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I-TASSER results for job id Rv2577

[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
10.55 48 4kkzD 1RF Rep, Mult 173,217,220,253,254,357,358,385,387
20.43 30 3zk4A MN Rep, Mult 173,217,253,348,385
30.02 3 2qfrA SO4 Rep, Mult 253,254,357,358,385,387
40.01 1 1xzwA PO4 Rep, Mult 522,523,524,527
50.01 1 1xzwB UUU Rep, Mult 335,339

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
10.3074kbpA0.7690.940.2280.7793.1.3.2253,307
20.1881kbpA0.7690.920.2260.7793.1.3.2NA
30.0601oidA0.3835.070.1070.4863.6.1.45,3.1.3.5215,268
40.0601warA0.4653.260.2160.5123.1.3.2254,383,387
50.0602je8B0.4367.330.0600.6993.2.1.25NA
60.0602z72A0.3655.510.0800.4843.1.3.48253,254,385
70.0601ho5A0.3835.020.1020.4863.1.3.5,3.6.1.45NA
80.0601fa9A0.3317.370.0660.5352.4.1.1NA
90.0602e9bA0.3677.080.0260.5673.2.1.41389,391
100.0602z1aA0.3664.720.1260.4543.1.3.5NA
110.0601bf2A0.3967.390.0450.6393.2.1.68NA
120.0602q1fA0.3597.660.0300.5904.2.2.21NA
130.0603fn9C0.4197.070.0520.6563.2.1.23NA
140.0603czkA0.3607.450.0640.5803.2.1.48NA
150.0601xzwB0.7741.220.2200.7903.1.3.2NA
160.0603m07A0.3766.680.0300.5653.2.1.141216
170.0602vncB0.3857.190.0480.6093.2.1.-NA
180.0602nxfA0.4183.760.1600.4803.6.1.16,3.6.1.53,3.6.1.13NA
190.0601m7xB0.3677.370.0540.5902.4.1.18NA
200.0602vr5A0.3747.400.0290.6053.2.1.-NA
210.0601eh9A0.3616.960.0500.5583.2.1.141NA

