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I-TASSER results for job id Rv0143c

[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
10.33 29 2ht4B BR Rep, Mult 130,131,132,134,372,473
20.29 25 2htlA BR Rep, Mult 131,133,172,173,379,380,381,470
30.12 10 1otuB CL Rep, Mult 170,171,172,173,174,379,381,382
40.06 7 2h2sB SEK Rep, Mult 329,330,331,356
50.04 4 2h2sB SEK Rep, Mult 130,131,301,372,473
60.02 3 2h2sA SEK Rep, Mult 294,298,472
70.01 1 2h2sA SEK Rep, Mult 59,63,249

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
10.0602pdaA0.3306.670.0710.5021.2.7.1381
20.0603bkkA0.3376.810.0710.5263.4.15.1NA
30.0602a4zA0.3607.190.0660.5852.7.1.153251
40.0601vlbA0.3077.840.0340.5281.2.99.7NA
50.0602vdcA0.3347.630.0370.5631.4.1.13NA
60.0602b3xA0.3167.090.0510.5084.2.1.3134
70.0601llwA0.3467.690.0560.5921.4.7.1NA
80.0601y8bA0.3197.640.0480.5392.3.3.9135
90.0602ow6A0.3437.900.0520.6003.2.1.114NA
100.0602gtqA0.3456.770.0300.5283.4.11.2NA
110.0602h1nA0.3416.300.0380.5043.4.24.-421
120.0602fhcA0.3197.230.0390.5143.2.1.41196,203
130.0601h7aA0.3277.510.0630.5531.17.4.2NA
140.0602wghB0.3247.670.0320.5471.17.4.1NA
150.0602fhbA0.3067.660.0320.5143.2.1.41NA
160.0602jg0A0.3337.630.0760.5633.2.1.28177
170.0602wyhA0.3277.230.0320.5283.2.1.24209
180.0601q16A0.3547.590.0620.5871.7.99.4NA
190.0601h16A0.3687.470.0420.6122.3.1.54NA

(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
00.360.8751.490.230.901kpkA GO:0005216 GO:0005247 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006821 GO:0015108 GO:0015297 GO:0015299 GO:0015706 GO:0016020 GO:0016021 GO:0031404 GO:0043168 GO:0055085 GO:1902476 GO:1902600 GO:1903959
10.330.8271.620.230.863nd0A GO:0005216 GO:0005247 GO:0006821 GO:0016020 GO:0016021 GO:0034220 GO:0055085 GO:1903959
20.330.8711.650.230.901kplB GO:0005216 GO:0005247 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006821 GO:0015108 GO:0015297 GO:0016020 GO:0016021 GO:0034220 GO:0055085 GO:1902476 GO:1903959
30.250.7532.790.200.813orgA
40.060.3847.320.040.635bweA GO:0003824 GO:0008152
50.060.3716.960.040.584mtjA GO:0003824 GO:0008152
60.060.3687.040.040.582yajC GO:0003824 GO:0008152 GO:0016829 GO:0043722
70.060.3497.780.060.602f3oA GO:0003824 GO:0008152 GO:0016829
80.060.3607.770.050.635i2aB GO:0003824 GO:0008152
90.060.3667.480.030.611cm5A GO:0003824 GO:0005737 GO:0005829 GO:0005975 GO:0006006 GO:0006567 GO:0008152 GO:0008861 GO:0016020 GO:0016740 GO:0016746
100.060.3577.850.050.635i2gA GO:0003824 GO:0008152
110.060.2857.060.050.454uvmA GO:0005215 GO:0006810 GO:0006857 GO:0015197 GO:0015833 GO:0016020 GO:0016021
120.060.2687.270.050.443pyzA GO:0000166 GO:0004326 GO:0005524 GO:0009058 GO:0009396 GO:0016874 GO:0046901
130.060.2967.260.050.482pffA GO:0000287 GO:0003824 GO:0004312 GO:0004315 GO:0004316 GO:0004321 GO:0005829 GO:0005835 GO:0006629 GO:0006631 GO:0006633 GO:0008152 GO:0008897 GO:0016491 GO:0016740 GO:0042759 GO:0046872 GO:0055114 GO:0102132
140.060.2637.470.060.453aw5A GO:0005507 GO:0016020 GO:0016021 GO:0016491 GO:0016722 GO:0046872 GO:0055114
150.060.2466.810.050.385einA GO:0003942 GO:0005737 GO:0006526 GO:0008652 GO:0009085 GO:0016491 GO:0016620 GO:0019878 GO:0046983 GO:0051287 GO:0055114
160.060.2228.390.020.412gh8A GO:0019012 GO:0019028 GO:0030430 GO:0039617
170.060.2166.370.050.321j6oA GO:0004536 GO:0006308 GO:0016788
180.060.2226.430.030.333cymA GO:0000166 GO:0003676 GO:0003824 GO:0005622 GO:0006139 GO:0008408 GO:0044237 GO:0090305


Consensus prediction of GO terms
 
Molecular Function GO:0005247 GO:0015299 GO:0031404
GO-Score 0.71 0.36 0.36
Biological Processes GO:1903959 GO:1902476 GO:0015706 GO:1902600
GO-Score 0.71 0.57 0.36 0.36
Cellular Component GO:0005887
GO-Score 0.57

(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.