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I-TASSER results for job id Rv0587

[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
10.05 3 2nwwB TB1 Rep, Mult 71,92,161,164,165,168
20.05 3 4z3bA MN Rep, Mult 215,232,236
30.03 2 5sy1A CLR Rep, Mult 247,250
40.03 2 3v2d2 MG Rep, Mult 145,149
50.03 2 2axtl UNK Rep, Mult 244,247
60.02 1 2x7qA CA Rep, Mult 123,129
70.02 1 3kcuA MA5 Rep, Mult 102,120,121,123,124,127
80.02 1 2o014 CLA Rep, Mult 237,240
90.02 1 2o01H CLA Rep, Mult 112,122
100.02 1 1jb0K CLA Rep, Mult 104,109
110.02 1 4czaA TL Rep, Mult 37,99,126,130
120.02 1 3nmvB MG Rep, Mult 130,168
130.02 1 1fipA III Rep, Mult 67,68
140.02 1 1nquA RDL Rep, Mult 209,210
150.02 1 3wmm7 CRT Rep, Mult 58,68
160.02 1 3mmhB MG Rep, Mult 103,104
170.02 1 1u7gA NH4 Rep, Mult 108,122,203
180.02 1 3zuyA PTY Rep, Mult 67,71,74,86,94,136,139
190.02 1 1wuuB MG Rep, Mult 65,132
200.02 1 3zuxA PTY Rep, Mult 162,166,170,241,245,248,249,252

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
10.0602zr3B0.4036.200.0630.6686.1.1.11199
20.0602j2fA0.4275.670.0590.6831.14.19.2,1.14.99.6NA
30.0603fg3A0.4386.100.0990.7404.2.1.92,1.13.11.40NA
40.0601sesA0.4096.080.0490.6686.1.1.11NA
50.0603dy5A0.3996.160.0470.6831.13.11.40,4.2.1.92NA
60.0601i7qA0.3945.850.0710.6304.1.3.27NA
70.0601mhyD0.3955.980.0560.6601.14.13.25NA
80.0601m56A0.3955.960.0490.6451.9.3.1NA
90.0601serB0.2696.720.0310.4946.1.1.11NA
100.0601ayxA0.3985.850.0550.6533.2.1.3135
110.0601gaiA0.4015.560.0470.6233.2.1.3135
120.0603errA0.4066.010.0450.6536.1.1.11NA
130.0601fziA0.3945.910.0520.6641.14.13.25NA
140.0601z1lA0.3855.410.0300.5853.1.4.17163
150.0603d3lA0.4075.970.0660.6871.13.11.31NA
160.0601wleB0.4105.760.0360.6496.1.1.11NA
170.0601j0mA0.3416.270.0440.5964.2.2.12200
180.0601hxgA0.3955.620.0830.6264.2.3.9,4.1.99.7105,106
190.0602dq3A0.3996.150.0550.6576.1.1.11112

(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
00.140.7263.510.120.884bwzA GO:0006810 GO:0006812 GO:0015299 GO:0016020 GO:0016021 GO:0046872 GO:0055085 GO:1902600
10.090.6723.720.060.844czbB GO:0005886 GO:0006810 GO:0006811 GO:0006812 GO:0006814 GO:0015297 GO:0015299 GO:0016020 GO:0016021 GO:0042802 GO:0055085 GO:1902600
20.080.3905.620.050.614atvA 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
30.080.6454.070.090.834cz8A GO:0006810 GO:0006812 GO:0015299 GO:0016020 GO:0016021 GO:0055085 GO:1902600
40.070.6124.470.070.854n7wA GO:0016020 GO:0016021
50.070.6124.420.080.843zuxA GO:0016020 GO:0016021
60.060.4575.960.050.775dgqA GO:0003824 GO:0004553 GO:0005975
70.060.4015.060.090.603x17A GO:0000272 GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798 GO:0030245 GO:0046872
80.060.4505.770.050.743h7lA GO:0003824 GO:0004553 GO:0005975 GO:0008810
90.060.3245.790.040.521g87B GO:0000272 GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798 GO:0030245 GO:0030246 GO:0030248
100.060.2926.520.030.511ia7A GO:0000272 GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0046872
110.060.3176.650.040.583gzkA GO:0000272 GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798 GO:0030245 GO:0046872
120.060.2936.250.040.514rpfA GO:0000166 GO:0004413 GO:0005524 GO:0005737 GO:0006566 GO:0008652 GO:0009088 GO:0016301 GO:0016310 GO:0016740
130.060.4055.000.060.614cj1A GO:0000272 GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798 GO:0030245
140.060.2736.060.060.464w65A GO:0004553 GO:0005975 GO:0016787 GO:0046872
150.060.3236.050.050.551u0uA GO:0003824 GO:0005737 GO:0008152 GO:0009058 GO:0016740 GO:0016746 GO:0016747 GO:0050198
160.060.3245.140.060.484b2tb GO:0000166 GO:0002199 GO:0005524 GO:0005737 GO:0005832 GO:0005874 GO:0006457 GO:0007339 GO:0031625 GO:0043209 GO:0044297 GO:0051082 GO:0051131 GO:0070062 GO:1901998
170.060.2665.880.030.443rq0A GO:0004553 GO:0005975 GO:0016787 GO:0046872
180.060.2475.940.060.423r0rA GO:0019069 GO:0042025


Consensus prediction of GO terms
 
Molecular Function GO:0015298 GO:0015078
GO-Score 0.56 0.56
Biological Processes GO:0098662 GO:0015992 GO:0030001
GO-Score 0.56 0.56 0.33
Cellular Component GO:0016021 GO:0071944
GO-Score 0.39 0.33

(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.