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

I-TASSER results for job id Rv1453

[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
10.09 5 1f59B III Rep, Mult 287,290,291,294,295,330,333,334
20.05 3 3du2L BPH Rep, Mult 282,286,289,290
30.04 2 3m9iA 3PE Rep, Mult 289,293
40.04 2 3q0oB NUC Rep, Mult 30,33,60,62,63,66,103,106,140,222,223,226,280,281,283,284,287,321,324,325,328
50.04 2 1e8dA CNH Rep, Mult 280,364,365
60.04 2 3sgfH MG Rep, Mult 370,373
70.02 1 1u6g0 III Rep, Mult 279,283,319,320,321
80.02 1 3ae4C N1M Rep, Mult 215,219
90.02 1 2vglA IHP Rep, Mult 330,331,355,359,369,373,374,377
100.02 1 2jdq0 III Rep, Mult 288,291,292,322,325,326,327,369,370,376
110.02 1 2e75G OPC Rep, Mult 342,346
120.02 1 2xo6D NUC Rep, Mult 349,353
130.02 1 1cgpA CMP Rep, Mult 335,339
140.02 1 4fe1J CLA Rep, Mult 366,370
150.02 1 3a6pF NUC Rep, Mult 63,225,368,372
160.02 1 1r6nA ALQ Rep, Mult 346,347,366
170.02 1 5kl8A NUC Rep, Mult 30,33,59,60,63,99,103,106,140,222,223,226,281,283,284,287,319,321,324,325,328,366,367,368,370
180.02 1 3jcuS CLA Rep, Mult 282,286

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
10.0601trkA0.3847.300.0630.6632.2.1.1269,291
20.0602fhbA0.3727.440.0580.6463.2.1.41NA
30.0601f1sA0.4026.780.0470.6674.2.2.1334,402
40.0601ea0A0.4166.980.0330.6891.4.1.13NA
50.0601ay0A0.3837.310.0570.6702.2.1.1NA
60.0601ug9A0.3886.930.0530.6413.2.1.70NA
70.0603draA0.3966.460.0710.6222.5.1.58,2.5.1.59NA
80.0602eabA0.3946.810.0560.6373.2.1.63NA
90.0602bs9E0.3777.200.0610.6373.2.1.37NA
100.0602j5wA0.4017.360.0500.6891.16.3.1NA
110.0602bfgA0.3827.200.0670.6413.2.1.37NA
120.0601djnA0.3926.750.0560.6221.5.8.2,1.5.99.7NA
130.0603h09B0.4196.730.0500.6793.4.21.72NA
140.0601l2aE0.3876.470.0450.6013.2.1.4288
150.0602dqmA0.4036.640.0770.6413.4.11.2NA
160.0603dpyA0.4206.210.0590.6342.5.1.58,2.5.1.59294,315,329,372
170.0602vdcA0.4267.110.0310.7101.4.1.13NA
180.0602vtfA0.3827.120.0430.6343.2.1.96333
190.0601ho8A0.4125.870.0600.6113.6.3.14332,374,380

