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I-TASSER results for job id Rv2635

[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
10.14 6 1sn5A T3 Rep, Mult 13,71
20.07 3 3l74P AZI Rep, Mult 15,32
30.07 3 1r2rB DMS Rep, Mult 29,30,71,73
40.05 2 2gezF CL Rep, Mult 2,29,56
50.02 1 2p3oA GTA Rep, Mult 20,24,31,34
60.02 1 1smyF MG Rep, Mult 63,65
70.02 1 2cjzA PTR Rep, Mult 13,14,15,16,17,18,19
80.02 1 5cuyB MG Rep, Mult 34,64
90.02 1 3mmzA CA Rep, Mult 10,21
100.02 1 3kh5A AMP Rep, Mult 32,59,60,61,67,69
110.02 1 2xbmB RQA Rep, Mult 20,21,23,24,25

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
10.0601yguB0.4523.900.1130.8003.1.3.4852
20.0602h6eA0.4143.930.0430.7621.1.1.129,30
30.0602ebaA0.4403.940.0960.8251.3.99.7NA
40.0602hwkA0.4163.870.0570.7383.4.11.1,2.7.7.4840
50.0602fh7A0.4423.920.0910.8253.1.3.48NA
60.0602dewX0.4234.550.0700.8633.5.3.15NA
70.0601wd8A0.3384.650.0750.7383.5.3.1534
80.0601jlnA0.4414.420.0670.8633.1.3.4834
90.0603enoA0.4354.070.0650.8503.4.24.57NA
100.0601r6aA0.4373.170.0880.7132.7.7.4851
110.0601larA0.4254.020.0390.8123.1.3.48NA
120.0602ivpA0.4033.900.0430.8003.4.24.5716
130.0602a3kA0.4473.870.0950.8253.1.3.48NA
140.0602hc1A0.4424.090.0540.8383.1.3.4836
150.0602gp0A0.4713.760.0680.8123.1.3.4834,60,66
160.0603evfA0.4343.210.1230.7132.7.7.4810,54
170.0602bijA0.4403.960.0280.8123.1.3.4820
180.0602r7oA0.4163.970.0930.8002.7.7.48NA
190.0602pbnA0.4254.210.0800.7873.1.3.48NA

