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I-TASSER results for job id Rv1301

[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
10.81 16 2eqaA AMP Rep, Mult 59,63,64,65,66,118,120,142,143,183,194,195
20.29 4 3ajeA THR Rep, Mult 36,37,38,39,66,68,122,141,180,181
30.03 1 3vthB MG Rep, Mult 143,180,195
40.02 1 3lrjA SO4 Rep, Mult 38,122,124,126,130
50.02 1 1hbmA NA Rep, Mult 112,115,117,118,119
60.02 1 3vesA MN Rep, Mult 57,143

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
10.0601k4iA0.5104.140.1090.6914.1.99.12,5.4.99.-NA
20.0601pvwA0.4904.430.0750.6824.1.99.12,5.4.99.-NA
30.0601e6vA0.4045.550.0930.6912.8.4.1NA
40.0601tksA0.5024.080.1030.6774.1.99.12,5.4.99.-NA
50.0601e6yA0.4055.260.1030.6642.8.4.1NA
60.0602uveA0.3926.450.0540.7513.2.1.82114
70.0601larA0.4045.580.0610.6773.1.3.48NA
80.0601adyD0.3265.610.0530.5536.1.1.21162
90.0602c6fA0.3905.930.0520.6873.4.15.1NA
100.0601j36A0.3955.910.0260.6913.4.15.142
110.0601i1iP0.3505.880.0370.5993.4.24.16NA
120.0601snnA0.4944.410.0750.6874.1.99.1299
130.0601k4lA0.5104.100.1150.6914.1.99.1227
140.0602z8gB0.3905.930.0390.6913.2.1.57NA
150.0601y4wA0.3965.800.0720.6823.2.1.80NA
160.0602b3oA0.3905.660.0440.6543.1.3.48NA
170.0602fy3A0.3965.410.0370.6592.3.1.6NA
180.0602gfiA0.3905.670.0660.6683.1.3.8NA
190.0602pm8A0.3865.660.0560.6593.1.1.8NA

(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
00.420.9590.680.320.974e1bA GO:0000166 GO:0003725 GO:0005524 GO:0005737 GO:0008033 GO:0016740 GO:0016779 GO:0061710
10.410.8451.950.230.931k7jA GO:0003725 GO:0005829
20.330.8282.130.200.933l7vA GO:0003725
30.300.6693.370.240.841jcuA GO:0003725
40.300.6513.470.230.832mx1A GO:0000049 GO:0000166 GO:0002949 GO:0003723 GO:0003725 GO:0005524 GO:0005737 GO:0005829 GO:0006364 GO:0006450 GO:0008033 GO:0016740 GO:0016779 GO:0042254 GO:0061710
50.260.7612.920.240.903tsqA GO:0003725 GO:0008270 GO:0016743 GO:0046872 GO:0046944
60.060.3455.760.060.584u3wA GO:0008152 GO:0016491 GO:0016620 GO:0046872 GO:0055114
70.060.3095.970.040.544eziA GO:0004806 GO:0016042
80.060.2846.290.030.523vueA GO:0004373 GO:0009501 GO:0009507 GO:0009536 GO:0016740 GO:0016757 GO:0019252 GO:0033840
90.060.2785.490.030.471sg9A GO:0003676 GO:0006479 GO:0008168 GO:0008276 GO:0016740 GO:0018364 GO:0032259 GO:0036009
100.060.3036.560.040.593eojA GO:0015979 GO:0016168 GO:0018298 GO:0042314 GO:0046872 GO:0055114
110.060.3256.080.060.591ixkA GO:0003723 GO:0006364 GO:0008168 GO:0008757 GO:0032259
120.060.3245.840.090.592frxA GO:0003723 GO:0005737 GO:0006364 GO:0008168 GO:0008649 GO:0008757 GO:0009383 GO:0016434 GO:0016740 GO:0031167 GO:0032259 GO:0070475
130.060.2806.180.030.514mecB GO:0001525 GO:0001666 GO:0002246 GO:0004392 GO:0004630 GO:0004871 GO:0005634 GO:0005730 GO:0005783 GO:0005789 GO:0005829 GO:0005886 GO:0005901 GO:0006644 GO:0006788 GO:0006879 GO:0006915 GO:0006979 GO:0007264 GO:0008217 GO:0008219 GO:0008285 GO:0008630 GO:0010656 GO:0016020 GO:0016491 GO:0019899 GO:0020037 GO:0031670 GO:0032764 GO:0034101 GO:0034395 GO:0034605 GO:0035094 GO:0035556 GO:0042167 GO:0042168 GO:0042542 GO:0042803 GO:0043123 GO:0043231 GO:0043305 GO:0043392 GO:0043433 GO:0043524 GO:0043619 GO:0043627 GO:0045766 GO:0046872 GO:0048471 GO:0048661 GO:0048662 GO:0051090 GO:0051260 GO:0055072 GO:0055114 GO:0071243 GO:0071276 GO:0071456 GO:0097421 GO:1902042 GO:1904036 GO:1904706
140.060.3035.920.050.553n75A GO:0003824 GO:0005737 GO:0006520 GO:0006554 GO:0008923 GO:0016829 GO:0016831 GO:0042802
150.060.3065.800.080.533jcty GO:0000054 GO:0000463 GO:0000466 GO:0003743 GO:0005634 GO:0005730 GO:0005737 GO:0005829 GO:0006364 GO:0006412 GO:0006413 GO:0030687 GO:0042254 GO:0042256 GO:0042273 GO:0042802 GO:0043022 GO:0043023 GO:1902626
160.060.2766.370.030.521ix3A GO:0001525 GO:0001666 GO:0002246 GO:0004392 GO:0004630 GO:0004871 GO:0005634 GO:0005730 GO:0005783 GO:0005789 GO:0005829 GO:0005886 GO:0005901 GO:0006644 GO:0006788 GO:0006879 GO:0006915 GO:0006979 GO:0007264 GO:0008217 GO:0008219 GO:0008285 GO:0008630 GO:0010656 GO:0016020 GO:0016491 GO:0019899 GO:0020037 GO:0031670 GO:0032764 GO:0034101 GO:0034395 GO:0034605 GO:0035094 GO:0035556 GO:0042167 GO:0042168 GO:0042542 GO:0042803 GO:0043123 GO:0043231 GO:0043305 GO:0043392 GO:0043433 GO:0043524 GO:0043619 GO:0043627 GO:0045766 GO:0046872 GO:0048471 GO:0048661 GO:0048662 GO:0051090 GO:0051260 GO:0055072 GO:0055114 GO:0071243 GO:0071276 GO:0071456 GO:0097421 GO:1902042 GO:1904036 GO:1904706
170.060.2714.720.090.401z4eA GO:0008080
180.060.2333.710.090.312yv4A GO:0000166 GO:0003725 GO:0005524 GO:0005737 GO:0008033 GO:0016740 GO:0016779 GO:0061710


Consensus prediction of GO terms
 
Molecular Function GO:0003725 GO:0005524 GO:0061710
GO-Score 0.89 0.59 0.59
Biological Processes GO:0006400 GO:0006448 GO:0070525 GO:0016072 GO:0065008 GO:0022613
GO-Score 0.60 0.60 0.60 0.60 0.60 0.60
Cellular Component GO:0005829
GO-Score 0.59

(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.