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I-TASSER results for job id Rv0406c

[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
10.20 45 1bc2A ZN Rep, Mult 85,87,181
20.19 48 2gfjB VI Rep, Mult 18,85,87,89,125,181,206,208,245
30.12 32 1vmeA FEO Rep, Mult 85,87,90,181,203,245
40.10 23 1smlA ZN Rep, Mult 89,90,245
50.10 30 2nypA ZN Rep, Mult 89,90,198,245
60.02 8 2bmiB NA Rep, Mult 39,40,54,89,201
70.01 3 3r2uA FE Rep, Mult 85,181,198
80.01 2 5b1uA HIW Rep, Mult 18,89,90,125,145,181,204,206,245,247,248,266
90.01 2 1x8gA CO3 Rep, Mult 89,181,198,212,245
100.00 1 4awyB CA Rep, Mult 199,243,244,245,248,256
110.00 1 2fhxA AZI Rep, Mult 55,84,85,195,197,198
120.00 1 1jt1A MCO Rep, Mult 181,204,206,248,259,263,266
130.00 1 4awyB MG Rep, Mult 58,59,60,61,62,93,96
140.00 1 3f9oA CO3 Rep, Mult 229,230,234,261
150.00 1 4awyB MG Rep, Mult 248,256
160.00 1 4awyB MG Rep, Mult 114,117,121
170.00 1 2fu9A MP2 Rep, Mult 10,87,89,126,149,181,207,209
180.00 1 2hb9A L13 Rep, Mult 75,76,98,99,101,102
190.00 1 4awyB MG Rep, Mult 22,67
200.00 1 3m8tA ZN Rep, Mult 23,70

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
10.2151znbB0.6342.750.1110.7353.5.2.692,245
20.1681smlA0.8062.190.1980.8903.5.2.689
30.1091m2xA0.6342.580.1410.7283.5.2.689
40.1081ko2A0.6372.880.1690.7463.5.2.6NA
50.0921bvtA0.6192.630.1550.7133.5.2.6232,236
60.0911a8tA0.6332.750.1210.7353.5.2.689
70.0681p9eA0.6333.720.1620.7833.1.8.1213
80.0671xm8A0.5932.680.1780.6803.1.2.6NA
90.0671qh5A0.5882.840.1660.6883.1.2.6179,183
100.0671qh3A0.5872.850.1660.6883.1.2.689
110.0672qedA0.5722.950.1860.6733.1.2.6179
120.0673dhaA0.5593.150.2050.6693.1.1.-NA
130.0601hqdA0.4046.010.0770.6623.1.1.333
140.0602gmnA0.7892.230.1510.8753.5.2.689
150.0602p18A0.6212.920.1560.7323.1.2.689
160.0601x8hA0.6553.120.1390.7873.5.2.6NA
170.0601tahA0.4235.670.1100.6733.1.1.3NA
180.0601e5dA0.6452.630.1350.7351.-.-.-NA
190.0601gnxA0.4265.130.0600.6293.2.1.21NA
200.0602fk6A0.4953.810.1370.6213.1.26.11NA
210.0602i7tA0.5224.170.1050.6843.1.27.-245
220.0602q42A0.5912.690.1780.6803.1.2.692,179
230.0601gonA0.4265.080.0600.6253.2.1.21NA
240.0602zoxA0.4215.280.0270.6363.2.1.2164,71,100,102
250.0601l9yA0.8221.770.1550.8793.5.2.689
260.0601ycfA0.6293.080.1880.7431.7.99.7NA
270.0602cbnA0.4944.160.1360.6403.1.26.1187,89
280.0602e9lA0.3346.070.0280.5593.2.1.21NA
290.0602i7vA0.5294.430.1170.7103.1.27.-89
300.0602zo4A0.6993.360.2040.8423.-.-.-NA
310.0603hnnA0.6223.310.1180.7461.-.-.-NA

(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
00.460.7942.380.150.893lvzB GO:0046872
10.410.6993.360.200.842zo4A GO:0046872
20.370.6313.220.170.763adrA GO:0008270 GO:0046872
30.370.8072.180.200.895evdA GO:0008270 GO:0008800 GO:0016787 GO:0017001 GO:0042597 GO:0046677 GO:0046872
40.370.7792.140.170.865axoA GO:0046872
50.360.7892.240.210.884awyB GO:0046872
60.310.6373.950.150.814zo2B GO:0052689
70.270.8221.770.150.881l9yA GO:0008800 GO:0016787 GO:0046872
80.240.5593.150.200.673dhaA GO:0016787 GO:0046872 GO:0102007
90.210.6093.340.180.744ad9A GO:0004521 GO:0005739 GO:0005759 GO:0008270 GO:0016787 GO:0046872 GO:0090502
100.150.5822.960.130.694chlB GO:0005506 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005759 GO:0006749 GO:0016491 GO:0046872 GO:0050313 GO:0051213 GO:0055114 GO:0070221 GO:0070813
110.130.6333.720.160.781p9eA GO:0016787 GO:0046872
120.070.6212.920.160.732p18A GO:0004416 GO:0016787 GO:0046872
130.070.6033.060.220.712zwrB GO:0046872
140.070.5563.030.190.651ztcA
150.070.6133.470.170.754efzA GO:0016787 GO:0046872
160.070.6033.270.190.722xf4A GO:0016787
170.070.6053.450.170.743tp9A GO:0046872
180.070.5722.950.190.672qedA GO:0004416 GO:0016787 GO:0019243 GO:0046872
190.070.5953.000.160.702gcuA GO:0005739 GO:0009651 GO:0009793 GO:0009960 GO:0016491 GO:0016788 GO:0046872 GO:0047951 GO:0048316 GO:0050313 GO:0051213 GO:0055114
200.070.5872.960.220.683aj3A GO:0016787 GO:0042820 GO:0046872 GO:0047585
210.070.5912.690.180.682q42A GO:0004416 GO:0005506 GO:0005739 GO:0008270 GO:0016787 GO:0019243 GO:0046872
220.070.6053.440.140.743r2uA


Consensus prediction of GO terms
 
Molecular Function GO:0008270 GO:0008800
GO-Score 0.60 0.37
Biological Processes GO:0046677 GO:0017001
GO-Score 0.37 0.37
Cellular Component GO:0042597
GO-Score 0.37

(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.