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I-TASSER results for job id Rv1525

[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
10.41 68 2d7iA UDP Rep, Mult 13,14,15,17,40,58,60,61,84,85,86,169,170,198,201,206
20.12 18 4fiyA MN Rep, Mult 17,84,86,198
30.03 6 2y4kA GDP Rep, Mult 13,14,15,17,38,40,60,61,64,84,85,86
40.01 2 2z86A UGA Rep, Mult 13,15,40,58,61,82,84,85,148,171,172,173,174
50.01 3 2fydD NGA Rep, Mult 61,84,87,113,142,144,145,171,173,174,198
60.01 1 4fiyB UDP Rep, Mult 15,17,40,58,60,61,169,170,171,198
70.01 3 3ee5A UUU Rep, Mult 142,143,170,171,172,174,175,219
80.00 1 1fgxB U5P Rep, Mult 15,16,17,60
90.00 1 2z86A MN Rep, Mult 86,201

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
10.1341kwsA0.5623.760.0680.7012.4.1.13524,86,90
20.1301on8A0.6193.840.0820.7742.4.1.22394
30.0963f1cB0.5263.830.0960.6632.7.7.60NA
40.0672agdA0.6153.040.1170.7282.4.1.9046
50.0672px7A0.5143.540.1290.6322.7.7.6013,16
60.0671v82A0.5583.580.0740.6972.4.1.135NA
70.0671fggA0.5593.580.0680.6942.4.1.135NA
80.0671vgwB0.5313.590.1090.6552.7.7.6017
90.0661vpaA0.5343.350.0860.6472.7.7.60NA
100.0662vsiB0.5273.790.0710.6632.7.7.60195
110.0661fgxB0.5793.310.1200.6972.4.1.3866
120.0661h7tA0.5263.990.0960.6742.7.7.3863
130.0661h7eA0.5264.060.0910.6782.7.7.38NA
140.0662j0aA0.5273.670.0950.6592.4.1.22269,86,188
150.0661i52A0.5313.460.1200.6512.7.7.60,2.7.7.-NA
160.0663hl3A0.5413.390.0860.6672.7.7.24101
170.0663k8dA0.5343.840.0900.6742.7.7.38101
180.0601hm8A0.5553.700.0710.6942.7.7.23NA
190.0602d7iA0.8522.440.1400.9582.4.1.41115,198
200.0602d0jC0.5633.590.0740.6972.4.1.13513,24,86,90,198
210.0601yp3C0.5753.470.0780.7092.7.7.27NA
220.0603lw6A0.5743.740.1220.7132.4.1.133171,173,174
230.0602pa4B0.5473.680.0910.6862.7.7.9NA
240.0602oi6B0.5603.590.0920.6862.3.1.157,2.7.7.23NA
250.0602rj7A0.5543.690.0690.6972.4.1.37,2.4.1.4050,88
260.0602icyB0.5463.920.0490.7012.7.7.9NA
270.0601jv3A0.5403.840.0530.6942.7.7.23NA
280.0602vd4A0.5483.560.0960.6782.3.1.157,2.7.7.2342,86
290.0601fxoB0.5323.730.0720.6702.7.7.2470
300.0601hm9B0.5553.540.0790.6862.3.1.157,2.7.7.2357,59,86
310.0602d0jA0.5663.620.0740.7012.4.1.135NA
320.0602vs4A0.5663.470.0750.7012.4.1.87NA
330.0602i5kB0.5403.960.0530.6972.7.7.943
340.0602v0hA0.5493.550.0920.6782.3.1.157,2.7.7.23NA
350.0602zu8A0.6193.870.1000.7932.4.1.217100
360.0602ffvA0.8152.910.1270.9392.4.1.41NA

