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I-TASSER results for job id Rv1075c

[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
10.30 6 3dt9A GD7 Rep, Mult 79,80,118,119,148,149,246,247
20.09 2 1u8uA OCA Rep, Mult 79,80,148,149,184,186,247
30.08 2 1gz7A GOL Rep, Mult 149,154,156
40.04 1 1u65A UUU Rep, Mult 142,171,172
50.04 1 1gz7A GOL Rep, Mult 95,256,259,260,263

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
10.4141vyhA0.5353.190.1540.6273.1.1.4780,119,149,244,247
20.1892q0sH0.4972.510.1680.5543.1.1.2149,247
30.1611vyhN0.5353.190.1540.6273.1.1.47121,149
40.1071ivnA0.5192.130.1850.5673.1.1.5,80,119,149,244,247
50.0811bwpA0.5223.090.1440.6083.1.1.4780,119,149,244,247
60.0771deoA0.4923.620.1810.5963.1.1.-80,119,149,244,247
70.0602o14A0.5434.710.1070.7073.1.-.-124
80.0603enkA0.4784.210.1030.6125.1.3.2NA
90.0601z45A0.4804.410.0730.6185.1.3.2,5.1.3.3202
100.0601mx9D0.5265.500.0410.7743.1.1.1NA
110.0602pffA0.4794.780.0830.6692.3.1.41,2.3.1.86NA
120.0601gy8C0.4834.620.0850.6375.1.3.2NA
130.0601lpsA0.5585.320.0580.8063.1.1.3NA
140.0603kvnX0.5533.810.1650.6723.1.1.1185,229,248,255
150.0602vptA0.5132.400.2000.5733.1.1.72247
160.0601wvgA0.4884.450.0660.6404.2.1.45NA
170.0603eifA0.4935.540.0720.7393.4.21.110NA
180.0601ga1A0.4765.420.0690.7043.4.21.100,3.4.23.37NA
190.0601cleA0.5605.450.0540.8153.1.1.3NA
200.0601gz7C0.5655.200.0700.8063.1.1.3178,264
210.0601rkxC0.4874.610.0710.6404.2.1.45NA
220.0603f98A0.4925.500.0350.7233.1.1.47170,172,224

