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I-TASSER results for job id Rv2566

[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 4 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
10.06 2 2j5wA OXY Rep, Mult 49,51,95,97,866,868,918
20.06 2 3ffzB NA Rep, Mult 62,65,66,68,69
30.03 1 1gk9B EDO Rep, Mult 721,756,758
40.03 1 2vo9A ZN Rep, Mult 267,283,415
50.03 1 1d7pM CYS Rep, Mult 92,183,216,218
60.03 1 2hryA MG Rep, Mult 220,362
70.03 1 1dvfD ZN Rep, Mult 267,283
80.03 1 1hfuA UUU Rep, Mult 46,47,48,103
90.03 1 2pi4A MG Rep, Mult 793,1058
100.03 1 3n3oB ADP Rep, Mult 786,790,904
110.03 1 1kcwA O Rep, Mult 49,50,51,55,866,868
120.03 1 2fuqA ZN Rep, Mult 771,793,843
130.03 1 1tt4A MG Rep, Mult 631,741,866
140.03 1 2io9A MG Rep, Mult 694,696
150.03 1 3lp1A MN Rep, Mult 730,843,850

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
10.0922j5wA0.6484.100.0900.7171.16.3.1NA
20.0603c46B0.2509.420.0420.3902.7.7.671
30.0601ea0A0.2689.640.0370.4281.4.1.13106
40.0602h5uA0.2874.540.0790.3231.10.3.2NA
50.0602pdaA0.2639.760.0380.4241.2.7.1NA
60.0602np0A0.2419.770.0240.3913.4.24.69NA
70.0602g49A0.2589.000.0510.3933.4.24.56NA
80.0603h09B0.2589.000.0340.3913.4.21.72NA
90.0602uv8G0.2949.180.0290.4552.3.1.86NA
100.0601ofdA0.2739.840.0370.4451.4.7.1NA
110.0602pffB0.2819.050.0600.4292.3.1.86107
120.0602fqfA0.2704.910.0850.3091.-.-.-NA
130.0602qt6A0.2874.510.0920.3221.10.3.2NA
140.0601a65A0.2884.700.0810.3261.10.3.2NA
150.0601v10A0.2844.650.0870.3211.10.3.2NA
160.0602dqmA0.2568.730.0390.3823.4.11.2NA
170.0601aozA0.2924.690.0900.3301.10.3.3NA
180.0602hrgA0.2904.430.0960.3251.10.3.2NA
190.0601asqA0.2934.490.0920.3301.10.3.356,84
200.0601bxrA0.2759.450.0340.4326.3.5.519

