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I-TASSER results for job id Rv1768

[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
10.12 6 5sxmA III Rep, Mult 126,127,128,167,170,171,187,209,211,212,224,246,247,266,333,378,396
20.04 2 1g9kA CA Rep, Mult 309,311,313,323,324,325,328
30.04 2 2quaA CA Rep, Mult 372,373,374,387,400,402,405
40.04 2 4w23g NUC Rep, Mult 166,204,205,207,208,229,240,471
50.04 2 1go7P CA Rep, Mult 299,301,335,337
60.02 1 1g9kA CA Rep, Mult 318,319,320,329,330,331,334
70.02 1 3a6zA CA Rep, Mult 343,344,345,347,349,362,363,364,367
80.02 1 1cpoA UUU Rep, Mult 176,178
90.02 1 3sbpA CUK Rep, Mult 250,293,332,333,353,380
100.02 1 3sbrC CUK Rep, Mult 129,130,171,250,293,332,333,379
110.02 1 3iurA III Rep, Mult 125,143,144,167,477
120.02 1 3iurA III Rep, Mult 129,143,172
130.02 1 1g9kA CA Rep, Mult 308,309,310,311,313,328,335
140.02 1 3odtA CA Rep, Mult 126,396,402
150.02 1 3sfzA GBL Rep, Mult 206,207,229
160.02 1 1p22A III Rep, Mult 128,168,171,187,211,224,226,247,249,266,288,289,307,332,353,377,379

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
10.0601kitA0.3666.340.0450.5083.2.1.18NA
20.0601e5tA0.4045.810.0350.5393.4.21.26NA
30.0602ebsB0.5345.240.0710.6733.2.1.150NA
40.0601yrzA0.3876.310.0550.5373.2.1.37NA
50.0601ofdA0.3907.600.0750.6181.4.7.1NA
60.0601fwxA0.4364.850.0490.5231.7.99.6214
70.0602bklB0.4015.500.0440.5193.4.21.26NA
80.0603fsnB0.3774.890.0490.4715.2.1.7NA
90.0603g0bB0.3986.850.0430.5713.4.14.5NA
100.0601llwA0.3837.700.0720.6171.4.7.1NA
110.0601jofA0.3942.950.0470.4325.5.1.5228
120.0602w68C0.1444.720.0610.1783.2.1.18NA
130.0601orvA0.3986.860.0500.5683.4.14.5NA
140.0601t3tA0.3667.720.0460.5796.3.5.3337,402,404
150.0602bixA0.3754.910.0560.4691.14.99.-331
160.0603elqB0.3855.830.0610.5152.8.2.22NA
170.0602d0vA0.4034.890.0870.4971.1.99.8NA
180.0601yr2A0.4356.690.0530.6213.4.21.26348
190.0602ecfA0.4186.920.0640.6023.4.14.5NA

