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I-TASSER results for job id Rv1927

[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 3 4jm3A EPE Rep, Mult 35,79,97,127,130,131,135,139,248
20.05 2 1qd6C HDS Rep, Mult 42,43,75,77,103,117,240
30.03 1 3csyO UUU Rep, Mult 101,105
40.03 1 3d04B SAK Rep, Mult 137,139,190
50.03 1 3bh3C PNH Rep, Mult 120,127,137,139
60.03 1 3fg4C ACD Rep, Mult 127,128,131
70.03 1 3cmbA NA Rep, Mult 31,32,33,249,250,251
80.03 1 2e9eA UUU Rep, Mult 101,110,211
90.03 1 2e9eB UUU Rep, Mult 101,110
100.03 1 1ykjB PSL Rep, Mult 113,212,214
110.03 1 2j0sT NUC Rep, Mult 92,97
120.03 1 1r3nF BIB Rep, Mult 160,230
130.03 1 1tgvB 5UD Rep, Mult 43,45
140.03 1 2axtK CA Rep, Mult 64,68
150.03 1 3doyB 2BE Rep, Mult 58,137,139,190
160.03 1 3cmbA NA Rep, Mult 72,104,105,106

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
10.2643bh3D0.8002.090.1100.8874.1.1.4132
20.0603bh2D0.7802.240.0880.8794.1.1.437,132
30.0601qwlA0.3635.800.0330.6151.11.1.645
40.0601llwA0.3735.750.0310.6111.4.7.1NA
50.0601fo4A0.3486.150.0450.6071.17.1.479
60.0601cf9A0.3635.860.0330.6191.11.1.645
70.0603b9jC0.3416.720.0640.6421.17.3.2,1.17.1.4NA
80.0603c8wD0.7612.420.0900.8604.1.1.4119,132
90.0602ckjA0.3327.040.0330.6461.17.1.4,1.17.3.2NA
100.0601u5uA0.3866.040.0580.6694.2.1.9242
110.0601ye9K0.2795.770.0340.4481.11.1.637
120.0601e39A0.3136.590.0270.5801.3.99.1NA
130.0603b9jJ0.2736.720.0670.5171.17.1.4,1.17.3.2115
140.0601ye9A0.2805.740.0230.4481.11.1.645
150.0602vdcF0.3796.040.0380.6461.4.1.1369
160.0603fg3A0.3316.400.0250.5954.2.1.92,1.13.11.40NA
170.0601lj1A0.3215.980.0360.5331.3.99.1139
180.0601i78A0.3755.220.0350.5723.4.23.49NA
190.0601iphA0.3625.760.0480.6111.11.1.6117
200.0601sy7B0.3625.670.0350.5721.11.1.6NA

(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
00.290.7682.830.100.903cmbB GO:0016829
10.270.7802.270.080.883bh2A GO:0016829 GO:0016831 GO:0047602
20.260.7752.330.100.873c8wA GO:0016829 GO:0047602
30.240.7613.100.120.904jm3B GO:0016829
40.230.8012.080.110.893bgtD GO:0016829 GO:0016831 GO:0047602
50.140.7442.660.120.864zboA GO:0016829
60.060.3426.060.060.593n2cA
70.060.2826.140.030.494pfeA GO:0006091 GO:0008218 GO:0018298
80.060.2616.110.030.444dg8A GO:0000166 GO:0003824 GO:0008152
90.060.2605.650.010.421ln1A GO:0005737 GO:0005829 GO:0006810 GO:0006869 GO:0008289 GO:0008525 GO:0015914 GO:0031210
100.060.2696.800.030.514dg9A GO:0000166 GO:0003824 GO:0008152
110.060.3036.460.040.554w5tA GO:0000340 GO:0000932 GO:0000993 GO:0001047 GO:0003676 GO:0003723 GO:0003725 GO:0003727 GO:0003729 GO:0003743 GO:0004518 GO:0004519 GO:0004521 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0005844 GO:0005845 GO:0006351 GO:0006355 GO:0006412 GO:0006413 GO:0006417 GO:0007223 GO:0008022 GO:0009791 GO:0010501 GO:0010586 GO:0010628 GO:0016020 GO:0016442 GO:0016787 GO:0016891 GO:0030425 GO:0030529 GO:0031047 GO:0031054 GO:0035068 GO:0035087 GO:0035194 GO:0035196 GO:0035197 GO:0035198 GO:0035278 GO:0035279 GO:0035280 GO:0044822 GO:0045944 GO:0045947 GO:0046872 GO:0048015 GO:0060213 GO:0070551 GO:0070578 GO:0090502 GO:0090624 GO:0090625 GO:1900153
120.060.2274.520.050.321wi1A GO:0005829 GO:0006810 GO:0006887 GO:0008289 GO:0015031 GO:0016020 GO:0016050 GO:0016079 GO:0016082 GO:0019901 GO:0030054 GO:0030659 GO:0031410 GO:0045202 GO:0046872 GO:0050432 GO:0098793 GO:1990504
130.060.2565.940.060.431etpA GO:0005506 GO:0009055 GO:0020037 GO:0042597 GO:0046872 GO:0055114
140.060.2055.340.050.324ka0A GO:0016491 GO:0055114
150.060.2135.670.040.332igfH
160.060.2295.070.010.341rzfH
170.060.1905.670.030.303macH
180.060.2144.110.070.285e7kA8 GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0019843 GO:0030529


Consensus prediction of GO terms
 
Molecular Function GO:0047602
GO-Score 0.59
Biological Processes
GO-Score
Cellular Component
GO-Score

(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.