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I-TASSER results for job id Rv2050

[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
10.08 4 1ocoB HEA Rep, Mult 97,98
20.06 3 3mnnG MML Rep, Mult 100,103,104
30.06 3 4reuD MG Rep, Mult 87,93
40.04 2 1sumB FE Rep, Mult 92,96
50.04 2 2h6bA 3C4 Rep, Mult 102,105
60.02 1 1urkA FUC Rep, Mult 8,12,18
70.02 1 3k7tA GP7 Rep, Mult 51,52
80.02 1 3e27A MG Rep, Mult 47,57
90.02 1 1xupO GOL Rep, Mult 27,38,82
100.02 1 3lxvN CO3 Rep, Mult 57,59
110.02 1 4rkuL CLA Rep, Mult 98,102
120.02 1 2zegB IMD Rep, Mult 19,49,83
130.02 1 1hotB 16G Rep, Mult 84,88
140.02 1 2vdcG SF4 Rep, Mult 9,10,11,101,102,106
150.02 1 1mbxA YBT Rep, Mult 84,95

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
10.0601pzhA0.4594.750.0380.8741.1.1.27NA
20.0602zbwB0.4604.320.0430.7751.18.1.297
30.0601llcA0.4594.470.0290.8201.1.1.27NA
40.0601gq7E0.4394.760.0630.7753.5.3.22NA
50.0601f8rA0.4794.160.0610.8021.4.3.2NA
60.0601jnrA0.4804.370.0400.8381.8.99.2NA
70.0601sowB0.4484.540.0620.8201.1.1.27NA
80.0601uxiA0.4634.550.0400.8471.1.1.37NA
90.0601d4cA0.4704.420.0300.8291.3.99.1NA
100.0601xfkA0.4684.550.0380.8203.5.3.868
110.0601smkA0.4684.760.0280.8741.1.1.37NA
120.0602dfdA0.4594.980.0380.9011.1.1.3788
130.0602jaeA0.4644.110.0710.7841.4.3.2NA
140.0601ldnA0.4604.750.0380.8561.1.1.27NA
150.0601uxgA0.4234.920.0460.8111.1.1.3731
160.0602ztgA0.4624.780.0560.8926.1.1.7NA
170.0601sevA0.4644.940.0470.9011.1.1.3788
180.0602jb2A0.4654.110.0710.7841.4.3.2NA
190.0602a0mA0.4694.460.0680.8023.5.3.8NA

