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

I-TASSER results for job id Rv2695

[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
10.45 64 1a8uA BEZ Rep, Mult 15,16,70,71,72,97,188,216
20.07 11 4g8cB C6L Rep, Mult 15,16,46,71,72,75,160,161,164,188,216
30.07 10 4etwA ZMK Rep, Mult 15,16,71,72,104,107,108,111,122,125,126,128,161,188,216
40.02 3 1ukbA BEZ Rep, Mult 24,127,130,142,217
50.02 3 4fblA SPD Rep, Mult 15,16,17,18,71,122,123,141,145,146,216
60.01 1 3hssB MLA Rep, Mult 130,145,149,217
70.01 2 3v1nA HPK Rep, Mult 14,15,20,21,24,25,131,138,142,217
80.01 1 1iunB ACT Rep, Mult 207,220,223
90.01 2 2xuaH SHF Rep, Mult 15,16,112,122,125,126,146,157,188
100.01 1 1uk8A LEA Rep, Mult 195,198,199,206
110.01 2 1iup0 III Rep, Mult 177,184,198,201,202,203,204,205,206,207,208,209,210,213,224,227,228,231
120.00 1 2wm2A CL Rep, Mult 105,109,112,157

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
10.3391a88A0.8682.240.1700.9791.11.1.1071,186
20.2592pu5A0.8392.960.1680.9873.7.1.882
30.1943cn7A0.5882.460.1480.6683.1.1.171,185
40.1672qvbB0.7933.010.1680.9623.8.1.5NA
50.1481j1iA0.8082.650.1320.9363.7.1.871
60.1421y37A0.8212.920.1390.9793.8.1.3NA
70.1401u2eA0.8382.890.1260.9833.7.1.-71
80.1353a2lA0.8072.900.1190.9663.8.1.532
90.1323bf7A0.7612.980.1360.9063.1.-.-71
100.1311mt3A0.8213.030.1040.9793.4.11.5NA
110.1311ehyA0.7943.290.1400.9753.3.2.10186
120.1273hjuA0.7902.870.1270.9233.1.1.2371
130.1162r11D0.7713.260.1180.9403.1.1.172,97
140.1151dwoA0.7413.140.0970.9024.1.2.3771,186
150.1101qj4A0.7413.150.0940.9024.1.2.3771,186
160.0671i6wB0.5352.780.1140.6303.1.1.3186
170.0601zoiA0.8642.310.1430.9793.1.1.-71,186
180.0601iunB0.8302.990.1390.9793.7.1.994,186
190.0601qtrA0.8202.670.1510.9573.4.11.5NA
200.0601mj5A0.7962.960.1550.9623.8.1.5NA
210.0601a7uA0.8712.130.1170.9791.11.1.1071,186
220.0601k8qA0.7943.210.0960.9703.1.1.3NA
230.0601m33A0.8232.350.1760.9403.1.1.1NA
240.0603g0iA0.7843.160.1340.9533.3.2.395,138
250.0601a88B0.8672.260.1700.9791.11.1.1094
260.0603nwoA0.7993.320.1350.9623.4.11.571
270.0602og1A0.8392.970.1680.9873.7.1.89
280.0601va4A0.8752.120.1260.9793.1.1.221,71,219
290.0601azwA0.8202.670.1730.9623.4.11.5NA
300.0601a8qA0.8742.150.1170.9791.11.1.1071,186
310.0601a8sA0.8662.300.1260.9791.11.1.1071,186
320.0602ocgA0.7932.320.1280.8983.1.-.-13,71,73,77,186,194,206
330.0601c4xA0.8452.640.1910.9793.7.1.8NA
340.0603e3aB0.8352.560.1320.9701.11.1.-15,17
350.0602vf2A0.8342.970.1900.9833.7.1.815,35,72

