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I-TASSER results for job id Rv2091c

[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
10.11 6 3usbA IMP Rep, Mult 62,167,168,169,170,197,198,199,241,242
20.06 3 3nm1B IFP Rep, Mult 58,60,82,113,143,159,162,195,197
30.06 3 3q4dI ALA Rep, Mult 82,84,113,115,143,164,241
40.04 2 2y7dA ZN Rep, Mult 60,62,242
50.02 1 3oahA CYT Rep, Mult 163,164,165
60.02 1 3uufA MAN Rep, Mult 184,185
70.02 1 3mi1B FE Rep, Mult 187,189
80.02 1 3cv1A CA Rep, Mult 99,102
90.02 1 2h3cA NUC Rep, Mult 226,228,230
100.02 1 1c9uB CA Rep, Mult 82,91
110.02 1 3fbyA CA Rep, Mult 10,12,14,16,17,18,21
120.02 1 3dyoB IPT Rep, Mult 93,95
130.02 1 4c6cA ZN Rep, Mult 59,197,233
140.02 1 4e0sB MAN Rep, Mult 43,44,77
150.02 1 1cklF UUU Rep, Mult 234,237
160.02 1 3pvbB ANP Rep, Mult 134,137

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
10.0661xi3A0.5133.790.0600.6762.5.1.3NA
20.0661xi3B0.5083.550.0660.6602.5.1.3143
30.0601zfjA0.5713.560.0640.7341.1.1.205NA
40.0601nf7A0.5733.680.0470.7461.1.1.205239
50.0602bmbA0.5695.140.0530.8812.5.1.15,2.7.6.3,4.1.2.25NA
60.0601f76A0.5503.880.0680.7381.3.3.171,116
70.0601rboB0.5564.470.0760.7834.1.1.39NA
80.0602uv8G0.7213.730.0560.9182.3.1.86NA
90.0601bxnA0.5334.990.0650.8074.1.1.39NA
100.0603cuxA0.5504.120.0370.7542.3.3.9NA
110.0602pffB0.7243.480.1260.8972.3.1.86116,123,140,158
120.0601gthA0.5573.790.0450.7341.3.1.2NA
130.0601vcgB0.5543.760.0570.7255.3.3.2NA
140.0602zryD0.5593.910.0530.7545.3.3.2115
150.0601iwaA0.5534.360.0560.7754.1.1.39NA
160.0602c6qG0.5513.740.0860.7301.7.1.765,116
170.0602i9uA0.5484.670.0280.7793.5.4.3NA
180.0602d69A0.5494.470.0750.7704.1.1.39NA
190.0601bxnE0.5335.020.0550.8074.1.1.39116
200.0602rdtA0.5153.990.0490.6971.1.3.15NA
210.0602a1yA0.5503.360.0410.7011.7.1.763,116

(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
00.070.4774.800.040.705c7hA GO:0000166 GO:0016491 GO:0055114
10.060.4513.770.040.603ceuA GO:0003824 GO:0004789 GO:0005737 GO:0009228
20.060.3166.180.030.574bmsF GO:0000166
30.060.3645.730.070.613anlA GO:0008299 GO:0016114 GO:0016491 GO:0019288 GO:0030145 GO:0030604 GO:0042802 GO:0046872 GO:0051484 GO:0055114 GO:0070402
40.060.3236.230.030.584bmnA GO:0000166
50.060.3076.660.050.592qo3B GO:0003824 GO:0008152 GO:0016491 GO:0016740 GO:0016746 GO:0017000 GO:0031177 GO:0033068 GO:0047879 GO:0048037 GO:0055114
60.060.3545.540.050.593omlA GO:0003824 GO:0004300 GO:0005777 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0016491 GO:0016616 GO:0016829 GO:0033540 GO:0042803 GO:0055114 GO:0080023
70.060.2526.540.030.481tzsA GO:0004190 GO:0005768 GO:0006508 GO:0007586 GO:0008233 GO:0016540 GO:0016787 GO:0019886 GO:0030163 GO:0042803 GO:0070062
80.060.3006.170.020.533g87A GO:0003824 GO:0004314 GO:0008152 GO:0016740 GO:0016746
90.060.3556.490.030.675f9tA GO:0004308 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0052794 GO:0052795 GO:0052796
100.060.3186.310.040.583hjvA GO:0003824 GO:0004314 GO:0006633 GO:0008152 GO:0016740 GO:0016746
110.060.3575.900.020.602ghiA GO:0000166 GO:0005524 GO:0006810 GO:0016020 GO:0016021 GO:0016887 GO:0042626 GO:0055085
120.060.3146.910.050.623tzwA GO:0003824 GO:0005618 GO:0005829 GO:0005886 GO:0008152 GO:0009058 GO:0016740 GO:0016747 GO:0016788 GO:0019367 GO:0031177 GO:0034081 GO:0040007 GO:0051260 GO:0071768 GO:0071769
130.060.3386.050.060.592aj4A GO:0000166 GO:0000411 GO:0004335 GO:0005524 GO:0005737 GO:0005975 GO:0006012 GO:0008152 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0033499 GO:0046835
140.060.2985.680.060.502h1yB GO:0003824 GO:0004314 GO:0008152 GO:0016740 GO:0016746
150.060.3256.220.020.583rgiA GO:0003824 GO:0004314 GO:0008152 GO:0016740
160.060.2996.780.050.583h0pB GO:0003824 GO:0004314 GO:0006629 GO:0006631 GO:0006633 GO:0008152 GO:0016740 GO:0016746
170.060.3096.630.040.594rl1A GO:0003824 GO:0008152 GO:0016740 GO:0031177
180.060.3266.110.050.583qatA GO:0003824 GO:0004314 GO:0008152 GO:0016740 GO:0016746


Consensus prediction of GO terms
 
Molecular Function GO:1901265 GO:0036094
GO-Score 0.36 0.36
Biological Processes GO:0055114 GO:0009228 GO:0051484
GO-Score 0.12 0.07 0.06
Cellular Component GO:0005737
GO-Score 0.07

(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.