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I-TASSER results for job id Rv2554c

[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
10.11 4 3gqcD MG Rep, Mult 28,115,116
20.09 3 4dkwA MG Rep, Mult 28,142
30.08 3 3u0oB MG Rep, Mult 40,115,119
40.06 2 1hkbA CA Rep, Mult 36,37,49,51
50.06 2 3v9sB MG Rep, Mult 28,29,145
60.03 1 3cj9A PO4 Rep, Mult 26,27,77,78,149
70.03 1 1z6kA MG Rep, Mult 116,142
80.03 1 4a59C AMP Rep, Mult 64,65,68,102
90.03 1 3s41A NA Rep, Mult 92,93,96,97,99,114

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
10.0661hjrC0.4944.260.1110.7413.1.22.428,111
20.0602e20A0.5553.880.1030.7882.7.2.15116
30.0602d4wA0.5444.480.0940.8242.7.1.30NA
40.0603enoA0.5204.250.1100.7763.4.24.57NA
50.0603ifrA0.5394.460.0820.8062.7.1.17NA
60.0601v4tA0.4594.750.0690.7352.7.1.2,2.7.1.1NA
70.0602nztA0.5074.590.0540.8062.7.1.1115
80.0602hoeA0.5444.480.1100.8292.7.1.59NA
90.0602o4iA0.5144.340.0870.7763.1.11.230
100.0603b8aX0.5394.840.0870.8762.7.1.1117
110.0603ezwG0.5374.470.0930.8122.7.1.30101
120.0601ig8A0.5244.950.0940.8532.7.1.1NA
130.0601x3mA0.5553.970.1170.7882.7.2.15,2.7.2.-NA
140.0602zf5Y0.5384.580.1070.8182.7.1.3099
150.0603mdqA0.5204.070.0840.7413.6.1.1147,52
160.0602jguA0.5334.270.0490.8122.7.7.728
170.0601tgoA0.5314.330.0480.8122.7.7.797,99,119
180.0602uytA0.5514.560.0730.8242.7.1.5NA
190.0603ge1A0.5364.410.0940.8002.7.1.30101
200.0602oa8B0.5154.440.0980.7883.1.11.230,102

(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
00.430.7721.180.280.811ovqA GO:0000967 GO:0003676 GO:0004518 GO:0005737 GO:0006139 GO:0006364 GO:0016787 GO:0016788 GO:0031564 GO:0042254 GO:0090305
10.290.5403.600.270.711vhxA GO:0000967 GO:0003676 GO:0004518 GO:0005737 GO:0006139 GO:0006364 GO:0016787 GO:0016788 GO:0042254 GO:0090305
20.290.5253.210.290.681nmnA GO:0000967 GO:0003676 GO:0004518 GO:0005737 GO:0006139 GO:0006364 GO:0016787 GO:0016788 GO:0031564 GO:0042254 GO:0090305
30.120.3593.600.160.481iv0A GO:0000967 GO:0003676 GO:0004518 GO:0005737 GO:0006139 GO:0006364 GO:0016787 GO:0016788 GO:0042254 GO:0090305
40.070.5974.330.110.881kcfA GO:0000002 GO:0000400 GO:0000402 GO:0000403 GO:0003676 GO:0003677 GO:0004518 GO:0004519 GO:0005737 GO:0005739 GO:0008821 GO:0016787 GO:0032042 GO:0046872 GO:0070336 GO:0090305
50.070.5753.890.110.825b43A GO:0004518 GO:0004519 GO:0016787 GO:0051607 GO:0090305
60.070.4873.390.070.655e6fA GO:0000287 GO:0000400 GO:0003676 GO:0006281 GO:0006310 GO:0016788
70.060.4425.090.050.751mqqA GO:0000272 GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0033939 GO:0045493 GO:0046559
80.060.3665.580.070.683qyjA GO:0003824
90.060.3695.160.050.634kifB GO:0008168 GO:0016740 GO:0017000 GO:0032259
100.060.3135.040.060.521obbA GO:0000023 GO:0003824 GO:0004553 GO:0004558 GO:0005975 GO:0008152 GO:0016616 GO:0016787 GO:0016798 GO:0032450 GO:0046872 GO:0055114
110.060.3764.660.070.603o8jA GO:0005737 GO:0006099 GO:0016740 GO:0019679 GO:0036440 GO:0046912 GO:0050440
120.060.3884.400.040.561to0D GO:0005737 GO:0006364 GO:0008168 GO:0016740 GO:0031167 GO:0032259 GO:0070038
130.060.3944.700.030.643x2fA GO:0004013 GO:0005737 GO:0005829 GO:0006730 GO:0016787 GO:0033353
140.060.3854.940.070.621tuoA GO:0005975 GO:0016868 GO:0071704
150.060.3665.040.040.631gvnB GO:0000166 GO:0005524 GO:0016301 GO:0016310 GO:0016740
160.060.3575.830.040.692v54A GO:0000166 GO:0004798 GO:0005524 GO:0006233 GO:0006235 GO:0009165 GO:0016301 GO:0016310 GO:0016740 GO:0046939
170.060.3905.840.070.733ed4B GO:0003824 GO:0008152 GO:0008484
180.060.3605.650.050.681ro7D GO:0016740 GO:0016757


Consensus prediction of GO terms
 
Molecular Function GO:0003676 GO:0004518
GO-Score 0.77 0.77
Biological Processes GO:0090305 GO:0000967 GO:0031564
GO-Score 0.77 0.75 0.60
Cellular Component GO:0005737
GO-Score 0.77

(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.