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I-TASSER results for job id Rv2366c

[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
10.35 16 3lfrA AMP Rep, Mult 205,209,210,211,231,232,233,235,299,312,314,317
20.06 3 2ckjC FES Rep, Mult 22,26,28,31,34,35,36
30.04 2 1ea0A F3S Rep, Mult 62,63,64,67,68,69,98,99
40.02 1 2ckjA FES Rep, Mult 20,22,25,27,31
50.02 1 3eubS FES Rep, Mult 101,102,103,105,106,107,108
60.02 1 2ckjB FES Rep, Mult 234,235,236,245,246,277
70.02 1 1jz6A MG Rep, Mult 390,392,399

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
10.0603hhsB0.3286.720.0320.5171.14.18.1NA
20.0603k1dA0.3297.230.0460.5542.4.1.18305
30.0602jfdA0.2397.290.0360.4072.3.1.85166
40.0602vdcA0.3507.300.0560.5951.4.1.13NA
50.0601h16A0.3287.620.0430.5842.3.1.54NA
60.0601ea0A0.3197.050.0400.5291.4.1.13227
70.0601bhgA0.3307.100.0460.5423.2.1.31167
80.0603ffzA0.3337.260.0570.5683.4.24.69NA
90.0603b9jI0.1645.880.0140.2411.17.1.4,1.17.3.2NA
100.0602qf7B0.3507.140.0420.5846.4.1.1NA
110.0602aryA0.2206.780.0440.3563.4.22.52NA
120.0602c6fA0.3366.810.0500.5293.4.15.1321
130.0601t3tA0.3457.800.0710.6256.3.5.3NA
140.0602ckjA0.3466.550.0510.5361.17.1.4,1.17.3.2NA
150.0601ofdA0.3337.100.0490.5541.4.7.1NA
160.0602pdaA0.2827.310.0340.4741.2.7.1NA
170.0601d8yA0.2917.980.0580.5312.7.7.7152,190
180.0602je8B0.3296.840.0270.5333.2.1.25325
190.0602vdcF0.3497.380.0560.6001.4.1.13237

(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
00.370.5131.520.350.534hg0A GO:0003824 GO:0006810 GO:0016614 GO:0050660 GO:0055114
10.220.2952.340.290.313oi8A GO:0003824 GO:0016614 GO:0046872 GO:0050660 GO:0055114
20.180.2892.700.270.324iysA GO:0005886 GO:0006810 GO:0006811 GO:0010960 GO:0015693 GO:0016020 GO:0016021 GO:0016323
30.090.3052.790.310.343ocmA GO:0000166 GO:0003824 GO:0016020 GO:0016021 GO:0016614 GO:0050660 GO:0055114
40.060.2407.380.060.415bp4L GO:0003824 GO:0008152 GO:0016491 GO:0016740 GO:0016746 GO:0031177 GO:0050111 GO:0055114
50.060.3337.850.070.605bp4A GO:0003824 GO:0008152 GO:0016491 GO:0016740 GO:0016746 GO:0031177 GO:0050111 GO:0055114
60.060.2477.510.050.432z5lA GO:0003824 GO:0008152 GO:0016740 GO:0031177
70.060.3027.010.040.495d2eA GO:0003824 GO:0008152 GO:0031177
80.060.2957.420.040.504difA GO:0000166 GO:0003824 GO:0008152 GO:0016740 GO:0031177 GO:0048037
90.060.3006.800.050.482fr0A GO:0003824 GO:0008152 GO:0016740 GO:0016746 GO:0017000 GO:0031177 GO:0033068 GO:0047879
100.060.2977.300.030.504impA GO:0000166 GO:0003824 GO:0008152 GO:0016740 GO:0031177 GO:0048037
110.060.2887.050.040.473qp9A GO:0003824 GO:0008152 GO:0008270 GO:0016491 GO:0016740 GO:0016746 GO:0016747 GO:0017000 GO:0031177 GO:0033068 GO:0048037 GO:0055114
120.060.3017.360.030.512et6A GO:0003824 GO:0005777 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0016491 GO:0016616 GO:0016829 GO:0016853 GO:0055114
130.060.2356.600.030.374opfA GO:0003824 GO:0008152 GO:0016874 GO:0031177
140.060.2647.580.040.474oqjA GO:0003824 GO:0008152 GO:0031177
150.060.2976.770.050.472zkmX GO:0004435 GO:0004629 GO:0004871 GO:0005509 GO:0005737 GO:0005829 GO:0006629 GO:0006644 GO:0007165 GO:0007202 GO:0007223 GO:0008081 GO:0016042 GO:0016787 GO:0035556 GO:0043647 GO:0046872 GO:0050913
160.060.2756.690.040.444j1qA GO:0003824 GO:0005737 GO:0008152 GO:0016740 GO:0016746 GO:0016874 GO:0017000 GO:0031177
170.060.2677.660.040.473hhdC GO:0001649 GO:0003824 GO:0004312 GO:0004313 GO:0004314 GO:0004315 GO:0004316 GO:0004317 GO:0004319 GO:0004320 GO:0005737 GO:0005739 GO:0005794 GO:0005829 GO:0005886 GO:0005913 GO:0006084 GO:0006629 GO:0006631 GO:0006633 GO:0008144 GO:0008152 GO:0009058 GO:0015939 GO:0016020 GO:0016295 GO:0016296 GO:0016297 GO:0016491 GO:0016740 GO:0016787 GO:0016788 GO:0016829 GO:0019171 GO:0030879 GO:0031177 GO:0031325 GO:0035338 GO:0042470 GO:0042587 GO:0042802 GO:0042803 GO:0044822 GO:0047117 GO:0047451 GO:0055114 GO:0070062 GO:0070402 GO:0071353 GO:0098609 GO:0098641 GO:0102132
180.060.2687.570.030.474z37A GO:0003824 GO:0008152 GO:0031177


Consensus prediction of GO terms
 
Molecular Function GO:0016614 GO:0050660 GO:0043169
GO-Score 0.55 0.55 0.43
Biological Processes GO:0055114 GO:0070838 GO:0055065 GO:0072507
GO-Score 0.58 0.37 0.37 0.37
Cellular Component GO:0031224 GO:0098590
GO-Score 0.41 0.37

(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.