(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
00.180.8453.380.090.914bxsV GO:0004252 GO:0005507 GO:0005576 GO:0006508 GO:0007596 GO:0010952 GO:0016504 GO:0035807 GO:0044469 GO:0046872
10.080.6524.000.090.724ejxA GO:0001889 GO:0004322 GO:0005507 GO:0005576 GO:0005615 GO:0005765 GO:0006810 GO:0006811 GO:0006825 GO:0006879 GO:0007568 GO:0007584 GO:0016491 GO:0030324 GO:0046658 GO:0046688 GO:0046872 GO:0051087 GO:0055114 GO:0070062 GO:0072562
20.060.4274.240.080.482r7eA GO:0000139 GO:0002576 GO:0005507 GO:0005576 GO:0005615 GO:0005788 GO:0005886 GO:0006888 GO:0006953 GO:0007596 GO:0007597 GO:0007599 GO:0016491 GO:0030134 GO:0030168 GO:0031093 GO:0033116 GO:0046872 GO:0048208 GO:0055114
30.060.4264.210.090.473cdzA GO:0000139 GO:0002576 GO:0005507 GO:0005576 GO:0005615 GO:0005788 GO:0005886 GO:0006888 GO:0006953 GO:0007596 GO:0007597 GO:0007599 GO:0016491 GO:0030134 GO:0030168 GO:0031093 GO:0033116 GO:0046872 GO:0048208 GO:0055114
40.060.3594.510.050.412r7eB GO:0000139 GO:0002576 GO:0005507 GO:0005576 GO:0005615 GO:0005788 GO:0005886 GO:0006888 GO:0006953 GO:0007596 GO:0007597 GO:0007599 GO:0016491 GO:0030134 GO:0030168 GO:0031093 GO:0033116 GO:0046872 GO:0048208 GO:0055114
50.060.3494.170.060.391sddB GO:0005507 GO:0005576 GO:0007596 GO:0007599 GO:0030168 GO:0046872
60.060.3564.310.060.404bdvB GO:0000139 GO:0002576 GO:0005507 GO:0005576 GO:0005615 GO:0005788 GO:0005886 GO:0006888 GO:0006953 GO:0007596 GO:0007597 GO:0007599 GO:0016491 GO:0030134 GO:0030168 GO:0031093 GO:0033116 GO:0046872 GO:0048208 GO:0055114
70.060.2924.690.090.331aozA GO:0005507 GO:0005576 GO:0008447 GO:0016491 GO:0046872 GO:0055114
80.060.2894.690.080.333ppsA GO:0005507 GO:0016491 GO:0046872 GO:0052716 GO:0055114
90.060.2884.540.090.325e9nA GO:0005507 GO:0016491 GO:0046872 GO:0052716 GO:0055114
100.060.2884.700.080.331a65A GO:0005507 GO:0016491 GO:0046872 GO:0052716 GO:0055114
110.060.2864.710.090.321zpuA GO:0004322 GO:0005381 GO:0005507 GO:0005886 GO:0006810 GO:0006811 GO:0006827 GO:0016020 GO:0016021 GO:0016491 GO:0033215 GO:0033573 GO:0046688 GO:0046872 GO:0055072 GO:0055114 GO:1901684
120.060.2604.230.090.293aw5A GO:0005507 GO:0016020 GO:0016021 GO:0016491 GO:0016722 GO:0046872 GO:0055114
130.060.2644.310.090.295afaA GO:0005507 GO:0016491 GO:0046872 GO:0052716 GO:0055114
140.060.2454.400.100.284f7kA GO:0005507 GO:0016491 GO:0052716 GO:0055114
150.060.1848.000.040.272qqlA GO:0001525 GO:0001938 GO:0002116 GO:0004872 GO:0005021 GO:0005576 GO:0005886 GO:0007155 GO:0007275 GO:0007399 GO:0007411 GO:0008201 GO:0010595 GO:0016020 GO:0016021 GO:0017154 GO:0019838 GO:0019955 GO:0021675 GO:0030154 GO:0038084 GO:0046872 GO:0048010 GO:0048846 GO:0061549 GO:0097490 GO:0097491 GO:1902285
160.060.2814.700.090.323sqrA GO:0005507 GO:0016491 GO:0046872 GO:0055114
170.060.1863.960.110.214knsA GO:0005507 GO:0006807 GO:0046872 GO:0050421 GO:0055114
180.060.1934.090.070.213g5wA GO:0005507 GO:0016491 GO:0046872 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0005507 GO:0061134 GO:0004175 GO:0008236 GO:0008047
GO-Score 0.38 0.36 0.36 0.36 0.36
Biological Processes GO:0044710 GO:0001775 GO:0002526 GO:0048207 GO:0006461 GO:0006901 GO:0045055 GO:0090114 GO:0072378 GO:0030194 GO:0044468 GO:0052547 GO:0035806 GO:0044483 GO:0051345 GO:0045862
GO-Score 0.49 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36
Cellular Component GO:0044421 GO:0071944 GO:0098588 GO:0005793 GO:0030135 GO:0070013 GO:0030133 GO:0031091 GO:0034774 GO:0044431 GO:0044432
GO-Score 0.49 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36

(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.