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I-TASSER results for job id Rv2305

[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 4 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
10.03 1 1xl7B MPD Rep, Mult 288,304,307,308,311
20.03 1 5duaA 5FQ Rep, Mult 10,13,14,127,383
30.03 1 3lw5K CLA Rep, Mult 282,286
40.03 1 1s1qA CU Rep, Mult 127,149
50.03 1 1jgtB MG Rep, Mult 131,258
60.03 1 3fp0A SWE Rep, Mult 209,210,211,212,421
70.03 1 1iujA ZN Rep, Mult 98,127
80.03 1 2wscJ CLA Rep, Mult 106,107
90.03 1 3b2sA B2S Rep, Mult 19,22,102,127,197,284,356,389,391
100.03 1 3gk0B PO4 Rep, Mult 103,126
110.03 1 2ii3B CAO Rep, Mult 208,408,412,413
120.03 1 1xl7B MPD Rep, Mult 235,236,301,302,305
130.03 1 1xl8B MPD Rep, Mult 242,246,257,260
140.03 1 3orcA NUC Rep, Mult 279,280
150.03 1 2xr7A MLC Rep, Mult 225,232,233,234,235
160.03 1 1f8iB MG Rep, Mult 77,131
170.03 1 3dfmA ZN Rep, Mult 126,131

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
10.0952bghA0.6614.180.0990.8282.3.1.160266,282
20.0602ckjA0.3386.840.0280.5341.17.1.4,1.17.3.2NA
30.0603aboA0.3527.230.0430.5874.3.1.7125
40.0603l60A0.3793.480.1050.4362.3.1.12127
50.0602debA0.5674.850.0710.7482.3.1.21NA
60.0603b9jC0.3077.400.0410.5241.17.3.2,1.17.1.455
70.0603bq5A0.3146.850.0430.5102.1.1.14NA
80.0602ii4A0.3793.470.0990.4382.3.1.168NA
90.0601bf2A0.3567.070.0590.5853.2.1.68325
100.0601sczA0.3753.520.0990.4382.3.1.61127
110.0603b9jJ0.2286.560.0820.3521.17.1.4,1.17.3.2NA
120.0601t7lA0.3467.060.0520.5662.1.1.14NA
130.0601eadA0.3823.540.1410.4432.3.1.12342
140.0601fo4A0.3547.000.0590.5761.17.1.4NA
150.0601xl7B0.5475.050.0720.7372.3.1.137NA
160.0601vlpB0.3527.120.0710.5782.4.2.11242
170.0602vr5A0.3557.100.0460.5873.2.1.-NA
180.0602fy3A0.5884.500.0890.7512.3.1.6NA
190.0602j5wA0.3587.010.0500.5851.16.3.1NA
200.0601q16A0.2777.260.0320.4661.7.99.4NA

(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
00.270.8352.690.140.924tx3B GO:0003824 GO:0008152 GO:0009058 GO:0016788 GO:0016874 GO:0031177
10.260.7833.410.160.914jn3B GO:0003824 GO:0008152 GO:0031177
20.210.7923.350.100.924zxjA GO:0000166 GO:0003824 GO:0005524 GO:0005829 GO:0005886 GO:0008152 GO:0009058 GO:0009239 GO:0009366 GO:0016740 GO:0016779 GO:0016788 GO:0016874 GO:0031177 GO:0043041 GO:0047527
30.190.7363.950.130.901l5aA GO:0016880 GO:0019290
40.170.8162.930.120.922jgpA GO:0003824 GO:0008152 GO:0009058 GO:0016788 GO:0016874 GO:0017000 GO:0031177
50.140.7653.800.090.922vsqA GO:0003824 GO:0008152 GO:0009058 GO:0016788 GO:0016874 GO:0017000 GO:0030435 GO:0031177
60.060.3206.710.060.514dg9A GO:0000166 GO:0003824 GO:0008152
70.060.3336.930.040.543kxwA GO:0003824 GO:0008152
80.060.3267.000.040.542p20A GO:0000166 GO:0003824 GO:0003987 GO:0005524 GO:0006935 GO:0008152 GO:0016208 GO:0016874 GO:0019427 GO:0046872
90.060.3216.780.050.524d56A GO:0003824 GO:0008152
100.060.3256.880.070.524dg8A GO:0000166 GO:0003824 GO:0008152
110.060.2847.540.040.494eatB GO:0003824 GO:0005524 GO:0008152 GO:0016405 GO:0016874
120.060.3287.590.060.584qflA GO:0043190 GO:0055085
130.060.2947.230.010.503a9vA GO:0000166 GO:0003824 GO:0008152 GO:0016874
140.060.3087.070.040.513e7wA GO:0000166 GO:0003824 GO:0005524 GO:0005737 GO:0008152 GO:0016874 GO:0016876 GO:0047473 GO:0070395
150.060.3036.840.070.493rg2C GO:0000166 GO:0003824 GO:0005524 GO:0005829 GO:0008152 GO:0008668 GO:0008908 GO:0009239 GO:0016020 GO:0016740 GO:0016746 GO:0016787 GO:0016874 GO:0019290 GO:0047527
160.060.3166.960.040.524r0mA GO:0003824 GO:0008152 GO:0016740 GO:0031177
170.060.3257.210.060.555es8B GO:0003824 GO:0008152 GO:0009058 GO:0016742 GO:0016874 GO:0017000 GO:0031177
180.060.2837.150.050.475ifiA GO:0000166 GO:0003824 GO:0003987 GO:0005524 GO:0008152 GO:0016208 GO:0016874 GO:0019427


Consensus prediction of GO terms
 
Molecular Function GO:0031177 GO:0016788 GO:0016881 GO:0032559 GO:0032550 GO:0016772 GO:0035639
GO-Score 0.65 0.53 0.43 0.43 0.43 0.43 0.43
Biological Processes GO:0018130 GO:0009713 GO:0009238 GO:0019540 GO:0043038 GO:0016999
GO-Score 0.43 0.43 0.43 0.43 0.43 0.34
Cellular Component GO:0043234 GO:0044444 GO:0071944 GO:0016020
GO-Score 0.43 0.43 0.43 0.32

(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.