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I-TASSER results for job id Rv0999

[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
10.17 8 4eneA DMU Rep, Mult 243,247
20.04 2 5hhjA GLY Rep, Mult 242,245
30.04 2 2xnvF VU3 Rep, Mult 138,217,219
40.04 2 2c5wB III Rep, Mult 11,14,120,121,122,123,124,125,126,127,128,129
50.02 1 2jkgA MG Rep, Mult 178,181
60.02 1 2y6pC MG Rep, Mult 100,235
70.02 1 4fmsA C8E Rep, Mult 208,210,219
80.02 1 2cqtA PO4 Rep, Mult 208,236,237
90.02 1 1izcA MG Rep, Mult 144,207
100.02 1 2cixA MAN Rep, Mult 185,186
110.02 1 5k1nB RE Rep, Mult 140,215
120.02 1 2hf8A ZN Rep, Mult 50,109
130.02 1 1agmA MAN Rep, Mult 103,106
140.02 1 1dq8D COA Rep, Mult 76,78

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
10.0603imhA0.4035.290.0390.6195.1.3.3NA
20.0601z45A0.4375.280.0510.6595.1.3.2,5.1.3.3208
30.0601lf6A0.3895.160.0550.5793.2.1.377
40.0601oqzB0.3925.960.0590.6473.5.1.93NA
50.0601l7kB0.4135.460.0430.6395.1.3.3NA
60.0603eqvA0.4285.740.0470.6793.4.16.4187
70.0602dqmA0.4195.830.0380.6913.4.11.2NA
80.0603fwlA0.3965.820.0300.6512.4.1.129NA
90.0603eifA0.4066.270.0500.7383.4.21.110NA
100.0601f1sA0.4355.270.0510.6474.2.2.1NA
110.0603mwxA0.3975.630.0470.6155.1.3.3NA
120.0602htaA0.4105.190.0510.6075.1.3.-NA
130.0601ffuB0.3956.000.0340.6751.2.99.2NA
140.0602wafA0.4066.050.0430.7063.4.-.-NA
150.0601rw9A0.4505.260.0660.6914.2.2.5NA
160.0602cqsA0.4515.020.0580.6552.4.1.20NA
170.0601i8qA0.4375.320.0560.6514.2.2.1244
180.0601snzA0.4115.490.0800.6315.1.3.3NA
190.0601sqiA0.3465.840.0640.5641.13.11.27NA

(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
00.160.5053.940.110.664esqA GO:0000166 GO:0004672 GO:0004674 GO:0005524 GO:0005618 GO:0005886 GO:0005887 GO:0006468 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0043085 GO:0043086 GO:0043388 GO:0045893 GO:0045926 GO:0046777 GO:0046890 GO:0052572
10.070.4724.970.100.693aflA GO:0016829
20.060.4745.220.080.713e80A GO:0008201 GO:0015021 GO:0016829 GO:0030211 GO:0042597 GO:0046872 GO:0047488
30.060.4375.130.070.645jmfA GO:0016829 GO:0042597
40.060.4525.070.070.655jmdA GO:0016829 GO:0042597
50.060.3236.170.050.583w9aB GO:0004553 GO:0005576 GO:0005975 GO:0030248 GO:0042802
60.060.3295.610.100.524n0qB GO:0006810 GO:0006865
70.060.3216.470.040.601np7A GO:0003677 GO:0003913 GO:0006281 GO:0006351 GO:0006355 GO:0018298
80.060.3845.840.050.614fnvA GO:0015021 GO:0016829 GO:0042597
90.060.3016.170.050.502cl2A GO:0004553 GO:0005975
100.060.2736.510.070.501b0aA GO:0000105 GO:0003824 GO:0004477 GO:0004488 GO:0005829 GO:0006164 GO:0006730 GO:0008152 GO:0008652 GO:0009086 GO:0009396 GO:0016491 GO:0016787 GO:0035999 GO:0055114
110.060.3125.700.040.512ykkA GO:0004553 GO:0005975 GO:0006080 GO:0016985 GO:0030246 GO:0030248 GO:0046872
120.060.2625.530.060.422ws2A GO:0016740
130.060.2765.250.070.432hyeB GO:0003723 GO:0016032 GO:0030430 GO:0030683 GO:0039502 GO:0039503 GO:0039554 GO:0039563 GO:0046872
140.060.2545.640.040.413etpA GO:0000166 GO:0000902 GO:0001525 GO:0001655 GO:0004672 GO:0004713 GO:0004714 GO:0004872 GO:0005003 GO:0005005 GO:0005102 GO:0005524 GO:0005886 GO:0005887 GO:0006468 GO:0007169 GO:0007275 GO:0007399 GO:0007411 GO:0007413 GO:0007612 GO:0008046 GO:0009887 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0018108 GO:0021631 GO:0021952 GO:0022038 GO:0030424 GO:0030425 GO:0031290 GO:0042472 GO:0042802 GO:0042995 GO:0043025 GO:0045202 GO:0048013 GO:0048168 GO:0048170 GO:0048593 GO:0050770 GO:0050771 GO:0050878 GO:0051965 GO:0060021 GO:0060996 GO:0060997 GO:0071679
150.060.2786.370.030.501h76A GO:0005576 GO:0005615 GO:0005623 GO:0006810 GO:0006811 GO:0006826 GO:0006879 GO:0008199 GO:0015091 GO:0015682 GO:0046872 GO:0055072
160.060.2356.270.060.411nzbA GO:0003677 GO:0006310 GO:0015074
170.060.2516.230.020.441pszA GO:0005886 GO:0006810 GO:0007155 GO:0016020 GO:0030001 GO:0046872
180.060.2635.580.060.423ivlA GO:0003824 GO:0004222 GO:0006508 GO:0008233 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0016773 GO:0032550 GO:0032559 GO:0035639 GO:0016301
GO-Score 0.32 0.32 0.32 0.32 0.32
Biological Processes GO:0051101 GO:0051099 GO:0040008 GO:0048519 GO:0052200 GO:0019216 GO:1903508 GO:0006468 GO:0008610 GO:0006355 GO:0010628 GO:0052564 GO:0050790 GO:0044092
GO-Score 0.32 0.32 0.32 0.32 0.32 0.32 0.32 0.32 0.32 0.32 0.32 0.32 0.32 0.32
Cellular Component GO:0030312 GO:0031226
GO-Score 0.32 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.