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I-TASSER results for job id Rv2325c

[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
10.08 4 4efcA MG Rep, Mult 232,236
20.06 3 2jj2G QUE Rep, Mult 237,240,241
30.04 2 1lghA DET Rep, Mult 172,179
40.04 2 2z1qB FAD Rep, Mult 73,75,78,81,134,135,136
50.04 2 4zzbA XE Rep, Mult 179,180,183
60.04 2 1hbnA UUU Rep, Mult 64,66,67,68,128,131,134
70.04 2 1bjeA AZI Rep, Mult 190,226
80.02 1 1diiA HEM Rep, Mult 155,159
90.02 1 2wse1 CLA Rep, Mult 226,230
100.02 1 1xmeC HAS Rep, Mult 171,175
110.02 1 3hykA A3P Rep, Mult 230,234,241
120.02 1 1e6vA UUU Rep, Mult 42,43,132,135
130.02 1 2z1qA FAD Rep, Mult 156,158,159,167,170
140.02 1 3e6sE FE Rep, Mult 186,190
150.02 1 3gxqB NUC Rep, Mult 32,34
160.02 1 4zgmA 32M Rep, Mult 220,224

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
10.0601fa9A0.3256.550.0600.5782.4.1.1142
20.0602azdB0.4046.070.0630.6632.4.1.1NA
30.0602ztgA0.3826.560.0860.6816.1.1.764,68,122
40.0603gpbA0.3936.030.0270.6522.4.1.1142
50.0602fonB0.4116.560.0580.7271.3.3.642
60.0602z1qB0.4236.220.0760.7201.3.99.394
70.0601is2A0.3976.730.0370.7271.3.3.6180
80.0602zxqA0.3896.630.0500.6923.2.1.9765,70
90.0601mhsA0.3766.360.0390.6493.6.3.6NA
100.0601e6vA0.4055.870.0480.6492.8.4.1NA
110.0601kqfA0.3636.500.0660.6381.2.1.2NA
120.0602hpiA0.3166.610.0360.5602.7.7.7185
130.0601a0eA0.3705.870.0850.5895.3.1.5NA
140.0603fvyA0.4595.850.0610.7383.4.14.436,151
150.0603eqlM0.3626.480.0410.6422.7.7.672,75
160.0602vumB0.2917.020.0150.5532.7.7.6NA
170.0601de5A0.3755.890.0740.5995.3.1.14NA
180.0601e6yA0.3876.350.0460.6602.8.4.1NA
190.0601t3tA0.3725.890.0270.6106.3.5.3NA

(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
00.420.8051.700.210.864huqT GO:0005215 GO:0005886 GO:0006810 GO:0016020 GO:0016021
10.410.8671.330.170.905d3mD GO:0005215 GO:0005886 GO:0006810 GO:0016020 GO:0016021
20.070.3506.580.030.613cskA GO:0004177 GO:0005737 GO:0006508 GO:0008233 GO:0008237 GO:0008239 GO:0016787 GO:0046872
30.060.4236.220.080.722z1qB GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
40.060.2825.880.080.452uxwA GO:0000062 GO:0001659 GO:0003995 GO:0004466 GO:0005634 GO:0005730 GO:0005737 GO:0005739 GO:0005743 GO:0005759 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0009055 GO:0015980 GO:0016020 GO:0016491 GO:0016627 GO:0017099 GO:0030855 GO:0033539 GO:0036498 GO:0042645 GO:0042760 GO:0045717 GO:0046322 GO:0050660 GO:0052890 GO:0055088 GO:0055114 GO:0090181
50.060.3316.390.060.595e2qA GO:0004177 GO:0005654 GO:0005737 GO:0005886 GO:0006508 GO:0008233 GO:0008237 GO:0008239 GO:0008270 GO:0016787 GO:0046872 GO:0070062
60.060.2976.560.070.523mxlB GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
70.060.2616.200.060.433r7kA GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
80.060.3936.050.070.643u33A GO:0000062 GO:0003677 GO:0003995 GO:0005737 GO:0006974 GO:0008152 GO:0008470 GO:0009055 GO:0016491 GO:0016627 GO:0033539 GO:0043565 GO:0045892 GO:0050660 GO:0052890 GO:0055088 GO:0055114
90.060.2906.230.030.483afeA GO:0000062 GO:0003995 GO:0004497 GO:0005886 GO:0006629 GO:0006694 GO:0006707 GO:0008152 GO:0008202 GO:0009055 GO:0016042 GO:0016491 GO:0016627 GO:0016712 GO:0019439 GO:0033539 GO:0036383 GO:0044117 GO:0050660 GO:0052890 GO:0055088 GO:0055114
100.060.2676.770.040.492ix4A GO:0003824 GO:0004315 GO:0005739 GO:0006629 GO:0006631 GO:0006633 GO:0008152 GO:0016740 GO:0016746 GO:0016747
110.060.4256.460.070.743owaC GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
120.060.2996.540.060.534kcfA GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
130.060.3976.730.040.731is2A GO:0000062 GO:0003995 GO:0003997 GO:0005504 GO:0005777 GO:0006091 GO:0006629 GO:0006631 GO:0006635 GO:0006693 GO:0008152 GO:0009055 GO:0016401 GO:0016491 GO:0016627 GO:0019395 GO:0033539 GO:0033540 GO:0050660 GO:0052890 GO:0055088 GO:0055114
140.060.2786.470.050.484n5fA GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
150.060.2845.970.050.473d9dA GO:0000166 GO:0003995 GO:0006807 GO:0008152 GO:0016491 GO:0016627 GO:0050141 GO:0050660 GO:0052664 GO:0055114 GO:0071949
160.060.2886.270.030.482rfqA GO:0004497 GO:0006629 GO:0006694 GO:0008152 GO:0008202 GO:0016042 GO:0016491 GO:0016627 GO:0019439 GO:0036383 GO:0050660 GO:0055114
170.060.2856.870.040.513affA GO:0000062 GO:0003995 GO:0004497 GO:0005886 GO:0006629 GO:0006694 GO:0006707 GO:0008152 GO:0008202 GO:0009055 GO:0016042 GO:0016491 GO:0016627 GO:0016712 GO:0019439 GO:0033539 GO:0036383 GO:0044117 GO:0050660 GO:0052890 GO:0055088 GO:0055114
180.060.2696.810.030.492pg0A GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0005215
GO-Score 0.66
Biological Processes GO:0006810
GO-Score 0.66
Cellular Component GO:0016021 GO:0005886
GO-Score 0.66 0.66

(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.