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I-TASSER results for job id Rv2125

[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
10.10 6 3ut6B PO4 Rep, Mult 22,23,129,130,131,205
20.07 4 1v2hE GUN Rep, Mult 16,17,96,124,125
30.05 3 1ampA ZN Rep, Mult 27,102,198
40.05 3 3djfC BC3 Rep, Mult 31,140,141,191,192,193,206,230
50.03 2 4zfzA ZN Rep, Mult 245,248
60.02 1 3uxmC MG Rep, Mult 102,235
70.02 1 1nquA RDL Rep, Mult 187,188
80.02 1 2oyyB HEM Rep, Mult 225,229
90.02 1 2anuA ZN Rep, Mult 245,256
100.02 1 4mchA 61N Rep, Mult 38,42,205,206
110.02 1 3hq9B BU3 Rep, Mult 276,280
120.02 1 3jsxE FAD Rep, Mult 61,77,79
130.02 1 3se1A MG Rep, Mult 259,262
140.02 1 5da5O CA Rep, Mult 243,245
150.02 1 2f1oD FAD Rep, Mult 77,79
160.02 1 1jm0D MN Rep, Mult 230,233
170.02 1 2hawA MG Rep, Mult 27,214

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
10.0601yw6A0.4594.480.0760.6273.5.1.9626,79,187
20.0601vhjB0.4733.380.0990.5792.4.2.1NA
30.0603eueA0.4743.860.1010.5992.4.2.3NA
40.0601t8rA0.4634.070.0810.5933.2.2.4NA
50.0601jdvC0.4683.440.0890.5792.4.2.28NA
60.0601tcuC0.5043.820.0790.6302.4.2.1NA
70.0601v4nB0.4574.010.0730.5792.4.2.28NA
80.0601a9oA0.4993.910.1260.6302.4.2.138
90.0601yqqA0.5024.090.1170.6402.4.2.1NA
100.0601qe5B0.4833.870.0660.6162.4.2.1NA
110.0601jpvA0.4673.480.0890.5792.4.2.28100
120.0601k3fA0.4663.640.0930.5862.4.2.3NA
130.0602a8yA0.4603.980.0800.5822.4.2.28NA
140.0601nc3A0.4633.420.1130.5583.2.2.9NA
150.0603bl6A0.4573.380.1430.5513.2.2.16NA
160.0602iscD0.4713.420.0750.5792.4.2.1NA
170.0603dp9C0.4563.440.1300.5513.2.2.9NA
180.0602qttA0.4543.980.1250.5793.2.2.1632
190.0603e0qC0.5043.830.0740.6302.4.2.1100

(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
00.490.9390.990.270.962wamA GO:0005886 GO:0006367 GO:0070207
10.430.8551.840.250.912p90B GO:0006367
20.390.8042.130.230.873e35A GO:0006367
30.060.3965.780.060.624goxA GO:0003824 GO:0008152 GO:0016740 GO:0031177
40.060.3256.180.050.522ap1A GO:0000166 GO:0005524 GO:0005975 GO:0006044 GO:0008270 GO:0009254 GO:0016301 GO:0016310 GO:0016740 GO:0045127 GO:0046835 GO:0046872
50.060.3485.510.040.532decA GO:0005975 GO:0030246
60.060.3606.420.050.614fuqC GO:0000166 GO:0003824 GO:0005524 GO:0008152 GO:0016874
70.060.2995.450.040.461narA GO:0004553 GO:0005975
80.060.3416.260.080.581iwpA GO:0003824 GO:0008152 GO:0016829 GO:0016836 GO:0031419 GO:0046405 GO:0050215
90.060.3034.420.070.413ewiB GO:0005634 GO:0005829 GO:0006054 GO:0006055 GO:0008781 GO:0016020 GO:0016740 GO:0016779
100.060.3006.510.040.513ezuA
110.060.2796.250.060.473istA GO:0006807 GO:0008152 GO:0008360 GO:0008881 GO:0009252 GO:0016853 GO:0016855 GO:0036361 GO:0071555
120.060.2895.070.080.414o6oD GO:0003677 GO:0006281 GO:0006310 GO:0006974 GO:0046872
130.060.2756.090.040.445ee7A GO:0003796 GO:0003824 GO:0004871 GO:0004888 GO:0004930 GO:0004967 GO:0005085 GO:0005768 GO:0005886 GO:0005887 GO:0006091 GO:0006887 GO:0007165 GO:0007166 GO:0007186 GO:0007188 GO:0007189 GO:0007584 GO:0008152 GO:0008217 GO:0009253 GO:0009755 GO:0016020 GO:0016021 GO:0016787 GO:0016798 GO:0016998 GO:0017046 GO:0019076 GO:0019835 GO:0030430 GO:0042593 GO:0042594 GO:0042742 GO:0043547 GO:0070873 GO:0071377
140.060.3184.780.080.442ohoA GO:0006807 GO:0008152 GO:0008360 GO:0008881 GO:0009252 GO:0016853 GO:0016855 GO:0036361 GO:0071555
150.060.2395.740.070.374uucA GO:0005622 GO:0016567 GO:0035556
160.060.2155.370.050.324v6iBs GO:0000027 GO:0002181 GO:0003735 GO:0005622 GO:0005737 GO:0005840 GO:0022625 GO:0030529 GO:0030687 GO:0042254 GO:0070180
170.060.2126.680.070.384djmD GO:0030288 GO:0042597 GO:0043711 GO:0061077 GO:0071555
180.060.2245.610.050.354stdA GO:0006582 GO:0016829 GO:0030411 GO:0042438 GO:0043581


Consensus prediction of GO terms
 
Molecular Function GO:0008270 GO:0045127 GO:0005524 GO:0031177
GO-Score 0.06 0.06 0.06 0.06
Biological Processes GO:0006367 GO:0070207
GO-Score 0.82 0.49
Cellular Component GO:0005886
GO-Score 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.