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I-TASSER results for job id Rv1986

[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 5 1v54B HEA Rep, Mult 19,121,124,125
20.09 5 4n7wB MPG Rep, Mult 30,119,122,123,125,126,129,138,194
30.04 2 5irxA 6EU Rep, Mult 27,116,119,120
40.02 1 2o013 CLA Rep, Mult 72,73
50.02 1 1xveD 3BB Rep, Mult 77,81,84
60.02 1 2wieA CVM Rep, Mult 51,55
70.02 1 1mhy1 III Rep, Mult 9,10,13,14,16,17,18,21,22,124,128
80.02 1 1xvfA 3CL Rep, Mult 7,14,129,131,132
90.02 1 1ea4J NUC Rep, Mult 196,197,199
100.02 1 2r9rB PGW Rep, Mult 181,196
110.02 1 3wguG CLR Rep, Mult 112,119
120.02 1 1xvgB BRJ Rep, Mult 12,13,16,74,78
130.02 1 1xvgA BRJ Rep, Mult 121,122,125,182,185,186
140.02 1 3zuxA PTY Rep, Mult 122,125,129,137,145,186,190,193,194
150.02 1 2zt9G III Rep, Mult 61,69
160.02 1 1jtxB CVI Rep, Mult 50,158
170.02 1 1xvbD 3BR Rep, Mult 81,84,85,88
180.02 1 2bhwA CLA Rep, Mult 17,19

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
10.0602dgaA0.4335.130.0370.6783.2.1.21NA
20.0601myrA0.4315.040.0300.6683.2.1.147NA
30.0602p0mA0.4285.190.0440.6941.13.11.33NA
40.0601up8A0.3555.700.0540.6181.11.1.18123
50.0601zchA0.4294.780.0970.6481.5.1.29132
60.0601h16A0.4775.410.0740.7842.3.1.54NA
70.0601p4kA0.4315.190.0340.6993.5.1.26147
80.0601mhyB0.5204.650.0550.7891.14.13.25NA
90.0601jk0A0.4355.370.0680.7091.17.4.1NA
100.0601biqB0.4764.970.0780.7641.17.4.1NA
110.0601dwaM0.4325.110.0300.6733.2.1.147NA
120.0601ayyD0.2734.830.0530.4223.5.1.26NA
130.0602vuxB0.4485.590.0560.7641.17.4.1NA
140.0601is2A0.4305.440.0440.7241.3.3.658
150.0602de3B0.4324.930.0860.6993.13.1.3NA
160.0601smsA0.4704.780.0610.7591.17.4.1NA
170.0602bq1I0.4984.520.0930.7541.17.4.1NA
180.0601fziA0.4985.280.0750.8141.14.13.25NA
190.0603hf1B0.4675.070.0610.7691.17.4.1NA

(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
00.210.5314.630.060.801fyzC GO:0004497 GO:0006725 GO:0006730 GO:0015049 GO:0015050 GO:0015947 GO:0016491 GO:0016709 GO:0055114
10.150.7872.590.130.944bwzA GO:0006810 GO:0006812 GO:0015299 GO:0016020 GO:0016021 GO:0046872 GO:0055085 GO:1902600
20.140.7203.230.060.944czbB GO:0005886 GO:0006810 GO:0006811 GO:0006812 GO:0006814 GO:0015297 GO:0015299 GO:0016020 GO:0016021 GO:0042802 GO:0055085 GO:1902600
30.120.7023.590.120.944n7wA GO:0016020 GO:0016021
40.120.6973.400.060.923zuxA GO:0016020 GO:0016021
50.120.7103.350.080.944cz8A GO:0006810 GO:0006812 GO:0015299 GO:0016020 GO:0016021 GO:0055085 GO:1902600
60.070.4985.280.070.811fziA GO:0004497 GO:0006725 GO:0006730 GO:0015049 GO:0015050 GO:0015947 GO:0016491 GO:0046872 GO:0055114
70.070.5204.650.060.791mhyB GO:0004497 GO:0006725 GO:0006730 GO:0015049 GO:0016491 GO:0016709 GO:0055114
80.060.4775.410.060.822innA GO:0006725 GO:0016491 GO:0046872 GO:0055114
90.060.5045.100.050.813dhiA GO:0004497 GO:0006725 GO:0016491 GO:0019439 GO:0042203 GO:0046872 GO:0055114
100.060.5244.970.070.851mhyD GO:0004497 GO:0006725 GO:0006730 GO:0015049 GO:0016491 GO:0046872 GO:0055114
110.060.4765.370.070.812incA GO:0004497 GO:0006725 GO:0016491 GO:0046872 GO:0055114
120.060.4634.580.040.722inpD GO:0006725 GO:0016491 GO:0016709 GO:0055114
130.060.7332.950.060.904atvA GO:0005886 GO:0006810 GO:0006811 GO:0006814 GO:0006885 GO:0015081 GO:0015297 GO:0015491 GO:0015992 GO:0016020 GO:0016021 GO:0035725 GO:0055085 GO:0098655
140.060.4474.020.090.613dhiB GO:0004497 GO:0006725 GO:0016491 GO:0016709 GO:0019439 GO:0042203 GO:0055114
150.060.3556.210.050.675aa5C GO:0016151
160.060.3505.510.030.591u0uA GO:0003824 GO:0005737 GO:0008152 GO:0009058 GO:0016740 GO:0016746 GO:0016747 GO:0050198
170.060.3105.230.050.492y1vA GO:0005618 GO:0016020 GO:0016021
180.060.3074.940.050.482fckA GO:0008080 GO:0016740 GO:0016746


Consensus prediction of GO terms
 
Molecular Function GO:0015078 GO:0015298 GO:0016705 GO:0004497 GO:0043169
GO-Score 0.54 0.54 0.42 0.42 0.31
Biological Processes GO:0098662 GO:0015992 GO:0043446 GO:0044281
GO-Score 0.54 0.54 0.42 0.42
Cellular Component GO:0016021 GO:1990204
GO-Score 0.43 0.42

(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.