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I-TASSER results for job id Rv0883c

[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 2nr9A PA6 Rep, Mult 126,130
20.04 2 2wtgA OXY Rep, Mult 91,243
30.04 2 4r6cA 6BP Rep, Mult 124,127,128
40.04 2 2wpnB UUU Rep, Mult 40,110
50.04 2 2ek8A ZN Rep, Mult 168,184,211
60.02 1 1lc3A PO4 Rep, Mult 92,93,97,98,99
70.02 1 2wssX III Rep, Mult 122,126
80.02 1 1h6dA NDP Rep, Mult 130,136,137,139,140,141
90.02 1 3kd3A MG Rep, Mult 10,12,185
100.02 1 1v51A ZN Rep, Mult 185,189
110.02 1 3rbvA NA Rep, Mult 106,107,108,109,111
120.02 1 4ep7B MG Rep, Mult 130,133
130.02 1 1shkA MG Rep, Mult 69,70,71
140.02 1 4dcaA MG Rep, Mult 165,184
150.02 1 2pnqA MG Rep, Mult 115,116
160.02 1 1c66A AR Rep, Mult 129,171
170.02 1 3oceC CO Rep, Mult 121,124
180.02 1 1h74B MG Rep, Mult 73,104

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
10.0662glxE0.5994.820.0850.8771.1.1.263157
20.0602ph5A0.4665.780.0870.7672.5.1.448,55
30.0601ml4A0.4595.100.0440.6962.1.3.2NA
40.0603euwD0.5655.140.0940.8741.1.1.1811,60
50.0602o48X0.6194.670.1150.8931.1.1.179,1.3.1.20NA
60.0601dpgA0.5555.500.0680.8931.1.1.49NA
70.0601gcuA0.5924.730.0590.8701.3.1.24NA
80.0601ydwB0.5965.290.0960.9091.-.-.-128
90.0602ixaA0.5975.080.0540.9093.2.1.49128
100.0602o4uX0.6194.660.1150.8931.3.1.2091
110.0601e5qA0.4745.780.0430.7751.5.1.10101,105
120.0601e5lA0.4625.570.0340.7391.5.1.10NA
130.0601p1jA0.4894.910.0700.7395.5.1.496,100,222
140.0602ejwA0.4895.340.0850.7671.1.1.3NA
150.0601o0sA0.4755.430.0550.7511.1.1.38NA
160.0601ebfA0.4835.370.0530.7671.1.1.3NA
170.0603mtjA0.4965.720.0900.8061.1.1.396,98,127
180.0601dxhA0.4645.450.0330.7272.1.3.369
190.0602h63D0.5854.710.0510.8581.3.1.24NA
200.0602glxA0.5984.800.0770.8741.1.1.292NA

(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
00.250.6064.730.060.893q2kC GO:0000166 GO:0008152 GO:0016491 GO:0055114
10.080.6394.750.140.933c1aA GO:0016491 GO:0055114
20.080.6094.700.090.884nheB GO:0016491 GO:0055114
30.080.6044.970.070.905a03C GO:0008152 GO:0016491 GO:0055114
40.070.6154.890.090.903rc1A GO:0000166 GO:0016491 GO:0055114
50.070.6194.670.120.892o48X GO:0016491 GO:0047115 GO:0047837 GO:0055114
60.070.6194.820.080.893evnA GO:0016491 GO:0055114
70.070.6004.710.090.871xeaA GO:0016491 GO:0055114
80.070.5934.930.080.883kuxA GO:0008152 GO:0016491 GO:0055114
90.070.6124.610.120.894h3vA GO:0008152 GO:0016491 GO:0055114
100.070.5964.880.110.893u3xA GO:0008152 GO:0016491 GO:0055114
110.070.6114.780.040.903dtyA GO:0008152 GO:0016491 GO:0055114
120.070.6134.830.070.893e9mA GO:0016491 GO:0055114
130.070.6024.730.090.884fb5A GO:0008152 GO:0016491 GO:0055114
140.070.5995.010.080.893db2A GO:0008152 GO:0016491 GO:0055114
150.070.6084.470.120.874gqaC GO:0008152 GO:0016491 GO:0055114
160.070.6065.040.070.903moiA GO:0008152 GO:0016491 GO:0055114
170.070.5964.840.100.882p2sA GO:0008152 GO:0016491 GO:0055114
180.070.5984.820.100.884koaA GO:0008152 GO:0016491 GO:0033712 GO:0055114
190.070.5975.040.090.893gfgB GO:0008152 GO:0016491 GO:0055114
200.070.5854.710.050.862h63D GO:0004074 GO:0005737 GO:0005829 GO:0008270 GO:0016491 GO:0042167 GO:0046872 GO:0055114 GO:0070062
210.070.5924.730.060.871gcuA GO:0004074 GO:0005737 GO:0008270 GO:0016491 GO:0042167 GO:0046872 GO:0055114
220.070.5854.960.050.874ew6A GO:0016491 GO:0019151 GO:0055114
230.070.6064.960.070.904hadA GO:0016491 GO:0055114
240.070.6004.800.100.883m2tA GO:0000166 GO:0016491 GO:0055114
250.070.5914.680.080.863ezyA GO:0008152 GO:0016491 GO:0050112 GO:0055114
260.070.5984.800.080.872glxA GO:0008152 GO:0016491 GO:0033712 GO:0055114
270.070.5954.900.090.893q2iA GO:0000166 GO:0008152 GO:0016491 GO:0055114
280.070.5835.090.050.883fhlC GO:0008152 GO:0016491 GO:0055114
290.070.5954.820.090.883f4lA GO:0005829 GO:0008152 GO:0016491 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0016491 GO:0000166
GO-Score 0.46 0.31
Biological Processes GO:0055114
GO-Score 0.46
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.