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I-TASSER results for job id Rv2917

[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
10.22 8 2fsgA ATP Rep, Mult 64,66,69,91,93,94,95,96
20.14 5 2y3tB MG Rep, Mult 94,95,184
30.03 1 3ebgA ZN Rep, Mult 166,170,175
40.03 1 2w00A ATP Rep, Mult 21,54,55,56,66,69,90,91,92,93,94,95,96,390,415,418
50.03 1 3af5A ZN Rep, Mult 242,243,361,587
60.03 1 4a36A UUU Rep, Mult 66,69,89,91,93,94,95,96,185,214,388,390,411,415,420
70.03 1 5e3hA BEF Rep, Mult 89,94,185,387

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
10.0601moqA0.2486.160.0550.3452.6.1.16121
20.0603kx2B0.4416.060.0680.6023.6.4.1391,95,159,187,192
30.0603pjrA0.3835.610.0770.5083.6.4.12NA
40.0602is6A0.3786.020.0880.5213.6.4.12NA
50.0602bhrA0.3864.930.0790.4793.4.21.91NA
60.0603ecqB0.3697.830.0390.5973.2.1.97NA
70.0601yksA0.3815.220.0930.4813.4.21.91119,185,187,216
80.0602is4B0.3775.910.0710.5113.6.1.-NA
90.0601ofdA0.3937.760.0430.6231.4.7.1NA
100.0601w36B0.4455.490.0800.5693.1.11.5NA
110.0608ohmA0.3684.760.0790.4552.7.7.48119,185,187,216
120.0603i62A0.4705.590.0840.6123.6.4.1369,95,388,390,392,418
130.0603e90D0.1205.650.0640.1613.4.21.91120,124
140.0602vsfA0.4284.310.1320.5033.6.4.1292,94,214
150.0601oyyA0.4465.110.1070.5573.6.4.1291,94,123,185,411,415,418
160.0602vf4X0.2486.030.0550.3422.6.1.16134
170.0601ea0A0.3837.670.0360.6021.4.1.13NA
180.0601bxrA0.3457.950.0320.5626.3.5.5NA
190.0602wwyA0.4355.620.0990.5723.6.4.12415,418

