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I-TASSER results for job id Rv2337c

[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
10.53 35 3gh8G FMN Rep, Mult 29,30,31,32,33,64,67,68,71
20.05 3 2ymvA FNR Rep, Mult 29,30,31,33,64,67,125,126,127,129,208,226,240,294,295,296,297,347
30.02 2 2wqfA FMN Rep, Mult 125,126,128,280,283,295,296,297

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
10.0603a2pA0.3376.880.0490.5673.5.2.12NA
20.0601v5yA0.3753.110.1250.4301.6.99.-NA
30.0602c6fA0.3616.830.0410.5973.4.15.131,188
40.0602q5lA0.3447.080.0790.5944.1.1.74,4.1.1.43275
50.0601q16A0.3357.220.0250.5941.7.99.4NA
60.0601dgjA0.3526.700.0680.5831.2.-.-47
70.0603dy5A0.3536.180.0430.5561.13.11.40,4.2.1.92NA
80.0601vlbA0.3566.770.0430.6001.2.99.754,269
90.0603hznH0.3653.310.1210.4221.-.-.-NA
100.0601xjjA0.3357.240.0380.5941.17.4.172,157
110.0602vdcA0.3597.050.0670.6241.4.1.13NA
120.0603hq2B0.3367.030.0490.5703.4.24.-NA
130.0602fugU0.2886.680.0390.4761.6.99.549
140.0602wghB0.3437.200.0300.5891.17.4.159
150.0602vdcF0.3696.850.0350.6131.4.1.13NA
160.0601ds7A0.3683.380.1250.4301.5.1.34,1.6.99.7189
170.0602cf2C0.3376.630.0480.5432.3.1.8573
180.0602zxcA0.3807.220.0520.6753.5.1.23203,210
190.0602iukA0.3896.180.0520.6021.13.11.12NA

(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
00.390.8411.290.190.872ymvA GO:0016491 GO:0055114
10.260.4063.180.110.473gfaA GO:0000166 GO:0016491 GO:0055114
20.190.4053.390.120.473eo8A GO:0000166 GO:0016491 GO:0055114
30.150.3673.080.080.423gbhB GO:0016491 GO:0055114
40.150.3763.910.110.454eo3A GO:0000166 GO:0016209 GO:0016491 GO:0055114 GO:0098869
50.130.4143.430.130.492isjA GO:0000166 GO:0009236 GO:0016491 GO:0016705 GO:0055114
60.080.4263.420.090.503tnzA GO:0004447 GO:0016020 GO:0016021 GO:0016491 GO:0055114 GO:0098869
70.070.3853.070.090.444ttbA GO:0004447 GO:0005886 GO:0006590 GO:0016020 GO:0016021 GO:0016491 GO:0055114 GO:0098869
80.070.3823.490.130.452i7hA GO:0000166 GO:0016491 GO:0055114
90.070.5683.660.130.683eo7A GO:0000166 GO:0016491 GO:0055114
100.060.4264.050.130.522wzvB GO:0000166 GO:0010181 GO:0016491 GO:0042802 GO:0042803 GO:0050661 GO:0055114 GO:2001039
110.060.4264.160.100.533gr3A GO:0016491 GO:0055114
120.060.4253.390.080.504ttcA GO:0004447 GO:0005886 GO:0006590 GO:0016020 GO:0016021 GO:0016491 GO:0055114 GO:0098869
130.060.3993.050.110.463ek3A GO:0000166 GO:0016491 GO:0055114
140.060.3923.380.060.451vkwA GO:0016491 GO:0055114
150.060.3823.080.100.443gb5A GO:0004447 GO:0016020 GO:0016021 GO:0016491 GO:0055114 GO:0098869
160.060.3663.180.130.423gagA GO:0000166 GO:0016491 GO:0055114
170.060.3733.000.110.433bemB GO:0005737 GO:0009636 GO:0016491 GO:0019439 GO:0055114
180.060.3753.110.120.431v5yA GO:0008218 GO:0016491 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0016491 GO:0000166
GO-Score 0.74 0.49
Biological Processes GO:0055114
GO-Score 0.74
Cellular Component
GO-Score

(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.