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I-TASSER results for job id Rv2824c

[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 1hbnB TP7 Rep, Mult 89,90,95,105,106
20.08 4 3qjjA NUC Rep, Mult 59,76,77,78,110,111,112,113,114,121,185,197,198,199,244,245,246,247,254,256,259,260,261,284,300,301
30.08 3 4c9dB NUC Rep, Mult 83,99,101,102,104,192,193,194,195,196,197,198,205,206,210,213,247,252,253,255,256,289,290,291,293,294
40.06 3 2c3oA SF4 Rep, Mult 185,203,207,208,209,288,289,290,298,299
50.04 2 3qjlA NUC Rep, Mult 59,112,113,114,121,163,175,176,185,187,203,241,242,243,261,300,302,303
60.03 1 4c8yA NUC Rep, Mult 80,81,83,84,85,87,91,96,99,100,101,102,103,104,146,148,192,193,205,206,209,210,213,289,290,291,293
70.02 1 3qjlA NUC Rep, Mult 76,77,78,110,111,197,198,199,244,245,246,247,254,256
80.02 1 2zozA ET Rep, Mult 98,99
90.02 1 1hbnB UUU Rep, Mult 214,218,219,220
100.02 1 1bjyA CTC Rep, Mult 82,86
110.02 1 2fuqA ZN Rep, Mult 56,67,99
120.02 1 1mroB COM Rep, Mult 282,286,288

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
10.0601sllA0.3687.020.0610.6664.2.2.15NA
20.0601hbmB0.3916.280.0640.6502.8.4.1NA
30.0602e9bA0.3546.270.0510.5833.2.1.41NA
40.0601f1hL0.3536.070.0290.5606.3.1.2NA
50.0602j5nB0.3506.540.0340.6021.5.1.12214
60.0601st8A0.3467.180.0440.6343.2.1.80NA
70.0601lgrA0.3416.280.0300.5576.3.1.2NA
80.0602e8yA0.3626.030.0410.5803.2.1.41NA
90.0601sliA0.3647.090.0530.6664.2.2.15,3.2.1.18NA
100.0601djnA0.3516.790.0540.6371.5.8.2,1.5.99.7NA
110.0601s76D0.2966.990.0540.5352.7.7.6NA
120.0602pdaA0.3686.440.0470.6181.2.7.1200
130.0601o01C0.3476.780.0540.6151.2.1.3121
140.0602wvhA0.3516.990.0360.6344.1.1.1234
150.0601htoA0.3476.410.0400.5766.3.1.2NA
160.0601l2aE0.3436.440.0400.5733.2.1.4NA
170.0601aroP0.3366.380.0410.5642.7.7.6NA
180.0601b0pA0.3686.570.0380.6211.2.7.1NA
190.0601xc6A0.3256.690.0400.5673.2.1.2365,84

(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
00.140.3916.260.030.653sqgB GO:0015948 GO:0016740 GO:0050524
10.110.3966.370.060.661e6vB GO:0015948 GO:0050524
20.100.4036.010.050.651e6yE GO:0015948 GO:0016740 GO:0050524
30.060.4006.030.070.624g2cB GO:0004601 GO:0005576 GO:0016491 GO:0016689 GO:0020037 GO:0030145 GO:0046872 GO:0052750 GO:0055114 GO:0098869
40.060.4196.150.070.665c2iA GO:0004601 GO:0020037 GO:0055114 GO:0098869
50.060.3875.890.060.614gs1B GO:0004601 GO:0020037 GO:0046872 GO:0055114 GO:0098869
60.060.3866.040.070.624gt2A GO:0004601 GO:0005623 GO:0015684 GO:0020037 GO:0033212 GO:0046872 GO:0055114 GO:0098869
70.060.3826.080.080.615fw4A GO:0004096 GO:0004601 GO:0005576 GO:0016491 GO:0020037 GO:0046872 GO:0055114 GO:0098869
80.060.3966.060.030.653fahA GO:0009055 GO:0016491 GO:0033727 GO:0046872 GO:0051536 GO:0051537 GO:0055114
90.060.3756.400.050.624grcA GO:0004601 GO:0005623 GO:0015684 GO:0020037 GO:0033212 GO:0046872 GO:0055114 GO:0098869
100.060.3986.330.060.642y4eA GO:0004601 GO:0006974 GO:0015684 GO:0016491 GO:0016675 GO:0020037 GO:0033212 GO:0042597 GO:0046872 GO:0055114 GO:0098869
110.060.3936.190.060.655a0yB GO:0015948 GO:0016740 GO:0050524
120.060.3756.350.070.603qnsA GO:0004601 GO:0020037 GO:0046872 GO:0055114 GO:0098869
130.060.3825.980.080.621jroB GO:0016491 GO:0030151 GO:0046872 GO:0055114
140.060.3397.170.030.631ffuB GO:0005507 GO:0016491 GO:0018492 GO:0030151 GO:0046872 GO:0055114
150.060.3396.770.050.601fo4A GO:0003824 GO:0004854 GO:0004855 GO:0005506 GO:0005576 GO:0005615 GO:0005737 GO:0005777 GO:0005829 GO:0009055 GO:0009115 GO:0016491 GO:0016614 GO:0016903 GO:0043546 GO:0046872 GO:0050660 GO:0051536 GO:0051537 GO:0055114
160.060.3615.990.080.574au9A GO:0004601 GO:0016491 GO:0020037 GO:0046872 GO:0055114 GO:0098869
170.060.3595.970.040.563afvA GO:0004601 GO:0020037 GO:0046872 GO:0055114 GO:0098869
180.060.3706.300.050.584gu7A GO:0004601 GO:0020037 GO:0046872 GO:0055114 GO:0098869


Consensus prediction of GO terms
 
Molecular Function GO:0050524
GO-Score 0.31
Biological Processes GO:0015948
GO-Score 0.31
Cellular Component GO:0005576
GO-Score 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.