rep, Mult 223,227,230
100.02 1 3muoA ZPR Rep, Mult 31,56,109,111,112,133,190,218,222
110.02 1 4bzzA ACT Rep, Mult 48,52,222
120.02 1 1tk3B NAG Rep, Mult 9,64,88

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
10.5811dinA0.8092.340.2450.9113.1.1.45112,159,190
20.2593cn7A0.6812.580.1410.7893.1.1.1159,190
30.2581auoA0.6962.660.1190.8063.1.1.1159,190
40.2581i6wB0.5743.040.1500.6883.1.1.3113,159,190
50.2092ocgA0.6792.990.1350.8103.1.-.-114,118,159,166,190
60.2061jjfA0.7022.990.1830.8443.2.1.837,41,60,113
70.1902h1iA0.6653.300.1240.8193.1.1.1136
80.1161fj2A0.7053.060.1430.8443.1.4.39NA
90.1003fcxB0.7213.260.1580.8823.1.2.12NA
100.0751vkhA0.6623.170.1240.8143.5.1.984,86
110.0673esbA0.5543.900.1050.7133.1.1.74NA
120.0673gbsA0.5413.710.0820.6883.1.1.74NA
130.0663dcnA0.5393.780.0850.6963.1.1.74NA
140.0601l7aA0.7532.630.1550.8613.1.1.72,3.1.1.41NA
150.0601orvA0.7503.070.1310.8903.4.14.5159,190
160.0601f6wA0.7283.120.1190.8693.1.1.13,3.1.1.3NA
170.0601lpsA0.7183.330.1100.8783.1.1.388
180.0601aknA0.7273.220.1180.8783.1.1.13,3.1.1.3NA
190.0602jbwD0.7552.700.1540.8653.7.1.-190
200.0602qr5A0.7672.580.1660.8823.4.19.195
210.0601e5tA0.7583.110.1700.9073.4.21.2695
220.0601z68A0.7373.030.1240.8783.4.21.-159,190
230.0601hlgA0.7323.180.1290.8693.1.1.3228
240.0601jjiA0.7392.470.1660.8403.1.1.1NA
250.0601r9mB0.7423.160.1270.8903.4.14.5159,190
260.0601yr2A0.7293.100.1560.8693.4.21.26159
270.0601k8qA0.7342.920.1390.8613.1.1.3228
280.0602bklB0.7503.100.1530.9033.4.21.26NA
290.0601vlqA0.7403.040.1650.8653.1.1.41NA
300.0602b4kA0.7343.340.1590.8993.1.1.43NA
310.0601gz7A0.7193.410.1140.8863.1.1.3NA
320.0603fvrA0.7542.830.1630.8733.1.1.6NA

(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
00.450.8212.040.260.904zv9A GO:0016787
10.370.8052.340.240.911dinA GO:0008806 GO:0016787 GO:0019439 GO:0052689
20.300.7053.060.140.841fj2A GO:0002084 GO:0004622 GO:0005737 GO:0005739 GO:0005829 GO:0006629 GO:0006631 GO:0008474 GO:0016298 GO:0016787 GO:0042997 GO:0050999 GO:0070062
30.270.7592.310.180.862o2gA GO:0016787
40.240.7222.420.150.823visA GO:0003847 GO:0015996 GO:0016042 GO:0046872 GO:0047746
50.230.7712.860.130.904q3kB GO:0006508 GO:0008152 GO:0008236 GO:0016787
60.220.7542.700.150.862jbwB GO:0009820 GO:0016787 GO:0019608
70.220.7173.130.170.854fhzA GO:0016787
80.210.7153.290.180.873dohA GO:0002084 GO:0005737 GO:0008474 GO:0016787 GO:0052689
90.210.7172.430.150.824eb0A GO:0003847 GO:0016042 GO:0016787 GO:0050525
100.180.8252.090.230.913f67A GO:0016787
110.180.7252.580.160.834cg3A GO:0003847 GO:0015996 GO:0016042 GO:0016787 GO:0047746 GO:0050525
120.180.6752.860.150.803ksrA GO:0004252 GO:0006508 GO:0008236 GO:0016787
130.160.7782.890.240.903hlkB GO:0000038 GO:0001676 GO:0005102 GO:0005739 GO:0005759 GO:0006637 GO:0016290 GO:0016787 GO:0016790 GO:0035338 GO:0047617 GO:0052689 GO:0070062
140.150.7712.920.120.904bzwA GO:0008152 GO:0016787 GO:0042802
150.140.7432.940.180.894n5hX GO:0008152 GO:0016787
160.130.6962.660.120.811auoA GO:0016787 GO:0052689
170.100.6802.980.170.804lheA GO:0016787 GO:0047372 GO:0052689
180.090.6712.750.170.784ke6E GO:0016787 GO:0047372 GO:0052689
190.080.6992.860.120.833h04A GO:0008152 GO:0016787
200.070.6803.150.140.821mt3A GO:0004177 GO:0006508 GO:0008233 GO:0016787
210.070.4813.900.080.654c20B GO:0005737 GO:0005975 GO:0005996 GO:0006004 GO:0008736 GO:0016853 GO:0016861 GO:0019317 GO:0030145 GO:0042355 GO:0046872
220.070.4315.460.050.704nf7A GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798 GO:0030245 GO:0030246 GO:0030247
230.060.3564.570.070.514rs3A GO:0005886 GO:0006810 GO:0008643 GO:0016020 GO:0030246 GO:0071322


Consensus prediction of GO terms
 
Molecular Function GO:0016790 GO:0098599 GO:0004620 GO:0043169 GO:0008806
GO-Score 0.59 0.59 0.59 0.47 0.36
Biological Processes GO:0032768 GO:0042159 GO:0090005 GO:0032787 GO:0098734 GO:0035601 GO:0044255 GO:0042996 GO:0051224 GO:0046149 GO:0006787 GO:0044712 GO:0015994
GO-Score 0.59 0.59 0.59 0.59 0.59 0.59 0.59 0.59 0.59 0.47 0.47 0.47 0.47
Cellular Component GO:0031988 GO:1903561 GO:0043231 GO:0044444
GO-Score 0.59 0.59 0.59 0.59

(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.