(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
00.090.6005.410.060.773j2tA GO:0000166 GO:0001666 GO:0001843 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0006915 GO:0006919 GO:0007275 GO:0007399 GO:0007420 GO:0007568 GO:0007584 GO:0008635 GO:0008656 GO:0010659 GO:0030154 GO:0030900 GO:0031072 GO:0034349 GO:0042802 GO:0042981 GO:0043065 GO:0043293 GO:0043531 GO:0051260 GO:0051402 GO:0070059 GO:0070062 GO:0071560 GO:0072432 GO:0097190 GO:0097193 GO:1902510 GO:2001235
10.070.5285.100.080.651nr0A GO:0003779 GO:0005737 GO:0005856 GO:0016528 GO:0030016 GO:0030240 GO:0030836 GO:0030837 GO:0040011 GO:0040012 GO:0042643 GO:0051015 GO:0071689
20.070.5405.210.060.672ymuA GO:0016020 GO:0016021
30.070.5205.250.070.651pguB GO:0003779 GO:0005737 GO:0005856 GO:0005884 GO:0006970 GO:0030042 GO:0030479 GO:0032466 GO:0051016
40.070.5375.160.050.674xfvA GO:0002098 GO:0005634 GO:0005654 GO:0005737 GO:0006351 GO:0006355 GO:0006357 GO:0006810 GO:0008017 GO:0015031 GO:0032447 GO:0033588
50.070.5226.470.060.733sfzA GO:0000166 GO:0001666 GO:0001843 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0006915 GO:0006919 GO:0007275 GO:0007420 GO:0007568 GO:0007584 GO:0008635 GO:0008656 GO:0010659 GO:0030154 GO:0030900 GO:0031072 GO:0034349 GO:0042802 GO:0042981 GO:0043293 GO:0043531 GO:0051260 GO:0051402 GO:0070059 GO:0070062 GO:0071560 GO:0097190 GO:1902510 GO:2001235
60.070.5435.220.050.674nsxA GO:0005634 GO:0005654 GO:0005730 GO:0006364 GO:0030529 GO:0031167 GO:0032040 GO:0034388 GO:0042254 GO:0042274
70.070.5215.940.060.684ci8A GO:0000226 GO:0002244 GO:0005509 GO:0005737 GO:0005829 GO:0005856 GO:0005874 GO:0005875 GO:0007052 GO:0007405 GO:0007420 GO:0008017 GO:0015631 GO:0048471 GO:0097431 GO:1990023
80.070.4674.260.050.545cvlA GO:0000724 GO:0005634 GO:0005737 GO:0005764 GO:0005768 GO:0005770 GO:0006974 GO:0007283 GO:0007338 GO:0008584 GO:0016032 GO:0016579 GO:0035264 GO:0043588 GO:0048568 GO:0048705 GO:0048872 GO:0050679 GO:0072520 GO:1902525
90.060.4122.790.070.455emkB GO:0000387 GO:0005634 GO:0005654 GO:0005737 GO:0005794 GO:0005829 GO:0006357 GO:0008284 GO:0008285 GO:0008327 GO:0016274 GO:0030374 GO:0034709 GO:0035246 GO:0060528 GO:0060770
100.060.3752.970.060.413i2nA GO:0006915 GO:0043130
110.060.4022.430.060.433jb9L GO:0005634 GO:0005681 GO:0005682 GO:0006397 GO:0008380 GO:0045292
120.060.4012.560.060.435a31R GO:0005634 GO:0005680 GO:0005737 GO:0007049 GO:0007067 GO:0010697 GO:0010997 GO:0030332 GO:0045842 GO:0051301 GO:0097027 GO:1904668 GO:2000060 GO:2000600
130.060.4032.510.100.433jcrL GO:0000375 GO:0000398 GO:0005634 GO:0005654 GO:0005681 GO:0006396 GO:0006397 GO:0008380 GO:0015030 GO:0016607 GO:0017070 GO:0030621 GO:0046540 GO:0071001 GO:0097525
140.060.3972.770.060.434u7aA GO:0000463 GO:0000466 GO:0005634 GO:0005654 GO:0005730 GO:0006364 GO:0030687 GO:0042254 GO:0042273 GO:0043021 GO:0070180 GO:0070545
150.060.3972.480.070.421b9xA GO:0001750 GO:0003924 GO:0004871 GO:0005622 GO:0005765 GO:0005834 GO:0007165 GO:0007186 GO:0007191 GO:0007200 GO:0008283 GO:0016020 GO:0016056 GO:0022400 GO:0032403 GO:0043209 GO:0050909 GO:0051020 GO:0060041 GO:0070062 GO:0071380 GO:0071870 GO:0097381 GO:1903561
160.060.4012.670.060.435g04R GO:0000922 GO:0005634 GO:0005654 GO:0005680 GO:0005737 GO:0005813 GO:0005815 GO:0005819 GO:0005829 GO:0005856 GO:0007049 GO:0007062 GO:0007067 GO:0007399 GO:0008022 GO:0008284 GO:0010997 GO:0016567 GO:0019899 GO:0030154 GO:0031145 GO:0031915 GO:0040020 GO:0042787 GO:0042826 GO:0043161 GO:0043234 GO:0048471 GO:0050773 GO:0051301 GO:0051436 GO:0051437 GO:0051439 GO:0090129 GO:0097027 GO:1904668
170.060.3993.000.030.443acpA GO:0000502 GO:0005634 GO:0005737 GO:0005829 GO:0006511 GO:0070682
180.060.3823.100.040.424v3pSa GO:0007165


Consensus prediction of GO terms
 
Molecular Function GO:0043531 GO:0031072 GO:0005524 GO:0042802 GO:0008656 GO:0051015 GO:0008017
GO-Score 0.09 0.09 0.09 0.09 0.09 0.07 0.07
Biological Processes GO:0030900 GO:0008635 GO:0007568 GO:0001843 GO:1902510 GO:2001235 GO:0001666 GO:0070059 GO:0071560 GO:0007584 GO:0034349 GO:0010659 GO:0072432 GO:0051260 GO:0051402 GO:0040012 GO:0071689 GO:0030836 GO:0030240 GO:0051016 GO:0002098 GO:0032466 GO:0006357 GO:0015031 GO:0006970 GO:0032447
GO-Score 0.09 0.09 0.09 0.09 0.09 0.09 0.09 0.09 0.09 0.09 0.09 0.09 0.09 0.09 0.09 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07
Cellular Component GO:0044424
GO-Score 0.52

(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.