(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
00.380.5541.270.220.574jggA GO:0004064 GO:0004622 GO:0005576 GO:0016787 GO:0052689
10.350.5192.130.180.571ivnA GO:0004620 GO:0004622 GO:0006508 GO:0006629 GO:0008233 GO:0016290 GO:0016298 GO:0016787 GO:0030288 GO:0042597 GO:0042802 GO:0047617
20.330.5272.200.190.583hp4A
30.310.5213.030.200.601yzfA GO:0016787
40.290.5163.030.130.604hf7A GO:0016787
50.290.5122.370.150.573x0hA GO:0004553 GO:0005576 GO:0005975 GO:0030248
60.280.5173.160.150.604jhlA GO:0000272 GO:0005737 GO:0005975 GO:0016787 GO:0045493 GO:0046555 GO:0052689
70.260.5012.990.200.573rjtA
80.240.5243.220.130.614ppyA GO:0016787
90.210.4942.260.150.544rshA GO:0016020 GO:0016021
100.210.5685.270.070.811gz7A GO:0004806 GO:0006629 GO:0016042 GO:0016787
110.190.4993.210.130.583p94A
120.170.5423.830.150.662waaA GO:0000272 GO:0005886 GO:0005975 GO:0008152 GO:0016020 GO:0016787 GO:0016798 GO:0045493 GO:0046555 GO:2000884
130.160.5082.640.170.574tx1A GO:0004064 GO:0016787
140.160.5163.240.110.603milA GO:0006083 GO:0006629 GO:0016042 GO:0016787 GO:0016788
150.140.5212.980.160.611z8hA
160.140.5365.320.070.773o9mA GO:0001540 GO:0003824 GO:0003990 GO:0004104 GO:0005576 GO:0005615 GO:0005641 GO:0005783 GO:0005788 GO:0007584 GO:0007612 GO:0008285 GO:0014016 GO:0016020 GO:0016787 GO:0016788 GO:0019695 GO:0019899 GO:0033265 GO:0042493 GO:0042802 GO:0043279 GO:0050783 GO:0050805 GO:0051384 GO:0051593 GO:0052689 GO:0072562
170.070.5605.450.050.821cleA GO:0004806 GO:0006629 GO:0008202 GO:0008203 GO:0016042 GO:0016787
180.070.5605.300.060.811crlA GO:0004806 GO:0006629 GO:0016042 GO:0016787
190.070.5615.530.060.821thgA GO:0004806 GO:0005576 GO:0006629 GO:0016042 GO:0016787
200.070.5555.450.070.814be4A GO:0016787
210.070.5554.100.150.682wabA GO:0000272 GO:0003824 GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798 GO:0030245 GO:0030248 GO:0045493 GO:0046555 GO:0046872 GO:2000884
220.070.5425.240.060.781eveA GO:0001507 GO:0003990 GO:0004104 GO:0005886 GO:0016020 GO:0016787 GO:0030054 GO:0031225 GO:0042135 GO:0043083 GO:0045202 GO:0052689
230.070.5305.670.060.791ukcA GO:0016787
240.070.5395.320.090.784bdtA GO:0001507 GO:0001540 GO:0001919 GO:0002076 GO:0003990 GO:0004104 GO:0005518 GO:0005576 GO:0005605 GO:0005615 GO:0005634 GO:0005794 GO:0005886 GO:0006260 GO:0006581 GO:0006656 GO:0007155 GO:0007399 GO:0007416 GO:0007517 GO:0008283 GO:0009611 GO:0009986 GO:0016020 GO:0016787 GO:0017171 GO:0030054 GO:0031225 GO:0031594 GO:0031623 GO:0032223 GO:0042135 GO:0042136 GO:0042166 GO:0042803 GO:0042982 GO:0043083 GO:0043236 GO:0043621 GO:0045202 GO:0045212 GO:0048471 GO:0050714 GO:0051262 GO:0052689 GO:0060041
250.070.5265.550.040.783k9bB GO:0005615 GO:0005783 GO:0005788 GO:0006805 GO:0008152 GO:0009636 GO:0016787 GO:0030855 GO:0047374 GO:0052689
260.070.5305.550.070.783vkfA GO:0002087 GO:0004872 GO:0005615 GO:0005794 GO:0005829 GO:0005886 GO:0005887 GO:0006605 GO:0007155 GO:0007157 GO:0007158 GO:0007399 GO:0007416 GO:0009897 GO:0009986 GO:0010841 GO:0014069 GO:0016020 GO:0016021 GO:0016080 GO:0016339 GO:0017146 GO:0030054 GO:0030165 GO:0030425 GO:0031175 GO:0032230 GO:0032433 GO:0035418 GO:0042043 GO:0043197 GO:0043198 GO:0045161 GO:0045184 GO:0045202 GO:0045211 GO:0045664 GO:0046983 GO:0048489 GO:0048511 GO:0048789 GO:0050804 GO:0050808 GO:0050839 GO:0051260 GO:0051290 GO:0051491 GO:0051965 GO:0051968 GO:0052689 GO:0060076 GO:0060080 GO:0060291 GO:0060999 GO:0061002 GO:0072553 GO:0097091 GO:0097104 GO:0097105 GO:0097110 GO:0097113 GO:0097114 GO:0097115 GO:0097119 GO:0097120 GO:0098793 GO:1900029 GO:1900244 GO:1902474 GO:1902533 GO:2000302 GO:2000310 GO:2000311 GO:2000463 GO:2000809