(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
00.150.7823.600.090.924ol0B GO:0004872 GO:0005634 GO:0005737 GO:0006810 GO:0008139 GO:0008565 GO:0015031 GO:0031965 GO:0035048 GO:0042802 GO:0043231
10.120.6304.900.070.842x1gF GO:0005737 GO:0006606 GO:0006886 GO:0007270 GO:0008139 GO:0008536 GO:0008565 GO:0031965 GO:0042331 GO:0050804
20.120.7463.820.090.894c0qA GO:0004872 GO:0005634 GO:0005737 GO:0006810 GO:0008139 GO:0008565 GO:0015031 GO:0031965 GO:0035048 GO:0042802 GO:0043231
30.120.7214.360.080.913zjyE GO:0005634 GO:0005737 GO:0006606 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0031965
40.120.7413.660.090.874c0qB GO:0004872 GO:0005634 GO:0005737 GO:0006810 GO:0008139 GO:0008565 GO:0015031 GO:0031965 GO:0035048 GO:0042802 GO:0043231
50.110.7104.370.080.912xwuB GO:0005634 GO:0005737 GO:0006606 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0031965
60.100.6834.900.080.903wyfC GO:0000055 GO:0000776 GO:0005634 GO:0005737 GO:0005816 GO:0006406 GO:0006611 GO:0006810 GO:0006886 GO:0008536 GO:0008565 GO:0015031 GO:0034501 GO:0048471
70.100.5665.740.040.835difC GO:0000055 GO:0000776 GO:0005634 GO:0005737 GO:0005816 GO:0006406 GO:0006611 GO:0006810 GO:0006886 GO:0008536 GO:0008565 GO:0015031 GO:0034501 GO:0048471
80.070.6084.310.090.773zkvA GO:0005737 GO:0006606 GO:0006886 GO:0007270 GO:0008139 GO:0008536 GO:0008565 GO:0031965 GO:0042331 GO:0050804
90.060.3886.770.040.622iw3B GO:0000166 GO:0001933 GO:0003723 GO:0003746 GO:0005524 GO:0005737 GO:0005840 GO:0006412 GO:0006414 GO:0006415 GO:0006469 GO:0010494 GO:0016887 GO:0019843 GO:0022626 GO:0042788
100.060.3737.040.060.622hivA GO:0000166 GO:0003677 GO:0003909 GO:0003910 GO:0005524 GO:0005737 GO:0006260 GO:0006273 GO:0006281 GO:0006310 GO:0006974 GO:0007049 GO:0016874 GO:0046872 GO:0051103 GO:0051301 GO:0071897
110.060.2445.710.060.352htmC GO:0003824 GO:0005737 GO:0009228 GO:0009229 GO:0016740 GO:0016783
120.060.2255.360.050.314muzA GO:0003824 GO:0004590 GO:0006207 GO:0006221 GO:0008152 GO:0016829 GO:0016831 GO:0044205
130.060.2226.930.030.374rk9A GO:0005215 GO:0006810
140.060.1846.490.030.282yn3C GO:0005509 GO:0007156 GO:0016020 GO:0016491 GO:0030151 GO:0046872 GO:0055114
150.060.1636.260.040.244gqnB GO:0016491 GO:0055114
160.060.1514.090.040.194exnA GO:0001934 GO:0002376 GO:0005125 GO:0005157 GO:0005576 GO:0005615 GO:0006954 GO:0008083 GO:0008284 GO:0045087 GO:0045651 GO:0045657
170.060.1285.600.010.194izeA GO:0002376 GO:0005125 GO:0005149 GO:0005576 GO:0005615 GO:0006954 GO:0007267 GO:0019221 GO:0045087
180.060.1385.210.020.192lbmA GO:0000166 GO:0000228 GO:0000781 GO:0000784 GO:0000792 GO:0003677 GO:0003678 GO:0003682 GO:0004386 GO:0005524 GO:0005634 GO:0005694 GO:0005720 GO:0005721 GO:0006281 GO:0006306 GO:0006310 GO:0006334 GO:0006336 GO:0006338 GO:0006351 GO:0006355 GO:0006974 GO:0007283 GO:0010571 GO:0015616 GO:0016568 GO:0016605 GO:0016787 GO:0030330 GO:0030900 GO:0031297 GO:0031933 GO:0032206 GO:0032508 GO:0035064 GO:0035128 GO:0035264 GO:0042393 GO:0045944 GO:0046872 GO:0060009 GO:0070087 GO:0070198 GO:0070603 GO:0072520 GO:0072711 GO:1900112 GO:1901581 GO:1901582 GO:1904908 GO:1990707


Consensus prediction of GO terms
 
Molecular Function GO:0008139 GO:0008565 GO:0017016 GO:0004872 GO:0042802
GO-Score 0.49 0.49 0.46 0.34 0.34
Biological Processes GO:0035048
GO-Score 0.34
Cellular Component GO:0005737 GO:0031965
GO-Score 0.49 0.49

(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.