(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
00.070.4434.090.060.823o4sA GO:0004721 GO:0004725 GO:0005737 GO:0005829 GO:0005856 GO:0006470 GO:0009898 GO:0016311 GO:0016787 GO:0016791 GO:0035335
10.070.3804.400.050.812ooqB GO:0004721 GO:0004725 GO:0005886 GO:0006470 GO:0007155 GO:0007156 GO:0007165 GO:0007169 GO:0008013 GO:0009986 GO:0016020 GO:0016021 GO:0016311 GO:0016787 GO:0016791 GO:0035335 GO:0045294 GO:0045295 GO:0045296 GO:0070097
20.070.3004.660.030.642c7sA GO:0001750 GO:0004721 GO:0004725 GO:0005001 GO:0005886 GO:0005887 GO:0005911 GO:0005912 GO:0006470 GO:0007155 GO:0007165 GO:0007179 GO:0008013 GO:0008285 GO:0009986 GO:0010839 GO:0016020 GO:0016021 GO:0016311 GO:0016477 GO:0016787 GO:0016791 GO:0019901 GO:0030054 GO:0030336 GO:0030424 GO:0030425 GO:0031175 GO:0031256 GO:0034394 GO:0034614 GO:0034644 GO:0035335 GO:0043025 GO:0045295 GO:0045786 GO:0045892 GO:0048041
30.070.3114.600.060.692nlkA GO:0004721 GO:0004725 GO:0005001 GO:0005887 GO:0006470 GO:0007169 GO:0010633 GO:0016020 GO:0016021 GO:0016311 GO:0016787 GO:0016791 GO:0035335 GO:0042802 GO:0070062 GO:1903385
40.070.4473.870.100.822a3kA GO:0004721 GO:0004725 GO:0005737 GO:0005829 GO:0005856 GO:0006470 GO:0009898 GO:0016311 GO:0016787 GO:0016791 GO:0035335
50.070.4403.960.030.812bijA GO:0001784 GO:0001934 GO:0001975 GO:0002092 GO:0004721 GO:0004725 GO:0005783 GO:0005789 GO:0005829 GO:0006470 GO:0010976 GO:0016020 GO:0016021 GO:0016311 GO:0016787 GO:0016791 GO:0019901 GO:0030424 GO:0033160 GO:0035254 GO:0035335 GO:0035640 GO:0035902 GO:0042493 GO:0043025 GO:0043204 GO:0043407 GO:0051019 GO:1900273 GO:1901216 GO:1903492 GO:1903955 GO:1990635 GO:2001025
60.060.3744.260.030.724ri5A GO:0001784 GO:0004721 GO:0004725 GO:0005737 GO:0005856 GO:0005886 GO:0006470 GO:0008092 GO:0009898 GO:0016020 GO:0016311 GO:0016787 GO:0016791 GO:0017080 GO:0035335 GO:0045930 GO:0051045 GO:0051117 GO:0097421 GO:0098902 GO:2000649
70.060.3154.950.040.755j8rA GO:0002102 GO:0004721 GO:0004725 GO:0004726 GO:0005737 GO:0005829 GO:0005886 GO:0005925 GO:0006470 GO:0016311 GO:0016787 GO:0016791 GO:0017124 GO:0030054 GO:0035335 GO:0042058 GO:0042246 GO:0042995 GO:0071364
80.060.3034.680.030.651rpmA GO:0001937 GO:0004721 GO:0004725 GO:0005001 GO:0005737 GO:0005887 GO:0005911 GO:0005913 GO:0006470 GO:0007155 GO:0007156 GO:0007165 GO:0010596 GO:0010842 GO:0016020 GO:0016021 GO:0016311 GO:0016525 GO:0016787 GO:0016791 GO:0030027 GO:0031175 GO:0031290 GO:0035335 GO:0042493 GO:0042802 GO:0045296 GO:0045909 GO:0048471
90.060.4254.020.040.811larA GO:0004721 GO:0004725 GO:0005001 GO:0005886 GO:0005887 GO:0006470 GO:0007155 GO:0007185 GO:0007268 GO:0008201 GO:0010975 GO:0016020 GO:0016021 GO:0016311 GO:0016477 GO:0016787 GO:0016791 GO:0031102 GO:0032403 GO:0035335 GO:0035373 GO:0043005 GO:0043025 GO:0048679 GO:0070062 GO:1900121
100.060.4424.340.050.853s3eA GO:0004721 GO:0004725 GO:0004728 GO:0005001 GO:0005886 GO:0006470 GO:0007275 GO:0007399 GO:0007411 GO:0007417 GO:0007424 GO:0007616 GO:0008045 GO:0016020 GO:0016021 GO:0016311 GO:0016787 GO:0016791 GO:0023014 GO:0030154 GO:0030424 GO:0035335 GO:0045177
