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I-TASSER results for job id Rv0725c

[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
10.45 18 2zw9A SAM Rep, Mult 15,18,19,22,26,85,108,109,110,130,131,134,158,159,160,184,185,186,189,190
20.14 3 1d2hD SAH Rep, Mult 130,131,134,159,160,185,186,189

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
10.0662cl5A0.4924.230.0970.6212.1.1.6NA
20.0663e05B0.4513.790.0630.5582.1.1.132NA
30.0663c3yA0.4954.050.0670.6282.1.1.104NA
40.0662ex4A0.4953.960.0750.6312.1.1.-NA
50.0663hnrA0.4623.700.0910.5812.1.1.-NA
60.0601bxsA0.4895.520.0570.7341.2.1.36NA
70.0602avdA0.4864.150.0770.6282.1.1.-NA
80.0603bwmA0.4944.310.0920.6252.1.1.6NA
90.0603fg0C0.4925.690.0640.7481.2.1.8NA
100.0603k2wB0.4885.490.0500.7241.2.1.8NA
110.0601suiA0.4954.170.0520.6352.1.1.104NA
120.0603bt7A0.4914.360.0770.6442.1.1.35204
130.0602opbB0.5344.140.0810.6912.1.1.28110,130,158
140.0603cbgA0.4903.950.0630.6182.1.1.-NA
150.0602iipA0.5313.900.0890.6642.1.1.1110,159
160.0601ej6A0.5324.790.0640.7282.7.7.50110
170.0601kphC0.5224.500.0560.7012.1.1.7915,17
180.0602a14A0.5383.980.0880.6812.1.1.49110
190.0601tpyA0.5234.580.0970.6982.1.1.79NA
200.0601susD0.4944.130.0420.6312.1.1.104NA
210.0601ri1A0.5233.770.0710.6582.1.1.56130
220.0601wznA0.5024.110.0910.6382.1.1.-NA
230.0603bt7B0.4914.370.0770.6442.1.1.3549
240.0601o9jA0.4865.500.0680.7311.2.1.3NA

(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
00.630.9500.870.370.972ckdA GO:0008168 GO:0016740 GO:0032259
10.560.8601.120.390.882uyoA GO:0008168 GO:0016740 GO:0032259
20.310.7163.090.160.833p71T GO:0003880 GO:0005829 GO:0006464 GO:0006479 GO:0006481 GO:0008168 GO:0008276 GO:0008757 GO:0010906 GO:0016740 GO:0018423 GO:0031333 GO:0032259 GO:0042981 GO:0090266
30.300.7313.140.120.861rjdC GO:0005829 GO:0006481 GO:0008168 GO:0010506 GO:0016740 GO:0018423 GO:0032259 GO:0043623
40.280.7123.590.110.872zwaB GO:0005737 GO:0005739 GO:0005829 GO:0006400 GO:0008033 GO:0008168 GO:0008175 GO:0008757 GO:0016740 GO:0030488 GO:0031591 GO:0032259
50.280.6503.090.160.753o7wA GO:0003880 GO:0005829 GO:0006464 GO:0006479 GO:0006481 GO:0008168 GO:0008276 GO:0008757 GO:0010906 GO:0016740 GO:0018423 GO:0031333 GO:0032259 GO:0042981 GO:0090266
60.260.6652.800.130.761rjgA GO:0005829 GO:0006481 GO:0008168 GO:0010506 GO:0016740 GO:0018423 GO:0032259 GO:0043623
70.070.5094.260.070.663ggdA
80.060.3495.640.070.533ingA GO:0000166 GO:0004412 GO:0006520 GO:0016491 GO:0050661 GO:0055114
90.060.3026.150.050.492zi8A GO:0003824 GO:0005506 GO:0006629 GO:0006707 GO:0006725 GO:0008198 GO:0008202 GO:0008203 GO:0009405 GO:0016042 GO:0016491 GO:0019439 GO:0046872 GO:0047071 GO:0051213 GO:0055114 GO:0070723
100.060.3046.620.020.542vpjA GO:0000139 GO:0004842 GO:0005815 GO:0005829 GO:0006513 GO:0006810 GO:0006888 GO:0016055 GO:0016192 GO:0016567 GO:0030134 GO:0031410 GO:0031463 GO:0043231 GO:0048208 GO:0090090
110.060.3066.680.020.542wozA GO:0001726 GO:0004842 GO:0005634 GO:0005737 GO:0005783 GO:0005789 GO:0005856 GO:0005886 GO:0016020 GO:0016529 GO:0016567 GO:0030239 GO:0031143 GO:0031275 GO:0031430 GO:0031463 GO:0033017 GO:0035914 GO:0042995 GO:0045214 GO:0045661 GO:0048741 GO:2000291 GO:2001014
120.060.4504.590.060.614dcmA GO:0003676 GO:0005737 GO:0006364 GO:0008168 GO:0008990 GO:0016740 GO:0031167 GO:0032259 GO:0052916 GO:0070475
130.060.3076.760.040.554ascA GO:0004842 GO:0005737 GO:0007275 GO:0016567 GO:0031397 GO:0031463 GO:0031672 GO:0031674 GO:0032435 GO:0048741
140.060.2865.110.020.412yc3A GO:0003824 GO:0008299 GO:0009507 GO:0009536 GO:0009570 GO:0016740 GO:0016779 GO:0019288 GO:0050518
150.060.2416.210.040.404f4wA GO:0000287 GO:0003677 GO:0003684 GO:0003887 GO:0005737 GO:0006260 GO:0006261 GO:0006281 GO:0006974 GO:0016740 GO:0016779 GO:0046872 GO:0071897
160.060.3005.390.060.461j1zA GO:0000166 GO:0004055 GO:0005524 GO:0005737 GO:0006526 GO:0008652 GO:0016874
170.060.2526.450.040.433fdsA GO:0000287 GO:0003677 GO:0003684 GO:0003887 GO:0005737 GO:0006260 GO:0006261 GO:0006281 GO:0006974 GO:0016740 GO:0016779 GO:0046872 GO:0071897
180.060.2007.560.030.403e1yC GO:0000184 GO:0003723 GO:0003747 GO:0005634 GO:0005737 GO:0005829 GO:0006412 GO:0006415 GO:0006449 GO:0006479 GO:0008079 GO:0016149 GO:0043022 GO:0044822


Consensus prediction of GO terms
 
Molecular Function GO:0008173 GO:0018423
GO-Score 0.56 0.52
Biological Processes GO:0006914 GO:0034622 GO:1901659 GO:1901566 GO:0008033 GO:0001510 GO:0031590 GO:0006481 GO:0042981 GO:0090266 GO:0010906 GO:0031333
GO-Score 0.60 0.60 0.56 0.56 0.56 0.56 0.56 0.52 0.31 0.31 0.31 0.31
Cellular Component GO:0005829 GO:0043231
GO-Score 0.65 0.56

(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.