270.070.5375.310.060.781qo9A GO:0001507 GO:0003990 GO:0004104 GO:0005615 GO:0005737 GO:0005886 GO:0006581 GO:0007268 GO:0016020 GO:0016787 GO:0030054 GO:0031225 GO:0042135 GO:0042331 GO:0042426 GO:0042803 GO:0043083 GO:0045202 GO:0052689
280.070.5275.540.060.783bixA GO:0002087 GO:0004872 GO:0005615 GO:0005794 GO:0005829 GO:0005886 GO:0005887 GO:0006605 GO:0007155 GO:0007157 GO:0007158 GO:0007399 GO:0007416 GO:0009897 GO:0009986 GO:0010841 GO:0014069 GO:0016020 GO:0016021 GO:0016080 GO:0016339 GO:0017146 GO:0030054 GO:0030165 GO:0030425 GO:0031175 GO:0032230 GO:0032433 GO:0035418 GO:0042043 GO:0043197 GO:0043198 GO:0045161 GO:0045184 GO:0045202 GO:0045211 GO:0045664 GO:0046983 GO:0048489 GO:0048511 GO:0048789 GO:0050804 GO:0050808 GO:0050839 GO:0051260 GO:0051290 GO:0051491 GO:0051965 GO:0051968 GO:0052689 GO:0060076 GO:0060080 GO:0060291 GO:0060999 GO:0061002 GO:0072553 GO:0097091 GO:0097104 GO:0097105 GO:0097110 GO:0097113 GO:0097114 GO:0097115 GO:0097119 GO:0097120 GO:0098793 GO:1900029 GO:1900244 GO:1902474 GO:1902533 GO:2000302 GO:2000310 GO:2000311 GO:2000463 GO:2000809
290.070.5265.530.060.782wqzA GO:0003360 GO:0004872 GO:0005615 GO:0005886 GO:0005887 GO:0007155 GO:0007158 GO:0007612 GO:0009986 GO:0014069 GO:0016020 GO:0016021 GO:0021549 GO:0030054 GO:0030182 GO:0030425 GO:0030534 GO:0031404 GO:0035176 GO:0035265 GO:0042043 GO:0042803 GO:0045202 GO:0045211 GO:0045216 GO:0050808 GO:0050839 GO:0052689 GO:0060076 GO:0071625 GO:0090394 GO:0097105 GO:0097110
300.070.5375.510.060.791f6wA GO:0003824 GO:0004771 GO:0004806 GO:0004872 GO:0005576 GO:0005615 GO:0005737 GO:0005887 GO:0006629 GO:0006641 GO:0006707 GO:0007158 GO:0007416 GO:0008201 GO:0009062 GO:0009986 GO:0016042 GO:0016787 GO:0018350 GO:0030157 GO:0030299 GO:0042043 GO:0044241 GO:0044258 GO:0045202 GO:0047372 GO:0050804 GO:0052689 GO:0070062
310.070.5215.700.080.793biwA GO:0002087 GO:0004872 GO:0005615 GO:0005794 GO:0005829 GO:0005886 GO:0005887 GO:0006605 GO:0007155 GO:0007157 GO:0007158 GO:0007399 GO:0007416 GO:0009897 GO:0009986 GO:0010841 GO:0014069 GO:0016020 GO:0016021 GO:0016080 GO:0016339 GO:0017146 GO:0030054 GO:0030165 GO:0030425 GO:0031175 GO:0032230 GO:0032433 GO:0035418 GO:0042043 GO:0043197 GO:0043198 GO:0045161 GO:0045184 GO:0045202 GO:0045211 GO:0045664 GO:0046983 GO:0048489 GO:0048511 GO:0048789 GO:0050804 GO:0050808 GO:0050839 GO:0051260 GO:0051290 GO:0051491 GO:0051965 GO:0051968 GO:0052689 GO:0060076 GO:0060080 GO:0060291 GO:0060999 GO:0061002 GO:0072553 GO:0097091 GO:0097104 GO:0097105 GO:0097110 GO:0097113 GO:0097114 GO:0097115 GO:0097119 GO:0097120 GO:0098793 GO:1900029 GO:1900244 GO:1902474 GO:1902533 GO:2000302 GO:2000310 GO:2000311 GO:2000463 GO:2000809
320.070.5365.540.050.804fnmA GO:0016787


Consensus prediction of GO terms
 
Molecular Function GO:0004622 GO:0004064 GO:0008233 GO:0016290 GO:0042802
GO-Score 0.59 0.38 0.35 0.35 0.35
Biological Processes GO:0006508 GO:0006629
GO-Score 0.35 0.35
Cellular Component GO:0005576 GO:0030288
GO-Score 0.38 0.35

(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.