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I-TASSER results for job id Rv3180c

[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 4xgqA MG Rep, Mult 7,8,43,101,102
20.08 4 2j5bB TYE Rep, Mult 5,7,8,102,105,121
30.06 3 2h1c0 III Rep, Mult 38,39,42,45,46,49,50,80,81,82,83,86,87,89,90,93,94,104
40.05 2 2fe10 III Rep, Mult 38,39,41,42,43,45,46,48,49,52,62,66,67,70,78,81,83,86,87,90,93,94,98,99,100,101,104
50.04 2 2h1cA III Rep, Mult 11,12,14,25,28,29,47,48,61,64,65,68,72,75
60.04 2 1tauA ZN Rep, Mult 7,9,102,123
70.04 2 3h87A MG Rep, Mult 102,123,127
80.02 1 2h1cA MG Rep, Mult 5,6,36,37,40
90.02 1 2h1cA MG Rep, Mult 45,49,66
100.02 1 2h1cA MG Rep, Mult 37,79,80,81,108
110.02 1 1v7pC MN Rep, Mult 7,9,21,123
120.02 1 1fx4A MG Rep, Mult 7,32

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
10.0602el7A0.5673.960.0800.8546.1.1.2NA
20.0603fnrA0.5924.400.0920.9726.1.1.19NA
30.0601irxB0.5744.180.0380.8966.1.1.6123
40.0602zufA0.5904.270.0870.9446.1.1.19NA
50.0601u0bB0.5564.370.0650.8966.1.1.16NA
60.0601li7B0.5294.670.0720.8756.1.1.16NA
70.0603a04A0.5554.230.0830.8686.1.1.243
80.0602zueA0.5854.350.0570.9446.1.1.19127
90.0601ileA0.5444.370.0650.8966.1.1.5NA
100.0601wz2A0.5934.380.0430.9656.1.1.4NA
110.0602j5bA0.5574.140.0610.8616.1.1.1NA
120.0601ffyA0.5414.290.0800.8966.1.1.5NA
130.0602pidB0.5444.240.0530.8546.1.1.1NA
140.0601iq0A0.5744.250.1080.9036.1.1.19105
150.0602ct8A0.5404.570.1100.9106.1.1.10NA
160.0603d6vA0.5583.810.0720.8266.1.1.16,13,20
170.0602cyaA0.5873.610.0630.8406.1.1.113
180.0602ja2A0.5394.210.0800.8616.1.1.17NA
190.0601q11A0.5643.750.0710.8336.1.1.1123

(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
00.360.8730.850.260.902fe1A GO:0000287 GO:0004518 GO:0004540 GO:0016787 GO:0046872 GO:0090305 GO:0090501
10.340.7262.620.210.851v8pF GO:0004518 GO:0004527 GO:0004540 GO:0016787 GO:0046872 GO:0090305 GO:0090501
20.300.6652.500.180.833dboB GO:0000287 GO:0004518 GO:0004521 GO:0004540 GO:0005576 GO:0016787 GO:0040007 GO:0040008 GO:0046872 GO:0090305 GO:0090501 GO:0090502
30.260.7132.170.170.854xgqA GO:0000287 GO:0004518 GO:0004540 GO:0016787 GO:0045926 GO:0046872 GO:0090305 GO:0090501
40.260.6852.720.100.873zvkA GO:0000287 GO:0004518 GO:0004540 GO:0016787 GO:0046872 GO:0090305 GO:0090501
50.260.7232.660.150.902bsqA GO:0000287 GO:0003677 GO:0004518 GO:0004540 GO:0016787 GO:0044001 GO:0046872 GO:0090305 GO:0090501
60.260.6463.420.140.881y82A GO:0000287 GO:0004518 GO:0004540 GO:0016787 GO:0046872 GO:0090305 GO:0090501
70.240.7032.700.100.885ecdA GO:0000287 GO:0004518 GO:0004519 GO:0004540 GO:0016787 GO:0046872 GO:0090305 GO:0090501
80.180.6013.090.140.771o4wA GO:0004518 GO:0004540 GO:0016787 GO:0046872 GO:0090305 GO:0090501
90.070.5064.020.110.781q7tA GO:0005886 GO:0008270 GO:0010125 GO:0016787 GO:0016811 GO:0019213 GO:0035595 GO:0046872
100.070.4404.440.120.744almA GO:0004318 GO:0006633 GO:0016491 GO:0047117 GO:0055114
110.060.4255.070.030.793k6jA GO:0003857 GO:0006631 GO:0016491 GO:0046872 GO:0055114
120.060.3735.220.040.653x0uA GO:0009405
130.060.3415.180.040.633ozcA GO:0003824 GO:0004645 GO:0005634 GO:0005737 GO:0005829 GO:0006139 GO:0006166 GO:0006738 GO:0009116 GO:0016740 GO:0016757 GO:0016763 GO:0017061 GO:0019509 GO:0032259 GO:0033574 GO:0043101 GO:0070062
140.060.3554.780.070.614igbB GO:0016020 GO:0016021
150.060.3594.890.040.621zxjD
160.060.3355.120.050.614e97B GO:0003796 GO:0003824 GO:0008152 GO:0009253 GO:0016787 GO:0016798 GO:0016998 GO:0019076 GO:0019835 GO:0030430 GO:0042742
170.060.3105.990.070.683r9cA GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114 GO:0070330
180.060.3055.680.080.611n0eB GO:0003677 GO:0003700 GO:0005737 GO:0006351 GO:0006355 GO:0009295


Consensus prediction of GO terms
 
Molecular Function GO:0004540 GO:0000287 GO:0004519 GO:0004527
GO-Score 0.84 0.76 0.60 0.34
Biological Processes GO:0090501 GO:0048519
GO-Score 0.84 0.53
Cellular Component GO:0005576
GO-Score 0.30

(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.