(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
00.580.6241.751.000.712m4vA GO:0001000 GO:0006351 GO:0006355 GO:0045893
10.070.4944.010.090.783cesA GO:0002098 GO:0005737 GO:0005829 GO:0008033 GO:0016491 GO:0030488 GO:0050660 GO:0055114
20.070.3785.060.060.722vqqA GO:0000118 GO:0000122 GO:0001025 GO:0001047 GO:0001501 GO:0002076 GO:0003677 GO:0003682 GO:0003714 GO:0004407 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0006338 GO:0006351 GO:0006355 GO:0006954 GO:0007399 GO:0008134 GO:0008270 GO:0008284 GO:0008285 GO:0010592 GO:0010832 GO:0010882 GO:0014894 GO:0014898 GO:0014911 GO:0016568 GO:0016575 GO:0016787 GO:0017053 GO:0019901 GO:0030017 GO:0030018 GO:0030183 GO:0030955 GO:0031594 GO:0031672 GO:0032041 GO:0033235 GO:0033558 GO:0033613 GO:0034983 GO:0040029 GO:0042113 GO:0042493 GO:0042641 GO:0042826 GO:0043234 GO:0043393 GO:0043433 GO:0043525 GO:0043565 GO:0044212 GO:0045668 GO:0045820 GO:0045892 GO:0045893 GO:0045944 GO:0046872 GO:0048661 GO:0048742 GO:0051091 GO:0051153 GO:0070491 GO:0070555 GO:0070932 GO:0070933 GO:0071260 GO:0071356 GO:0071374 GO:1903428
30.070.3724.780.070.693c0zC GO:0000118 GO:0000122 GO:0001570 GO:0003682 GO:0003714 GO:0004407 GO:0005080 GO:0005634 GO:0005654 GO:0005737 GO:0006351 GO:0006355 GO:0007043 GO:0016568 GO:0016575 GO:0016787 GO:0016925 GO:0019789 GO:0019901 GO:0030182 GO:0032041 GO:0032703 GO:0033613 GO:0045668 GO:0045892 GO:0046872 GO:0051402 GO:0070491 GO:0070932 GO:0071260 GO:0071889 GO:0090050 GO:1901215 GO:1901223
40.070.4264.910.030.822vvmA GO:0005777 GO:0016491 GO:0055114
50.070.3584.920.010.723q9bA GO:0016787 GO:0046872
60.070.4164.700.060.773bdvA GO:0016787 GO:0046872
70.070.3324.540.040.613nepX GO:0003824 GO:0005975 GO:0006099 GO:0016491 GO:0016616 GO:0019752 GO:0030060 GO:0055114
80.070.3964.860.080.723g5sA GO:0005737 GO:0008033 GO:0008168 GO:0016491 GO:0016740 GO:0030698 GO:0032259 GO:0047151 GO:0050660 GO:0055114
90.070.4634.090.050.774jn9A GO:0000166 GO:0016491 GO:0055114
100.060.4614.360.050.785ikkA GO:0000122 GO:0000183 GO:0000775 GO:0000781 GO:0000790 GO:0004407 GO:0005634 GO:0005694 GO:0006348 GO:0006351 GO:0006355 GO:0016568 GO:0016575 GO:0016584 GO:0016787 GO:0030466 GO:0030702 GO:0030874 GO:0031078 GO:0031618 GO:0031934 GO:0032041 GO:0033553 GO:0035391 GO:0070824 GO:0070932 GO:1990707
110.060.4224.770.080.792vhyB GO:0000166 GO:0000286 GO:0001666 GO:0005576 GO:0005618 GO:0005829 GO:0005886 GO:0006524 GO:0016491 GO:0042853 GO:0046872 GO:0055114
120.060.3495.080.050.713menB GO:0016787 GO:0046872
130.060.4254.690.030.801rp0A GO:0005739 GO:0005829 GO:0006950 GO:0006974 GO:0008270 GO:0009228 GO:0009409 GO:0009507 GO:0009536 GO:0009570 GO:0009579 GO:0009941 GO:0010319 GO:0016491 GO:0018131 GO:0042803 GO:0046872 GO:0052837 GO:0055114
140.060.3285.220.040.694bz5B GO:0016787 GO:0046872
150.060.3634.840.030.672apoA GO:0000495 GO:0001522 GO:0003723 GO:0006396 GO:0008033 GO:0009451 GO:0009982 GO:0016853 GO:0031118 GO:0031119 GO:0031120 GO:0031429 GO:1990481
160.060.4063.990.080.673wnbA GO:0003746 GO:0006414
170.060.4834.320.060.823c0yA GO:0000118 GO:0000122 GO:0001570 GO:0003682 GO:0003714 GO:0004407 GO:0005080 GO:0005634 GO:0005654 GO:0005737 GO:0006351 GO:0006355 GO:0007043 GO:0016568 GO:0016575 GO:0016787 GO:0016925 GO:0019789 GO:0019901 GO:0030182 GO:0032041 GO:0032703 GO:0033613 GO:0045668 GO:0045892 GO:0046872 GO:0051402 GO:0070491 GO:0070932 GO:0071260 GO:0071889 GO:0090050 GO:1901215 GO:1901223
180.060.3084.640.030.593sfhA GO:0000118 GO:0000122 GO:0000228 GO:0004407 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0005886 GO:0006333 GO:0006351 GO:0006355 GO:0007062 GO:0008134 GO:0016568 GO:0016575 GO:0016787 GO:0030544 GO:0031397 GO:0031647 GO:0032041 GO:0032204 GO:0046872 GO:0051879 GO:0070932 GO:0071922


Consensus prediction of GO terms
 
Molecular Function GO:0001000
GO-Score 0.58
Biological Processes GO:0045893
GO-Score 0.60
Cellular Component GO:0044424
GO-Score 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.