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I-TASSER results for job id Rv0359

[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
10.37 4 3b4rA ZN Rep, Mult 60,61,64,186
20.08 2 1xvgB BRJ Rep, Mult 56,57,61,171
30.08 2 1xvgA BRJ Rep, Mult 59,138,141,142
40.04 1 1xvfA 3CL Rep, Mult 132,172,175,176
50.04 1 1mhy1 III Rep, Mult 59,60,63,64,66,67,68,70,71,76,84
60.04 1 1xveA 3BB Rep, Mult 57,61,62,83
70.04 1 3en9B TBR Rep, Mult 83,85,114,116

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
10.0602h1nA0.4215.610.0530.6723.4.24.-NA
20.0603en9A0.4275.610.0480.6493.4.24.57NA
30.0603lomA0.4085.010.0710.6062.5.1.1054,175
40.0602ewgA0.4095.470.0310.6412.5.1.10NA
50.0603b8eC0.4255.020.0430.6293.6.3.9123
60.0601mhsA0.4185.180.0510.6253.6.3.6NA
70.0601eulA0.4165.270.0630.6413.6.3.8NA
80.0603g61A0.4365.370.0520.6643.6.3.44NA
90.0601qleA0.4015.430.0420.6141.9.3.1NA
100.0601v4eA0.4075.290.0990.6292.5.1.1187
110.0601fziA0.4466.160.0480.7571.14.13.25NA
120.0602yr4A0.4116.060.0480.7141.13.12.921
130.0603b8eA0.4244.930.0340.6223.6.3.9NA
140.0602gwdA0.3806.270.0530.6726.3.2.2NA
150.0602q80A0.4075.380.0440.6372.5.1.29,2.5.1.10,2.5.1.1NA
160.0601vncA0.4066.370.0490.6991.11.1.10135
170.0601zklA0.4076.000.0550.6993.1.4.17NA
180.0601wmwA0.4295.140.0480.6412.5.1.-NA
190.0601rqiA0.4115.450.0790.6452.5.1.10NA

(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
00.570.7741.360.190.813b4rA GO:0004222 GO:0005886 GO:0006508 GO:0008233 GO:0008237 GO:0016020 GO:0016021 GO:0016787 GO:0046872
10.070.4584.760.080.654av6A GO:0000287 GO:0004427 GO:0005509 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006814 GO:0009678 GO:0015081 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030955 GO:0035725 GO:0042803 GO:0046872
20.070.4065.910.040.663dhiA GO:0004497 GO:0006725 GO:0016491 GO:0019439 GO:0042203 GO:0046872 GO:0055114
30.060.4525.330.060.684av3B GO:0000287 GO:0004427 GO:0005509 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006814 GO:0009678 GO:0015081 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030955 GO:0035725 GO:0042803 GO:0046872
40.060.4494.900.050.643perA GO:0016491 GO:0019439 GO:0046872 GO:0051213 GO:0055114
50.060.4366.400.060.762innA GO:0006725 GO:0016491 GO:0046872 GO:0055114
60.060.4466.160.050.761fziA GO:0004497 GO:0006725 GO:0006730 GO:0015049 GO:0015050 GO:0015947 GO:0016491 GO:0046872 GO:0055114
70.060.4486.060.060.751mhyD GO:0004497 GO:0006725 GO:0006730 GO:0015049 GO:0016491 GO:0046872 GO:0055114
80.060.4085.960.050.662incA GO:0004497 GO:0006725 GO:0016491 GO:0046872 GO:0055114
90.060.3356.040.040.572wm4A GO:0004497 GO:0005506 GO:0005886 GO:0006629 GO:0006631 GO:0006707 GO:0008395 GO:0010430 GO:0016491 GO:0016705 GO:0020037 GO:0036199 GO:0046872 GO:0055114 GO:0070402 GO:0097089
100.060.3346.440.040.605bv7A GO:0004607 GO:0004623 GO:0005576 GO:0005615 GO:0006629 GO:0006644 GO:0006656 GO:0008202 GO:0008203 GO:0008374 GO:0016740 GO:0016746 GO:0030301 GO:0034186 GO:0034364 GO:0034372 GO:0034375 GO:0034435 GO:0042157 GO:0042158 GO:0042632 GO:0043691 GO:0046470 GO:0046688 GO:0051384 GO:0070062 GO:0090107
110.060.4705.740.070.764a01A GO:0004427 GO:0005773 GO:0005774 GO:0006810 GO:0006811 GO:0009678 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0046872 GO:0055085
120.060.3306.100.040.563juvA GO:0004497 GO:0005506 GO:0005783 GO:0005789 GO:0005886 GO:0006629 GO:0006694 GO:0006695 GO:0008202 GO:0008203 GO:0008398 GO:0016020 GO:0016021 GO:0016125 GO:0016126 GO:0016491 GO:0016705 GO:0020037 GO:0031090 GO:0033488 GO:0043231 GO:0046872 GO:0055114 GO:0070988
130.060.3515.700.040.574mudD GO:0005829 GO:0010124
140.060.3066.870.050.593dhiB GO:0004497 GO:0006725 GO:0016491 GO:0016709 GO:0019439 GO:0042203 GO:0055114
150.060.2805.750.050.442zsmA GO:0003824 GO:0005737 GO:0006779 GO:0006782 GO:0008483 GO:0016853 GO:0030170 GO:0033014 GO:0042286
160.060.2985.920.080.502rjqA GO:0004222 GO:0005178 GO:0005576 GO:0005578 GO:0005615 GO:0005788 GO:0006508 GO:0008201 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0022617 GO:0031012 GO:0036066 GO:0042742 GO:0046872 GO:0050840
170.060.3185.570.030.493l0mA GO:0000166 GO:0003824 GO:0005085 GO:0005524 GO:0005576 GO:0005622 GO:0006612 GO:0008152 GO:0008289 GO:0009405 GO:0016020 GO:0016740 GO:0016779 GO:0017137 GO:0018117 GO:0018260 GO:0033644 GO:0043087 GO:0043547 GO:0044161 GO:0044162 GO:0044600 GO:0070273 GO:0070733
180.060.2795.500.060.453l0iC GO:0000166 GO:0003824 GO:0005085 GO:0005524 GO:0005576 GO:0005622 GO:0006612 GO:0008152 GO:0008289 GO:0009405 GO:0016020 GO:0016740 GO:0016779 GO:0017137 GO:0018117 GO:0018260 GO:0033644 GO:0043087 GO:0043547 GO:0044161 GO:0044162 GO:0044600 GO:0070273 GO:0070733


Consensus prediction of GO terms
 
Molecular Function GO:0046872 GO:0004222
GO-Score 0.67 0.57
Biological Processes GO:0006508
GO-Score 0.57
Cellular Component GO:0005886 GO:0016021
GO-Score 0.63 0.63

(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.