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I-TASSER results for job id Rv2260

[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
10.73 268 1ycfB FEO Rep, Mult 63,65,67,68,126,149,190
20.43 146 2zo4A ZN Rep, Mult 63,65,126,149
30.02 12 2bmiB NA Rep, Mult 24,25,39,67,146
40.02 12 1qh5A GSH Rep, Mult 67,126,149,152,156,157,158,161,190
50.01 4 2fhxA AZI Rep, Mult 39,62,63,146,148,149
60.01 8 1wupC ZN Rep, Mult 67,149,152,190
70.00 1 1qh3A CAC Rep, Mult 170,171,175
80.00 1 2hb9A L13 Rep, Mult 54,76,77,79,80
90.00 3 2bfkB AZI Rep, Mult 126,152,160,161
100.00 1 4awyB CA Rep, Mult 150,188,189,190,193
110.00 1 4awyB MG Rep, Mult 92,95,99
120.00 4 2p18A SPD Rep, Mult 156,157,158,192,205
130.00 2 1jjeA ZN Rep, Mult 25,192
140.00 1 4awyB MG Rep, Mult 1,50
150.00 1 3m8tA ZN Rep, Mult 48,74,78
160.00 1 2fu7A PHN Rep, Mult 18,32,114,115,116,136,138
170.00 3 2ohjA FE Rep, Mult 125,126
180.00 1 3m8tA ZN Rep, Mult 5
190.00 1 4awyB MG Rep, Mult 193
200.00 1 4awzA MG Rep, Mult 200

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
10.4592p18A0.8352.110.1990.9383.1.2.667
20.4501qh3A0.8241.770.2540.8963.1.2.667
30.1461bvtA0.7843.030.1460.9433.5.2.667,153
40.1191m2xA0.7662.970.1640.9293.5.2.667
50.1042gmnA0.7533.120.2000.9153.5.2.667
60.0961smlA0.7503.210.2400.9153.5.2.667
70.0822zo4A0.7832.570.2350.9153.-.-.-67
80.0673dhaA0.6853.070.1440.8253.1.1.-74
90.0602ohhA0.7613.100.2340.9291.-.-.-67
100.0601djnA0.4745.010.0710.7541.5.8.2,1.5.99.763
110.0601l9yA0.7523.320.1690.9243.5.2.667
120.0601jjeB0.7662.850.1650.9193.5.2.667
130.0603maxA0.4775.560.0980.8063.5.1.9865
140.0601p9eA0.7533.120.2040.9193.1.8.1NA
150.0602fk6A0.6023.650.1510.7773.1.26.1124,73
160.0602qedA0.7911.850.2790.8673.1.2.669,124
170.0602fhxA0.7652.860.1730.9153.5.2.6NA
180.0601a8tA0.7902.930.1630.9433.5.2.623,66
190.0601e5dA0.7572.910.1530.9151.-.-.-NA
200.0601qh5A0.8251.770.2540.8963.1.2.688,124,152
210.0601x8hA0.7553.040.1500.9193.5.2.667
220.0602q42A0.8081.980.2800.8813.1.2.623,124,152
230.0601xm8A0.8091.970.2800.8813.1.2.667
240.0604kbpA0.4865.130.0500.7583.1.3.266
250.0601ko2A0.7633.170.1610.9293.5.2.667
260.0601kbpA0.4845.100.0500.7543.1.3.2NA
270.0601ycfA0.7483.070.1680.9191.7.99.7169

(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
00.590.8182.520.230.933r2uA
10.590.8241.770.250.901qh3A GO:0004416 GO:0005737 GO:0005739 GO:0005759 GO:0005829 GO:0005975 GO:0006090 GO:0006749 GO:0006750 GO:0016787 GO:0019243 GO:0046872 GO:0070062
20.580.8332.030.230.912gcuA GO:0005739 GO:0009651 GO:0009793 GO:0009960 GO:0016491 GO:0016788 GO:0046872 GO:0047951 GO:0048316 GO:0050313 GO:0051213 GO:0055114
30.550.8341.650.310.902zwrB GO:0046872
40.530.7832.570.230.912zo4A GO:0046872
50.520.7702.890.210.912q0jA GO:0044550
60.500.7382.730.200.873adrA GO:0008270 GO:0046872
70.480.7911.850.280.872qedA GO:0004416 GO:0016787 GO:0019243 GO:0046872
80.450.7533.120.200.921p9eA GO:0016787 GO:0046872
90.430.8242.070.240.904chlB 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
100.400.6153.570.150.793g1pB GO:0008081 GO:0016787 GO:0019700 GO:0030145 GO:0046872
110.400.7752.990.190.924ad9A GO:0004521 GO:0005739 GO:0005759 GO:0008270 GO:0016787 GO:0046872 GO:0090502
120.380.6853.070.140.823dhaA GO:0016787 GO:0046872 GO:0102007
130.360.7543.000.190.913lvzB GO:0046872
140.350.8081.980.280.882q42A GO:0004416 GO:0005506 GO:0005739 GO:0008270 GO:0016787 GO:0019243 GO:0046872
150.350.8840.980.290.912xf4A GO:0016787
160.340.8352.110.200.942p18A GO:0004416 GO:0016787 GO:0046872
170.310.7333.400.210.914awyB GO:0046872
180.300.7523.180.240.915evdA GO:0008270 GO:0008800 GO:0016787 GO:0017001 GO:0042597 GO:0046677 GO:0046872
190.280.7612.410.200.872p97A GO:0046872
200.260.7523.320.170.921l9yA GO:0008800 GO:0016787 GO:0046872
210.260.7343.270.190.915axoA GO:0046872
220.240.7373.310.160.924xukA GO:0016787
230.190.6693.230.170.824le6A GO:0004063 GO:0016311 GO:0016787 GO:0046872
240.190.8522.480.260.964efzA GO:0016787 GO:0046872
250.170.8232.330.270.933tp9A GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0046872 GO:0004416 GO:0050313 GO:0047951
GO-Score 0.96 0.59 0.58 0.58
Biological Processes GO:0006750 GO:0005975 GO:0006090 GO:0019243 GO:0009960 GO:0009793 GO:0055114 GO:0009651
GO-Score 0.59 0.59 0.59 0.59 0.58 0.58 0.58 0.58
Cellular Component GO:0070062 GO:0005759 GO:0005829
GO-Score 0.59 0.59 0.59

(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.