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I-TASSER results for job id Rv0744c

[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
10.06 3 4niqB III Rep, Mult 51,54,55,58,62,65,68,69,80,92,93,94,98,99,101,102,105,106,109,112,113,116
20.06 3 2yf3A MN Rep, Mult 80,83,113,116
30.04 2 3q73B 3CX Rep, Mult 9,10,42,43,44,45
40.04 2 2ze7A ZN Rep, Mult 113,161,162
50.04 2 3mpsA FEO Rep, Mult 53,86
60.04 2 3sfyB 3FX Rep, Mult 2,3,9,10,11,12,13
70.04 2 4fhvA MG Rep, Mult 36,37,47
80.02 1 3a5cE ADP Rep, Mult 17,18
90.02 1 4ev6E MG Rep, Mult 64,119
100.02 1 3rkoL LFA Rep, Mult 20,23,24
110.02 1 3bnxD POP Rep, Mult 7,11,15
120.02 1 1bf5A QNA Rep, Mult 10,11,25
130.02 1 3o2nB MZX Rep, Mult 114,119,141
140.02 1 3f1f2 MG Rep, Mult 5,9
150.02 1 3b6aD ZCT Rep, Mult 115,116
160.02 1 4mhlA ARF Rep, Mult 105,109
170.02 1 2yxhA MG Rep, Mult 87,113

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
10.0601k62B0.4914.780.0700.7684.3.2.1NA
20.0602v8tA0.5084.600.0230.7561.11.1.6NA
30.0601m56A0.4935.300.0390.8041.9.3.1NA
40.0601jk0A0.4844.120.1070.6961.17.4.1NA
50.0601tazA0.4944.660.0510.7923.1.4.17NA
60.0602jbwD0.5773.910.0920.7683.7.1.-NA
70.0601qd1B0.3655.400.0400.6732.1.2.5,4.3.1.4NA
80.0601gaiA0.4814.870.0390.7683.2.1.358
90.0602ozoA0.4874.660.0670.7682.7.10.2NA
100.0602occN0.4835.340.0380.8091.9.3.191
110.0601j0mA0.4915.090.0460.8274.2.2.12NA
120.0602oa6D0.5004.260.0560.7324.2.3.9NA
130.0602pfdB0.4933.610.0830.6672.1.2.5,4.3.1.450
140.0602cqsA0.5084.790.0730.7802.4.1.20NA
150.0601ihgA0.5023.560.0750.6555.2.1.8NA
160.0603ckeD0.4874.200.0500.7144.2.3.9NA
170.0601ojnA0.4844.250.0680.7204.2.2.152
180.0603evhA0.4895.060.0840.7804.2.2.3NA
190.0601ug9A0.4934.470.0420.7323.2.1.70NA

(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
00.070.5803.870.090.821ciyA GO:0005102 GO:0006952 GO:0009405 GO:0030435
10.070.5953.890.090.841ji6A GO:0005102 GO:0006952 GO:0009405 GO:0030435
20.070.5804.080.060.843x0uA GO:0009405
30.070.5634.170.080.784d8mA GO:0009405 GO:0030435
40.070.5783.790.070.804w8jA GO:0005102 GO:0006952 GO:0009405 GO:0030435
50.070.6134.020.060.864moaA GO:0005102 GO:0006952 GO:0009405 GO:0030435
60.070.5894.500.070.882c9kA GO:0005102 GO:0006952 GO:0009405 GO:0030435
70.070.6013.680.070.823eb7A GO:0005102 GO:0006952 GO:0009405 GO:0030435
80.070.5953.680.060.801dlcA GO:0005102 GO:0006952 GO:0009405 GO:0030435
90.070.5594.180.070.821i5pA GO:0005102 GO:0006952 GO:0009405 GO:0030435
100.060.4025.000.060.674p4oA GO:0003677 GO:0003887 GO:0005634 GO:0006281 GO:0034061 GO:0071897
110.060.4604.280.090.673ck6E GO:0005886 GO:0016020 GO:0016021 GO:0030001 GO:0046873 GO:0055085
120.060.3873.740.040.521yo7A GO:0006351 GO:0006355
130.060.3605.960.070.703o38A GO:0004316 GO:0016491 GO:0055114 GO:0102132
140.060.3235.150.050.544k3vB GO:0006810 GO:0007155 GO:0030001 GO:0046872
150.060.3755.020.040.664bvkB GO:0016787
160.060.3875.160.040.653odpA GO:0005975 GO:0016853 GO:0030246
170.060.3294.050.100.493nrwA GO:0003677 GO:0006310 GO:0015074
180.060.3094.460.010.481g6oA GO:0000166 GO:0005524 GO:0005737 GO:0006810 GO:0009405


Consensus prediction of GO terms
 
Molecular Function GO:0005515
GO-Score 0.37
Biological Processes GO:0051704 GO:0048646 GO:0030154 GO:0043934 GO:0006950
GO-Score 0.58 0.48 0.48 0.48 0.37
Cellular Component
GO-Score

(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.