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I-TASSER results for job id Rv1831

[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
10.12 5 1llzA F3S Rep, Mult 4,5,7,14,15,20
20.07 3 2xctS NUC Rep, Mult 39,63,65,66
30.05 2 3bbxE MG Rep, Mult 44,45,46
40.05 2 3aoeD LEU Rep, Mult 8,57,60,61,68,69
50.02 1 3wmnA MQ8 Rep, Mult 75,79
60.02 1 4a0uA CO3 Rep, Mult 30,33
70.02 1 2xz6E ETM Rep, Mult 11,47
80.02 1 3nmvB MG Rep, Mult 20,40
90.02 1 3ao4A 833 Rep, Mult 19,21,22,23,79,82
100.02 1 2xtvA MC3 Rep, Mult 60,71,75,78
110.02 1 2a5hA UUU Rep, Mult 39,40
120.02 1 2v46I NUC Rep, Mult 52,53

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
10.0601h3gA0.4814.190.0480.8243.2.1.54NA
20.0603h9eB0.4824.210.0490.8351.2.1.12NA
30.0601y6jA0.5293.510.0410.8121.1.1.37NA
40.0601ea0A0.4884.060.0830.8821.4.1.13NA
50.0601lldB0.4753.420.0280.8001.1.1.2767
60.0601xkjA0.4714.460.0770.8591.14.14.372
70.0603gayA0.4843.870.0500.8944.1.2.13NA
80.0602vdcA0.4884.060.0830.8821.4.1.13NA
90.0602v8tA0.5053.290.0150.7651.11.1.6NA
100.0602fhbA0.3334.680.0000.6713.2.1.41NA
110.0602vynD0.4783.770.0740.7881.2.1.12NA
120.0601nboA0.4774.160.0630.8351.2.1.13NA
130.0601lldA0.4803.320.0420.7881.1.1.27NA
140.0602d2iA0.4834.230.1140.8471.2.1.13NA
150.0602fhcA0.3354.500.0130.6593.2.1.41NA
160.0601ofdA0.3904.260.0850.7881.4.7.1NA
170.0603f9kI0.5203.590.0960.8472.7.7.49NA
180.0603b45A0.5073.020.0430.7413.4.21.10554,61
190.0603hpgB0.5073.590.0360.8242.7.7.4939

(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
00.070.3493.840.020.563pqeA GO:0003824 GO:0004459 GO:0005737 GO:0005975 GO:0006096 GO:0016491 GO:0016616 GO:0019752 GO:0055114
10.070.3573.640.040.563p7mB GO:0003824 GO:0005975 GO:0006099 GO:0016491 GO:0016616 GO:0019752 GO:0030060 GO:0055114
20.070.5343.420.040.804j05A GO:0005215 GO:0016020 GO:0016021 GO:0022857 GO:0055085
30.070.3443.130.030.494m1qA GO:0003824 GO:0004459 GO:0005737 GO:0005975 GO:0006096 GO:0016491 GO:0016616 GO:0019752 GO:0055114
40.070.4833.540.050.804zp0A GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015385 GO:0015386 GO:0016020 GO:0016021 GO:0030641 GO:0035725 GO:0046677 GO:0055085 GO:0071805
50.070.3584.600.130.654cl3A GO:0003824 GO:0005975 GO:0006099 GO:0016491 GO:0016616 GO:0019752 GO:0030060 GO:0055114
60.070.4053.680.040.614tvoA GO:0003824 GO:0005618 GO:0005829 GO:0005886 GO:0005975 GO:0006099 GO:0006108 GO:0016491 GO:0016615 GO:0016616 GO:0019752 GO:0030060 GO:0055114
70.070.5013.510.070.804uuoA GO:0003824 GO:0005975 GO:0006108 GO:0016491 GO:0016615 GO:0016616 GO:0019752 GO:0030060 GO:0055114
80.070.3553.660.020.553h3jB GO:0003824 GO:0004459 GO:0005737 GO:0005975 GO:0006096 GO:0016491 GO:0016616 GO:0019752 GO:0055114
90.070.3543.760.000.561ez4B GO:0003824 GO:0004459 GO:0005737 GO:0005975 GO:0006096 GO:0016491 GO:0016616 GO:0019752 GO:0055114
100.070.4013.970.020.624kdeA GO:0003824 GO:0005975 GO:0006099 GO:0006108 GO:0016491 GO:0016615 GO:0016616 GO:0019752 GO:0030060 GO:0055114
110.060.5333.120.080.804mdhA GO:0003824 GO:0005737 GO:0005829 GO:0005975 GO:0006099 GO:0006108 GO:0016491 GO:0016615 GO:0016616 GO:0019752 GO:0030060 GO:0055114
120.060.3644.820.100.692hjrB GO:0003824 GO:0005975 GO:0016491 GO:0016616 GO:0019752 GO:0055114
130.060.3445.190.010.781b8pA GO:0003824 GO:0005975 GO:0006099 GO:0006108 GO:0016491 GO:0016615 GO:0016616 GO:0019752 GO:0030060 GO:0055114
140.060.4444.040.010.794ldsA GO:0005215 GO:0006810 GO:0016020 GO:0016021 GO:0022857 GO:0022891 GO:0055085
150.060.5363.090.100.792gfpA GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0015893 GO:0016020 GO:0016021 GO:0055085
160.060.4783.300.090.764xnjA GO:0005215 GO:0006810 GO:0006857 GO:0015197 GO:0015833 GO:0016020 GO:0016021 GO:0042802
170.060.3553.660.090.593tl2A GO:0003824 GO:0004470 GO:0005975 GO:0006099 GO:0016491 GO:0016616 GO:0019752 GO:0030060 GO:0055114
180.060.5323.420.070.822cmdA GO:0003824 GO:0005737 GO:0005829 GO:0005975 GO:0006096 GO:0006099 GO:0006108 GO:0006113 GO:0009061 GO:0016020 GO:0016491 GO:0016615 GO:0016616 GO:0019752 GO:0019898 GO:0030060 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0016614
GO-Score 0.37
Biological Processes GO:0043436 GO:0044238
GO-Score 0.37 0.32
Cellular Component GO:0005737 GO:0005887
GO-Score 0.13 0.07

(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.