(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
00.310.8522.440.140.962d7iA GO:0000139 GO:0004653 GO:0005794 GO:0006486 GO:0006493 GO:0016020 GO:0016021 GO:0016266 GO:0016740 GO:0016757 GO:0030246 GO:0046872
10.290.8572.660.140.974d0tA GO:0000139 GO:0002378 GO:0004653 GO:0005576 GO:0005789 GO:0005794 GO:0005795 GO:0006486 GO:0006493 GO:0016020 GO:0016021 GO:0016266 GO:0016740 GO:0016757 GO:0018242 GO:0018243 GO:0030145 GO:0030173 GO:0030246 GO:0032580 GO:0046872 GO:0048471 GO:0070062
20.280.8102.730.120.921xhbA GO:0004653 GO:0005576 GO:0005794 GO:0006486 GO:0006493 GO:0016020 GO:0016021 GO:0016740 GO:0016757 GO:0018242 GO:0018243 GO:0030145 GO:0030246 GO:0032580 GO:0046872 GO:0048471
30.280.7443.800.130.922z86C GO:0016740 GO:0016757 GO:0047238 GO:0050510
40.260.8372.600.130.944d11C GO:0000139 GO:0002378 GO:0004653 GO:0005576 GO:0005789 GO:0005794 GO:0005795 GO:0006486 GO:0006493 GO:0016020 GO:0016021 GO:0016266 GO:0016740 GO:0016757 GO:0018242 GO:0018243 GO:0030145 GO:0030173 GO:0030246 GO:0032580 GO:0046872 GO:0048471 GO:0070062
50.200.8082.560.140.924fixA GO:0005829 GO:0005886 GO:0008921 GO:0009103 GO:0016020 GO:0016740 GO:0016757 GO:0035250 GO:0035496 GO:0040007 GO:0044038 GO:0045227 GO:0046872 GO:0052573 GO:0070592 GO:0071555 GO:0071769
60.180.5873.900.110.755ekeC GO:0005886 GO:0016020 GO:0016021 GO:0016740 GO:0016757
70.120.5242.900.110.613bcvA GO:0016740
80.070.5093.240.090.622we9B GO:0046872
90.070.4963.360.090.612e8bA GO:0000166 GO:0003824 GO:0005525 GO:0005737 GO:0006777 GO:0016740 GO:0019720 GO:0046872 GO:0061603 GO:0070568
100.070.4992.820.130.593d5nA
110.070.5193.200.090.622wawA
120.060.2946.330.040.514z8sB GO:0006952 GO:0016787 GO:0017148 GO:0030598
130.060.2996.980.030.604eb2B GO:0006952 GO:0016787 GO:0017148 GO:0030246 GO:0030598
140.060.2897.180.040.581vclA GO:0030246 GO:0046872
150.060.3426.320.070.613a21A GO:0003824 GO:0004553 GO:0004557 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0052692
160.060.3016.900.030.601abrB GO:0005534 GO:0006952 GO:0016787 GO:0017148 GO:0030246 GO:0030598 GO:0045807
170.060.2996.930.050.591onkB GO:0006952 GO:0016787 GO:0017148 GO:0030246 GO:0030598
180.060.2936.890.040.594hr6C GO:0017148 GO:0030246 GO:0030598
190.060.3036.950.050.612zr1B GO:0005829 GO:0006952 GO:0007157 GO:0016787 GO:0017148 GO:0030246 GO:0030598 GO:0044533
200.060.2996.850.030.592aaiB GO:0000166 GO:0005783 GO:0006952 GO:0016787 GO:0017148 GO:0030246 GO:0030598 GO:0031640
210.060.2946.840.060.593c9zA GO:0006952 GO:0016787 GO:0017148 GO:0030246 GO:0030598
220.060.2936.370.030.521unbA GO:0005506 GO:0009058 GO:0016491 GO:0017000 GO:0031418 GO:0050599 GO:0055114
230.060.3056.650.050.571rzoB GO:0000166 GO:0005783 GO:0006952 GO:0016787 GO:0017148 GO:0030246 GO:0030598


Consensus prediction of GO terms
 
Molecular Function GO:0004653 GO:0030246 GO:0030145 GO:0015020
GO-Score 0.74 0.74 0.62 0.55
Biological Processes GO:0016266 GO:0018242 GO:0018243 GO:0002378
GO-Score 0.64 0.62 0.62 0.47
Cellular Component GO:0048471 GO:0032580 GO:0030173 GO:0070062 GO:0005789
GO-Score 0.62 0.62 0.47 0.47 0.47

(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.