(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
00.600.7741.220.220.791xzwB GO:0003993 GO:0005576 GO:0016311 GO:0016787 GO:0046872
10.460.4622.970.210.501qhwA GO:0001503 GO:0003993 GO:0005615 GO:0005764 GO:0007162 GO:0008198 GO:0008199 GO:0010043 GO:0014070 GO:0016021 GO:0016311 GO:0016787 GO:0030316 GO:0030335 GO:0033555 GO:0033591 GO:0045453 GO:0046872 GO:0070723
20.400.4653.260.220.511warA GO:0001503 GO:0003993 GO:0005615 GO:0005764 GO:0005829 GO:0006771 GO:0007162 GO:0008198 GO:0008199 GO:0010043 GO:0014070 GO:0016021 GO:0016311 GO:0016787 GO:0030316 GO:0030335 GO:0032496 GO:0032691 GO:0032695 GO:0032720 GO:0032929 GO:0033555 GO:0033591 GO:0034097 GO:0045019 GO:0045453 GO:0046872 GO:0050728 GO:0050830 GO:0060349 GO:0070062 GO:0070723
30.350.4633.220.210.511uteA GO:0003993 GO:0005576 GO:0006810 GO:0006811 GO:0008198 GO:0008199 GO:0016311 GO:0016787 GO:0046872 GO:0055072
40.300.7103.210.230.783zk4B GO:0003993 GO:0016311 GO:0016787 GO:0046872
50.280.7720.980.220.784dsyB GO:0003993 GO:0005576 GO:0008199 GO:0008270 GO:0016311 GO:0016787 GO:0046872
60.160.4552.960.180.503tghA GO:0003993 GO:0005783 GO:0005886 GO:0016020 GO:0016021 GO:0016311 GO:0016787 GO:0043495 GO:0070258
70.060.2637.800.030.441on3E GO:0003989 GO:0006633 GO:0009317 GO:0016740 GO:0016874 GO:0047154
80.060.3317.370.070.542yikA GO:0000272 GO:0003824 GO:0004553 GO:0005975 GO:0016787 GO:0046872
90.060.2887.120.060.452iv0A GO:0000287 GO:0004450 GO:0006097 GO:0006099 GO:0016491 GO:0016616 GO:0046872 GO:0051287 GO:0055114
100.060.2537.010.020.401x0xA GO:0004367 GO:0004368 GO:0005737 GO:0005739 GO:0005829 GO:0005975 GO:0006072 GO:0006094 GO:0006116 GO:0006127 GO:0006654 GO:0006734 GO:0009331 GO:0016491 GO:0016616 GO:0019432 GO:0042803 GO:0045821 GO:0046168 GO:0046486 GO:0051287 GO:0055114 GO:0070062 GO:0071320 GO:0071356
110.060.2217.030.050.351f0kA GO:0005886 GO:0005975 GO:0007049 GO:0008360 GO:0009252 GO:0016020 GO:0016740 GO:0016757 GO:0016758 GO:0030259 GO:0050511 GO:0051301 GO:0051991 GO:0071555
120.060.2126.570.020.311bg0A GO:0000166 GO:0003824 GO:0004054 GO:0005524 GO:0005737 GO:0016301 GO:0016310 GO:0016740 GO:0016772
130.060.2496.030.090.363vvbA GO:0003978 GO:0009103
140.060.2046.520.050.314j3oH GO:0005537 GO:0007155 GO:0009289
150.060.2186.910.040.333w1vA GO:0003978 GO:0009103
160.060.1815.800.050.251fn8A GO:0004252 GO:0005576 GO:0006508 GO:0008233 GO:0008236 GO:0016787
170.060.1856.870.040.285aooB GO:0000166 GO:0001172 GO:0003723 GO:0003724 GO:0003968 GO:0004197 GO:0004386 GO:0005198 GO:0005216 GO:0005524 GO:0006351 GO:0006508 GO:0006810 GO:0006811 GO:0008233 GO:0008234 GO:0016020 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0019012 GO:0019028 GO:0019062 GO:0030430 GO:0033644 GO:0034220 GO:0039694 GO:0039707 GO:0044161 GO:0044162 GO:0044385 GO:0046718 GO:0051259
180.060.1655.510.040.235buvC GO:0008830
190.060.1366.330.040.204urtB GO:0001764 GO:0004888 GO:0005042 GO:0005829 GO:0005886 GO:0006915 GO:0007275 GO:0007399 GO:0007409 GO:0007411 GO:0010977 GO:0016020 GO:0016021 GO:0021965 GO:0030424 GO:0033563 GO:0033564 GO:0038007 GO:0048671 GO:0097192 GO:1901214 GO:2000171
200.060.1623.040.110.182edeA GO:0001764 GO:0004888 GO:0005042 GO:0005829 GO:0005886 GO:0006915 GO:0007275 GO:0007399 GO:0007409 GO:0007411 GO:0010977 GO:0016020 GO:0016021 GO:0021965 GO:0030424 GO:0033563 GO:0033564 GO:0038007 GO:0048671 GO:0097192 GO:1901214 GO:2000171


Consensus prediction of GO terms
 
Molecular Function GO:0003993 GO:0008199 GO:0008198
GO-Score 0.94 0.79 0.79
Biological Processes GO:0016311 GO:0030335 GO:0045453 GO:0001503 GO:0033555 GO:0070723 GO:0030316 GO:0033591 GO:0010043 GO:0007162 GO:0006771 GO:0032496 GO:0034097 GO:0050830 GO:0032691 GO:0032720 GO:0045019 GO:0032929 GO:0050728 GO:0032695 GO:0060349 GO:0055072 GO:0006811
GO-Score 0.94 0.68 0.68 0.68 0.68 0.68 0.68 0.68 0.68 0.68 0.40 0.40 0.40 0.40 0.40 0.40 0.40 0.40 0.40 0.40 0.40 0.35 0.35
Cellular Component GO:0005615 GO:0005764 GO:0016021 GO:0070062 GO:0005829
GO-Score 0.68 0.68 0.68 0.40 0.40

(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.