(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
00.250.6842.230.150.725ivwV GO:0000166 GO:0000439 GO:0000717 GO:0001666 GO:0003677 GO:0003684 GO:0004003 GO:0004386 GO:0004672 GO:0005524 GO:0005525 GO:0005634 GO:0005654 GO:0005675 GO:0006265 GO:0006281 GO:0006283 GO:0006289 GO:0006293 GO:0006294 GO:0006295 GO:0006296 GO:0006351 GO:0006355 GO:0006361 GO:0006362 GO:0006363 GO:0006366 GO:0006367 GO:0006368 GO:0006370 GO:0006468 GO:0006915 GO:0006974 GO:0006979 GO:0008022 GO:0008094 GO:0008104 GO:0008134 GO:0008353 GO:0009411 GO:0009650 GO:0016032 GO:0016787 GO:0016887 GO:0032564 GO:0033683 GO:0035315 GO:0042277 GO:0043065 GO:0043138 GO:0045944 GO:0047485 GO:0048568 GO:0070911 GO:1901990
10.240.6193.710.150.715fmf1 GO:0000019 GO:0000112 GO:0000166 GO:0000439 GO:0000990 GO:0001111 GO:0001113 GO:0003677 GO:0004003 GO:0004386 GO:0005524 GO:0005634 GO:0005675 GO:0005829 GO:0006281 GO:0006289 GO:0006351 GO:0006355 GO:0006366 GO:0006367 GO:0006974 GO:0010525 GO:0015616 GO:0016787 GO:0016973 GO:0032508 GO:0033683 GO:0070816 GO:0097550
20.150.4424.860.130.551wp9A GO:0000166 GO:0003676 GO:0003677 GO:0004386 GO:0004518 GO:0005524 GO:0006259 GO:0006281 GO:0046872 GO:0090305
30.150.4395.670.120.575jbjA GO:0003677 GO:0005524 GO:0016787 GO:0016817
40.070.5155.780.100.674qqwA GO:0000166 GO:0005524 GO:0046872
50.070.5075.940.090.674qqxG GO:0000166 GO:0005524 GO:0046872
60.070.4916.300.090.664q2dA GO:0000166 GO:0005524
70.070.4815.670.120.635jb2A GO:0003677 GO:0005524 GO:0016787 GO:0016817
80.070.4565.310.080.582zj8A GO:0000166 GO:0003676 GO:0003677 GO:0004386 GO:0005524 GO:0006281 GO:0006974 GO:0016787 GO:0016818
90.070.4654.380.140.563h1tA GO:0000166 GO:0003677 GO:0003824 GO:0005524 GO:0006304 GO:0016787
100.060.3035.610.100.391z6aA GO:0004386 GO:0005524
110.060.3113.770.100.362fwrA GO:0000166 GO:0003677 GO:0005524 GO:0016787
120.060.2886.660.030.423k9dA GO:0004029 GO:0008152 GO:0016491 GO:0016620 GO:0055114
130.060.3896.250.080.542eyqA GO:0000166 GO:0000716 GO:0003676 GO:0003677 GO:0003684 GO:0004386 GO:0005524 GO:0005737 GO:0005829 GO:0006281 GO:0006355 GO:0006974 GO:0008026 GO:0015616 GO:0016787 GO:0043175
140.060.2078.380.040.354o1pC GO:0000166 GO:0004540 GO:0004672 GO:0005524 GO:0006397 GO:0006468 GO:0046872 GO:0090501
150.060.2333.620.110.273i32A GO:0000166 GO:0003676 GO:0004386 GO:0005524 GO:0016787
160.060.2017.310.030.311gttA GO:0003824 GO:0008152 GO:0008704 GO:0016829 GO:0016853 GO:0018800 GO:0019439 GO:0046872 GO:1901023
170.060.2003.160.170.223b6eA GO:0000166 GO:0002376 GO:0003677 GO:0003723 GO:0003725 GO:0003727 GO:0004386 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0008270 GO:0009597 GO:0009615 GO:0016032 GO:0016787 GO:0016817 GO:0016925 GO:0032480 GO:0032727 GO:0032728 GO:0034344 GO:0039528 GO:0039530 GO:0043021 GO:0045087 GO:0046872 GO:0051607
180.060.1777.080.060.274g6zA GO:0000049 GO:0000166 GO:0004812 GO:0004818 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006424 GO:0016874 GO:0016876 GO:0043039


Consensus prediction of GO terms
 
Molecular Function GO:0005524 GO:0003677 GO:0032558 GO:0032561 GO:0004674 GO:0033218 GO:0005515 GO:0000988 GO:0004003 GO:0043169 GO:0016788
GO-Score 0.62 0.59 0.50 0.50 0.50 0.50 0.50 0.48 0.43 0.42 0.31
Biological Processes GO:1901987 GO:0007346 GO:0009416 GO:0043068 GO:0006464 GO:0006354 GO:0048513 GO:0042981 GO:0009452 GO:0016310 GO:0044764 GO:0006397 GO:0044772 GO:0030182 GO:0032508 GO:0006360 GO:0044403 GO:0065004 GO:0036293 GO:0006353 GO:0031334 GO:0006357 GO:0009790 GO:0045893 GO:0009913 GO:0000018 GO:0001109 GO:0032197 GO:0001112 GO:0006406 GO:0006312 GO:0010528 GO:0006367 GO:0033683
GO-Score 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.48 0.48 0.48 0.48 0.48 0.48 0.48 0.43 0.43
Cellular Component GO:0032993 GO:0044444 GO:0000109 GO:0000439 GO:0005675
GO-Score 0.48 0.48 0.48 0.43 0.43

(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.