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I-TASSER results for job id Rv2286c

[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
10.42 13 2imeA GSH Rep, Mult 12,13,14,40,143,144,155,156,158
20.06 2 3fz5B GSH Rep, Mult 12,13,14,143,144,145,155,156,166,167
30.03 1 3dksA III Rep, Mult 40,41,142,143,144,145
40.03 1 2imdA UUU Rep, Mult 11,13,14,40,44,53,54,55,61
50.03 1 3fz5C GSH Rep, Mult 12,13,14,41,56,144,156,166,167

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
10.1921r4wC0.6162.890.1170.7352.5.1.1811,36,155
20.0602gtqA0.3976.150.0320.7353.4.11.2NA
30.0601mpxA0.4236.150.0590.7613.2.1.43NA
40.0602gq3A0.4125.510.0540.6782.3.3.942
50.0601fsuA0.4335.860.0820.7483.1.6.12NA
60.0601q0lA0.4055.710.0750.6831.1.1.267NA
70.0601h19A0.4026.000.0560.7093.3.2.687,99,101
80.0601ehiA0.3984.280.0660.5526.3.2.4104
90.0601lnsA0.4185.870.0360.7223.4.14.11132
100.0601ofdA0.3496.110.0690.6131.4.7.1NA
110.0601yzxB0.6162.710.1300.7262.5.1.1811,36,65
120.0602akjA0.3925.580.0350.6481.7.7.1NA
130.0601l7qA0.4515.890.0850.7743.1.1.1NA
140.0601t3bA0.4702.390.1220.5355.3.4.112
150.0602bmaA0.4174.850.0500.6221.4.1.4150
160.0601ug9A0.4366.150.0320.7783.2.1.70NA
170.0603ebgA0.4186.120.0500.7523.4.11.-41
180.0602ff2B0.4015.410.0530.6563.2.2.1NA
190.0601v9lA0.3994.890.0760.6041.4.1.2NA
200.0601h54B0.4135.750.0200.6912.4.1.8NA

(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
00.380.7652.040.270.844zilA GO:0005618 GO:0005737 GO:0015035 GO:0016491 GO:0055114
10.270.6102.940.140.722imdA GO:0015035 GO:0016853 GO:0018845 GO:0019439 GO:0055114 GO:1901170
20.260.7382.090.280.824wkwA GO:0015035 GO:0055114
30.220.5873.000.190.693fz5C GO:0015035 GO:0016853 GO:0046872 GO:0055114
40.210.6142.910.120.731r4wA GO:0004364 GO:0004602 GO:0005102 GO:0005622 GO:0005739 GO:0005743 GO:0005759 GO:0005777 GO:0006749 GO:0015035 GO:0016020 GO:0016740 GO:0030855 GO:0043231 GO:0055114 GO:0070062 GO:0098869
50.210.5293.190.130.674p3yB GO:0015035 GO:0016853 GO:0042597 GO:0055114
60.200.5653.060.130.684pwoA GO:0016020 GO:0016021
70.170.5582.920.140.674n30A GO:0016853
80.160.5303.590.150.704k2dA GO:0015035 GO:0042597 GO:0045454 GO:0055114
90.150.5333.150.120.663gmfA GO:0016020 GO:0016021 GO:0016853
100.150.5513.320.150.693l9vA GO:0015035 GO:0016853 GO:0042597 GO:0045454 GO:0055114
110.140.5422.800.130.654gxzA GO:0005623 GO:0015035 GO:0045454 GO:0055114
120.130.5302.880.150.633gykA
130.130.5272.850.090.634xvwL GO:0005623 GO:0045454
140.120.5392.870.100.654xvwA GO:0005623 GO:0045454
150.120.5213.420.070.653bciA GO:0016853
160.120.5463.040.090.673f4tA GO:0003756 GO:0019153 GO:0055114
170.070.5992.990.180.723gl5A GO:0015035 GO:0055114
180.070.6192.840.130.733rpnA GO:0004364 GO:0004602 GO:0005102 GO:0005622 GO:0005739 GO:0005743 GO:0005759 GO:0005777 GO:0006749 GO:0015035 GO:0016020 GO:0016740 GO:0030855 GO:0043231 GO:0055114 GO:0070062 GO:0098869 GO:1901687
190.070.5683.210.090.693eu3A GO:0016491 GO:0030420 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0015035 GO:0016860 GO:0043169 GO:0016765 GO:0004601 GO:0005515
GO-Score 0.79 0.53 0.43 0.43 0.43 0.43
Biological Processes GO:0055114 GO:1901361 GO:0044248 GO:0018931 GO:0030154 GO:0006790 GO:0060429 GO:0006575 GO:1990748 GO:0006518
GO-Score 0.79 0.53 0.53 0.53 0.43 0.43 0.43 0.43 0.43 0.43
Cellular Component GO:0070013 GO:1903561 GO:0031966 GO:0019866 GO:0042579 GO:0031988 GO:0005618
GO-Score 0.43 0.43 0.43 0.43 0.43 0.43 0.38

(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.