(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
00.380.8632.410.140.993v48A GO:0006212 GO:0016787 GO:0016811 GO:0019740
10.360.8861.730.160.964ihaA GO:0005634 GO:0005737 GO:0010223 GO:0016787 GO:1901601
20.330.8691.890.130.964ih4A GO:0005634 GO:0005737 GO:0010223 GO:0016787 GO:1901601 GO:1902348
30.320.8692.160.130.981hkhA GO:0003824 GO:0004601 GO:0098869
40.320.8362.370.160.961m33A GO:0005737 GO:0009102 GO:0016787 GO:0052689 GO:0090499
50.310.8023.110.190.964psuA GO:0016787
60.310.8722.040.120.974dnqI GO:0010223 GO:0016787 GO:0016788 GO:1901601
70.300.8402.340.140.964x00A GO:0016787
80.300.8342.430.160.964nmwA GO:0005737 GO:0009102 GO:0016787 GO:0052689
90.290.8712.060.140.972xuaH GO:0016787 GO:0042952 GO:0047570
100.290.8482.460.140.974rncA GO:0016787 GO:0052689
110.280.7943.290.140.971ehyA GO:0003824 GO:0016787
120.280.8682.240.170.981a88A GO:0003824 GO:0004601 GO:0016491 GO:0016691 GO:0055114 GO:0098869
130.270.7973.120.170.963kxpA GO:0016787 GO:0042803 GO:0042820 GO:0047411
140.260.7973.060.140.962yysA GO:0006508 GO:0008233
150.250.7142.690.120.843pf8A GO:0016787
160.250.8332.810.130.982xmzA GO:0009234 GO:0016787 GO:0016829 GO:0070205
170.220.7862.910.160.944gdmC GO:0005829 GO:0009234 GO:0016787 GO:0016829 GO:0070205
180.220.8702.010.140.971womA GO:0016787
190.210.7612.980.140.913bf7A GO:0005829 GO:0016787 GO:0016790 GO:0052689
200.210.8542.380.180.973om8B GO:0016787 GO:0042952 GO:0047570
210.200.8722.010.120.974htaA GO:0005634 GO:0005737 GO:0005829 GO:0009640 GO:0009704 GO:0016787 GO:0080167
220.200.8392.970.170.992og1A GO:0003824 GO:0016787 GO:0016823 GO:0018771 GO:0018774 GO:0019439
230.200.8452.780.140.994f0jA GO:0003824 GO:0016787
240.190.8213.180.130.984opmA GO:0004806 GO:0016787
250.190.8282.820.140.983b12A GO:0003824 GO:0016787 GO:0018785
260.190.8242.980.180.982e3jA GO:0003824 GO:0016787
270.190.8262.870.150.983r3uA GO:0003824 GO:0016787 GO:0018785
280.190.8262.790.170.974nvrA GO:0016740 GO:0016746 GO:0016787 GO:0046872
290.170.8742.150.120.981a8qA GO:0003824 GO:0004601 GO:0016491 GO:0017000 GO:0055114 GO:0098869
300.150.8102.660.140.944ns4A GO:0016787 GO:0016788
310.150.7932.320.130.902ocgA GO:0005739 GO:0005741 GO:0006520 GO:0006805 GO:0009636 GO:0016787 GO:0047658 GO:0070062
320.140.8412.910.170.984i3fA GO:0016787
330.140.8213.030.100.981mt3A GO:0004177 GO:0006508 GO:0008233 GO:0016787
340.130.8023.030.160.964b9aA GO:0003824 GO:0009062 GO:0016298 GO:0016787
350.070.7033.380.100.873fnbA GO:0004252 GO:0006508


Consensus prediction of GO terms
 
Molecular Function GO:0016811 GO:0004601 GO:0090499
GO-Score 0.38 0.32 0.32
Biological Processes GO:1901601 GO:0010223 GO:0019740 GO:0006212 GO:1902348 GO:0098869 GO:0009102
GO-Score 0.57 0.57 0.38 0.38 0.33 0.32 0.32
Cellular Component GO:0005737 GO:0005634
GO-Score 0.71 0.57

(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.