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I-TASSER results for job id Rv1230c

[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
10.23 10 5anzA CA Rep, Mult 214,216,218,220,228
20.06 3 5ao8A NAG Rep, Mult 96,148,149,155,156,157,318
30.06 3 1d0kA NAG Rep, Mult 96,107,148,149,155,318
40.04 2 1d0lA BLG Rep, Mult 149,165,168,193,195,197,202,203,204,207,236,257,258,259
50.04 2 2z90A MG Rep, Mult 225,228
60.02 1 6r1rC III Rep, Mult 168,171,172,197,198
70.02 1 5ao7A NAG Rep, Mult 200,201,204,207,236
80.02 1 1d0kA AMU Rep, Mult 149,195,201,204
90.02 1 1qutA NAG Rep, Mult 203,204,207,236,257,259
100.02 1 1d0mA NAG Rep, Mult 149,155,156,157,193,201
110.02 1 1d0kA UUU Rep, Mult 96,99,100,148,149,151,155,202,258,262,263

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
10.0602vkzG0.3607.160.0480.6112.3.1.38,3.1.2.14144,146,198
20.0601ordA0.3567.140.0580.6014.1.1.17NA
30.0602vdcF0.3487.310.0470.6011.4.1.13NA
40.0601yqyA0.2597.400.0410.4533.4.24.83231
50.0601d0kA0.5783.630.1320.6844.2.2.-176,195,197,202,211,236
60.0602gtqA0.3667.270.0510.6233.4.11.2NA
70.0601pj6A0.3577.130.0400.5991.5.3.10NA
80.0602r72A0.3697.150.0480.6182.7.7.48107
90.0601bxrA0.3516.670.0360.5576.3.5.5148
100.0603c46B0.3217.170.0390.5452.7.7.6140
110.0602cqsA0.3427.230.0400.5822.4.1.20NA
120.0601ofdA0.3507.720.0520.6331.4.7.1211
130.0602z8yP0.3627.800.0540.6692.3.1.169200
140.0601ea0A0.3767.060.0400.6201.4.1.13NA
150.0603elqB0.3587.710.0490.6502.8.2.22147,215
160.0601h54B0.3446.840.0590.5622.4.1.8NA
170.0601s46A0.3697.290.0310.6352.4.1.4237
180.0602fhcA0.3217.260.0420.5553.2.1.41232
190.0601zxvA0.3357.220.0250.5693.4.24.83NA

(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
00.280.5783.630.130.681d0kA GO:0008933 GO:0009252 GO:0009279 GO:0016020 GO:0016829 GO:0016837 GO:0071555
10.180.5583.430.120.654anrA GO:0008933 GO:0009252 GO:0046872
20.060.3507.720.050.631ofdA GO:0003824 GO:0005737 GO:0006537 GO:0006541 GO:0006807 GO:0008152 GO:0008652 GO:0015930 GO:0016041 GO:0016491 GO:0016638 GO:0019676 GO:0046872 GO:0051536 GO:0051538 GO:0055114 GO:0097054
30.060.3777.180.040.632vdcA GO:0003824 GO:0004355 GO:0006537 GO:0006541 GO:0006807 GO:0008152 GO:0008652 GO:0015930 GO:0016491 GO:0016638 GO:0046872 GO:0051536 GO:0051538 GO:0055114 GO:0097054
40.060.3767.060.040.621ea0A GO:0003824 GO:0004355 GO:0006537 GO:0006541 GO:0006807 GO:0008152 GO:0008652 GO:0015930 GO:0016491 GO:0016638 GO:0046872 GO:0051536 GO:0051538 GO:0055114 GO:0097054
50.060.3827.090.040.631llwA GO:0003824 GO:0005737 GO:0006537 GO:0006541 GO:0006807 GO:0008152 GO:0008652 GO:0015930 GO:0016041 GO:0016491 GO:0016638 GO:0019676 GO:0046872 GO:0051536 GO:0051538 GO:0055114 GO:0097054
60.060.2757.060.060.471hr6A GO:0003824 GO:0004222 GO:0005739 GO:0005743 GO:0005759 GO:0006508 GO:0006626 GO:0006627 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0017087 GO:0046872
70.060.2857.220.050.484jgaA GO:0003824 GO:0006633 GO:0008152 GO:0016740 GO:0016746 GO:0016747 GO:0033817
80.060.2817.590.020.504a0kA GO:0000082 GO:0000715 GO:0000717 GO:0001701 GO:0005654 GO:0006281 GO:0006283 GO:0006293 GO:0006294 GO:0006295 GO:0006296 GO:0006511 GO:0006974 GO:0007050 GO:0008284 GO:0008285 GO:0016032 GO:0016567 GO:0030097 GO:0030853 GO:0031461 GO:0031464 GO:0031625 GO:0033683 GO:0035019 GO:0042769 GO:0042787 GO:0043161 GO:0051246 GO:0061630 GO:0070911 GO:0080008 GO:0097193 GO:1900087 GO:2000001 GO:2000819
90.060.2813.600.100.334g9sA GO:0003796 GO:0009253 GO:0016998
100.060.2587.500.030.451kbiA GO:0003824 GO:0004460 GO:0005739 GO:0005743 GO:0005758 GO:0005829 GO:0006089 GO:0006626 GO:0010181 GO:0016491 GO:0020037 GO:0046872 GO:0055114 GO:0070469
110.060.2296.730.080.371vrdA GO:0000166 GO:0003824 GO:0003938 GO:0006164 GO:0006177 GO:0016491 GO:0046872 GO:0055114
120.060.2256.910.040.374z7rA GO:0006810 GO:0018189
130.060.2137.370.070.371ldcB GO:0003824 GO:0004460 GO:0005739 GO:0005743 GO:0005758 GO:0005829 GO:0006089 GO:0006626 GO:0010181 GO:0016491 GO:0020037 GO:0046872 GO:0055114 GO:0070469
140.060.2267.360.030.394n02A GO:0000287 GO:0003824 GO:0004452 GO:0005737 GO:0008299 GO:0010181 GO:0016491 GO:0016853 GO:0046872 GO:0055114 GO:0070402
150.060.2217.070.020.373kd6A GO:0000166 GO:0016301 GO:0016310 GO:0016740 GO:0016773
160.060.2346.460.050.374z6yA GO:0005096 GO:0016023 GO:0017137 GO:0031398 GO:0031410 GO:0032007 GO:0036064 GO:0070848 GO:0090630 GO:1902018
170.060.2076.330.040.323mybA GO:0003824 GO:0004300 GO:0008152 GO:0016829 GO:0016853
180.060.2026.920.060.332g5gX GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0016835 GO:0008933 GO:0051536 GO:0016638 GO:0046872
GO-Score 0.55 0.41 0.36 0.36 0.33
Biological Processes GO:0045229 GO:0009252 GO:0006537 GO:0006520
GO-Score 0.55 0.41 0.36 0.36
Cellular Component GO:0044462 GO:0030313 GO:0019867
GO-Score 0.55 0.55 0.55

(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.