110.060.3254.600.000.694ikcA GO:0004721 GO:0004725 GO:0006470 GO:0016020 GO:0016021 GO:0016311 GO:0016787 GO:0016791 GO:0030154 GO:0035335 GO:0042472 GO:0045598 GO:0046856
120.060.3014.990.050.682i75A GO:0004721 GO:0004725 GO:0004726 GO:0005737 GO:0005856 GO:0005886 GO:0006470 GO:0008092 GO:0009898 GO:0016020 GO:0016311 GO:0016787 GO:0016791 GO:0035335
130.060.3974.500.030.792i1yB GO:0000302 GO:0001553 GO:0004725 GO:0005768 GO:0005794 GO:0005886 GO:0008021 GO:0009749 GO:0016020 GO:0016021 GO:0019221 GO:0030054 GO:0030073 GO:0030141 GO:0030424 GO:0030507 GO:0030658 GO:0031410 GO:0032868 GO:0035773 GO:0042995 GO:0043025 GO:0043204 GO:0043627 GO:0043679 GO:0045202 GO:0051020 GO:0051591 GO:1990502
140.060.3974.160.040.755awxA GO:0002244 GO:0004721 GO:0004725 GO:0005001 GO:0005576 GO:0005578 GO:0005615 GO:0005737 GO:0005886 GO:0005887 GO:0006470 GO:0007409 GO:0007413 GO:0007417 GO:0007420 GO:0007611 GO:0008285 GO:0008542 GO:0010812 GO:0010976 GO:0016020 GO:0016021 GO:0016311 GO:0016787 GO:0016791 GO:0017134 GO:0021766 GO:0030027 GO:0030175 GO:0030335 GO:0030424 GO:0030425 GO:0030426 GO:0031226 GO:0032587 GO:0035335 GO:0043025 GO:0043197 GO:0045211 GO:0048146 GO:0048666 GO:0048709 GO:0048814 GO:0050731 GO:0070445 GO:0072534 GO:1900006 GO:1900149 GO:1901216 GO:2000171 GO:2001224
150.060.3094.800.070.701l8kA GO:0004721 GO:0004725 GO:0004726 GO:0005178 GO:0005634 GO:0005654 GO:0005737 GO:0005783 GO:0005793 GO:0005886 GO:0006470 GO:0008285 GO:0008286 GO:0010804 GO:0010888 GO:0016020 GO:0016311 GO:0016787 GO:0016791 GO:0019901 GO:0019905 GO:0030183 GO:0030217 GO:0030218 GO:0030971 GO:0035335 GO:0042059 GO:0042512 GO:0042518 GO:0042524 GO:0042527 GO:0042593 GO:0045650 GO:0045722 GO:0046627 GO:0050728 GO:0050860 GO:0050922 GO:0060334 GO:0060336 GO:0060339 GO:0061099 GO:0070104 GO:0070373 GO:1902202 GO:1902206 GO:1902212 GO:1902215 GO:1902227 GO:1902233 GO:1902237 GO:1903899 GO:2000587
160.060.4384.220.030.821yguB GO:0001915 GO:0001960 GO:0002244 GO:0002378 GO:0004721 GO:0004725 GO:0005001 GO:0005622 GO:0005886 GO:0005887 GO:0005925 GO:0006469 GO:0006470 GO:0006933 GO:0007166 GO:0009897 GO:0009986 GO:0016020 GO:0016021 GO:0016311 GO:0016787 GO:0016791 GO:0019901 GO:0030217 GO:0030890 GO:0035335 GO:0042100 GO:0042102 GO:0044770 GO:0045121 GO:0045860 GO:0048539 GO:0048864 GO:0050852 GO:0050853 GO:0050857 GO:0051209 GO:0051607 GO:0051726 GO:0070062 GO:2000473 GO:2000648
170.060.4324.000.010.844fjvA GO:0004843 GO:0005634 GO:0006508 GO:0008233 GO:0008234 GO:0016579 GO:0016787 GO:0019784 GO:0035871 GO:0036459 GO:0043130 GO:0070536 GO:0071108
180.060.4353.760.070.792nv5A


Consensus prediction of GO terms
 
Molecular Function GO:0042578
GO-Score 0.57
Biological Processes GO:0006470
GO-Score 0.57
Cellular Component GO:0005829 GO:0005856 GO:0009986 GO:0009898 GO:0005887 GO:0031256 GO:0043025 GO:0030425 GO:0070062 GO:0030424 GO:0001750 GO:0005912 GO:0005911
GO-Score 0.13 0.13 0.13 0.13 0.13 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07

(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.