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I-TASSER results for job id Rv2288

[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
10.09 4 1lziA MN Rep, Mult 52,54
20.05 2 1fk0A DKA Rep, Mult 45,48,79,85,92
30.05 2 4qvpK MG Rep, Mult 41,45
40.05 2 1k61C NUC Rep, Mult 43,47
50.05 2 2npiA MG Rep, Mult 39,123
60.02 1 3e27A MG Rep, Mult 84,99
70.02 1 2dfdB HIS Rep, Mult 46,61,62
80.02 1 3tvwB 07H Rep, Mult 11,14,15
90.02 1 4h7oA ARG Rep, Mult 24,46
100.02 1 1j3gA ZN Rep, Mult 29,110,121
110.02 1 2bkmA OXY Rep, Mult 52,103
120.02 1 2wse4 CLA Rep, Mult 92,96
130.02 1 4zk0A ZN Rep, Mult 14,74
140.02 1 1gwvA MN Rep, Mult 52,54,119

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
10.0604mdhA0.4294.360.0190.7281.1.1.37NA
20.0602v65A0.4304.820.0240.8001.1.1.27NA
30.0601a59A0.4274.510.0360.7362.3.3.1NA
40.0603msuA0.4274.450.0630.7442.3.3.1NA
50.0601iz9A0.4304.240.0560.7281.1.1.3711,85,93
60.0601guzA0.4314.430.0500.7681.1.1.37NA
70.0601uxgA0.4214.880.0450.7601.1.1.37NA
80.0601ldxA0.4164.330.0460.7201.1.1.2727,38
90.0605ldhA0.4164.940.0450.7601.1.1.27NA
100.0601y6jA0.4364.540.0710.7681.1.1.37NA
110.0601b8pA0.3765.110.0870.7441.1.1.37NA
120.0601a39A0.4345.150.0410.8643.2.1.419
130.0603gvhA0.4314.660.0370.7761.1.1.3747
140.0603ovwA0.4355.240.0420.8643.2.1.4NA
150.0601sowB0.4364.370.0560.7681.1.1.27NA
160.0601bdmB0.3875.040.0540.7441.1.1.37NA
170.0601smkA0.4434.470.0610.7601.1.1.37NA
180.0602e37C0.3575.470.0250.7281.1.1.27NA
190.0601ldnA0.4324.540.0560.7681.1.1.27NA

(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
00.070.5074.200.090.862l6nA
10.070.4564.150.150.762l6pA GO:0016853
20.060.3844.240.060.653luuA GO:0046872
30.060.3474.790.040.611xi6A GO:0046854
40.060.2515.370.100.514ubqA GO:0008270 GO:0008800 GO:0016787 GO:0017001 GO:0046677 GO:0046872
50.060.3334.920.010.641qftA GO:0005576 GO:0030682 GO:0043176
60.060.2765.090.030.511tuzA GO:0000166 GO:0004143 GO:0005509 GO:0005524 GO:0005543 GO:0005829 GO:0005886 GO:0007205 GO:0016020 GO:0016301 GO:0016310 GO:0016740 GO:0030168 GO:0035556 GO:0046872
70.060.3185.510.040.671c9wA GO:0004032 GO:0005737 GO:0016491 GO:0055114
80.060.3175.780.040.702cb1A GO:0003824 GO:0016829 GO:0030170
90.060.2815.130.040.532q0aA GO:0000166 GO:0005216 GO:0005222 GO:0005244 GO:0005248 GO:0005249 GO:0005267 GO:0005272 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0016020 GO:0016021 GO:0030552 GO:0034765 GO:0035725 GO:0042391 GO:0042802 GO:0055085 GO:0060078 GO:0071320 GO:0071321 GO:0071805
100.060.3425.190.040.655chsB GO:0000166 GO:0001172 GO:0003824 GO:0003968 GO:0004482 GO:0005524 GO:0006139 GO:0006370 GO:0006397 GO:0008152 GO:0008168 GO:0016740 GO:0016779 GO:0019012 GO:0030430 GO:0032259 GO:0036265 GO:0039689
110.060.3235.220.030.654cnjA GO:0000166 GO:0016491 GO:0055114
120.060.3205.140.100.623bo5A GO:0000014 GO:0000729 GO:0000737 GO:0000793 GO:0003677 GO:0003690 GO:0003697 GO:0003824 GO:0004518 GO:0004519 GO:0005634 GO:0005694 GO:0006281 GO:0006303 GO:0006974 GO:0008152 GO:0008168 GO:0008270 GO:0008283 GO:0010452 GO:0015074 GO:0016568 GO:0016740 GO:0016787 GO:0018024 GO:0031297 GO:0032259 GO:0034968 GO:0035861 GO:0042800 GO:0042803 GO:0043566 GO:0044547 GO:0044774 GO:0046872 GO:0046975 GO:0051568 GO:0071157 GO:0090305 GO:0097676 GO:2000373 GO:2001034 GO:2001251
130.060.2724.280.030.452ip2A GO:0008168 GO:0008171 GO:0008757 GO:0016740 GO:0019438 GO:0032259
140.060.2895.050.060.521b4wA GO:0004623 GO:0005509 GO:0005576 GO:0006629 GO:0016042 GO:0016787 GO:0046872
150.060.3045.340.030.581qzzA GO:0008168 GO:0008171 GO:0016829 GO:0016831 GO:0017000 GO:0032259
160.060.3534.280.050.603ictA GO:0000166 GO:0003756 GO:0005623 GO:0016491 GO:0045454 GO:0050451 GO:0050660 GO:0050661 GO:0055114
170.060.2914.990.030.541a0iA GO:0000166 GO:0003677 GO:0003909 GO:0003910 GO:0005524 GO:0006260 GO:0006281 GO:0006310 GO:0006974 GO:0016874 GO:0046872 GO:0051103
180.060.2885.410.030.561sezA GO:0004729 GO:0005739 GO:0006779 GO:0006782 GO:0006783 GO:0016491 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0016853 GO:0008800 GO:0008270
GO-Score 0.07 0.06 0.06
Biological Processes GO:0046854 GO:0046677 GO:0017001
GO-Score 0.06 0.06 0.06
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.