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I-TASSER results for job id Rv0518

[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
10.35 9 3dt9A GD7 Rep, Mult 45,46,86,87,119,120,207,208
20.23 6 1u8uA OCA Rep, Mult 45,46,87,119,120,158,160,208
30.05 2 1v2gA IMD Rep, Mult 69,77,78,226,229
40.03 1 3dc7B NA Rep, Mult 44,45,47,48,116
50.02 1 3i26D UUU Rep, Mult 161,163,173,176,186,188
60.02 1 3x0hA BOG Rep, Mult 50,120,203,208
70.02 1 1v2gA IMD Rep, Mult 66,80,222,225

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
10.3172q0sH0.6802.620.2150.7833.1.1.283,120,208
20.1181ivnA0.6952.000.1690.7713.1.1.5,46,87,120,205,208
30.1141uqrK0.4503.720.0880.5934.2.1.10NA
40.0671h0rA0.4583.340.0820.5674.2.1.10NA
50.0661gqoB0.4523.390.0750.5674.2.1.10NA
60.0661d0iH0.4723.660.0770.6154.2.1.10NA
70.0662uygL0.4563.190.1210.5634.2.1.10NA
80.0662uygA0.4563.290.1210.5634.2.1.10NA
90.0662c4wA0.4813.510.0740.6194.2.1.10120,198
100.0663lwzA0.4593.370.0590.5844.2.1.10NA
110.0661uqrD0.4653.230.0810.5844.2.1.10NA
120.0602pd6D0.5514.130.1030.7401.1.1.62,1.1.1.63NA
130.0601h5qF0.5504.170.0670.7401.1.1.13844
140.0601pp4A0.6283.360.1670.7713.1.1.-87
150.0601flcC0.5634.000.0900.7363.1.1.53183,231
160.0602b4qA0.5514.020.0740.7321.1.1.100NA
170.0603gr6D0.5604.060.0770.7491.3.1.9NA
180.0601vyhN0.6422.460.1370.7403.1.1.47120
190.0601vyhA0.6422.450.1370.7403.1.1.4746,87,120,205,208
200.0601deoA0.6273.360.1670.7713.1.1.-46,87,120,205,208
210.0601bwpA0.6372.550.1280.7363.1.1.4746,87,120,205,208
220.0602vz8B0.5624.490.0810.7922.3.1.85116
230.0602jfdA0.3666.130.0650.6542.3.1.85101
240.0601uzmB0.5393.920.0920.7191.1.1.100NA
250.0601uznA0.5543.900.0910.7361.1.1.100NA
260.0601gegE0.5603.840.0990.7321.1.1.5NA
270.0602vz8A0.5494.390.0790.7622.3.1.85116
280.0603kvnX0.6533.190.1740.8013.1.1.1207,209
290.0601escA0.6972.690.2220.8183.1.1.-NA

(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
00.370.6952.000.170.771ivnA GO:0004620 GO:0004622 GO:0006508 GO:0006629 GO:0008233 GO:0016290 GO:0016298 GO:0016787 GO:0030288 GO:0042597 GO:0042802 GO:0047617
10.350.7401.350.230.784jggA GO:0004064 GO:0004622 GO:0005576 GO:0016787 GO:0052689
20.330.7193.420.190.894k3uA GO:0016787
30.310.6522.270.170.744rshA GO:0016020 GO:0016021
40.290.6872.640.200.801yzfA GO:0016787
50.290.6762.790.210.804tx1A GO:0004064 GO:0016787
60.270.6862.890.190.814jhlA GO:0000272 GO:0005737 GO:0005975 GO:0016787 GO:0045493 GO:0046555 GO:0052689
70.270.6872.390.180.783x0hA GO:0004553 GO:0005576 GO:0005975 GO:0030248
80.260.7112.050.140.793hp4A
90.250.6692.660.170.773rjtA
100.200.6332.600.150.744hf7A GO:0016787
110.180.6392.540.170.744ppyA GO:0016787
120.170.6202.640.140.723p94A
130.130.5743.050.080.695cd9A GO:0005938 GO:0007275 GO:0007277 GO:0007278 GO:0007279 GO:0007281 GO:0007314 GO:0007315 GO:0007318 GO:0007359 GO:0007616 GO:0007632 GO:0008103 GO:0008542 GO:0008595 GO:0019094 GO:0030719 GO:0035282 GO:0040040 GO:0043186 GO:0043488 GO:0045495 GO:0045727 GO:0046011 GO:0046594 GO:0048477
140.130.6762.810.170.801z8hA
150.100.6573.150.160.793milA GO:0006083 GO:0006629 GO:0016042 GO:0016787 GO:0016788
160.080.6262.470.120.722hsjD
170.070.4575.280.050.721r30B GO:0003824 GO:0004076 GO:0005506 GO:0009102 GO:0016740 GO:0046872 GO:0051536 GO:0051537 GO:0051539
180.070.4345.000.060.673e38B GO:0003677 GO:0003824 GO:0003887 GO:0006260 GO:0046872 GO:0071897
190.060.4404.530.050.652g0tB
200.060.2906.060.030.513uonA GO:0003796 GO:0003824 GO:0004871 GO:0004930 GO:0005886 GO:0005887 GO:0006940 GO:0007165 GO:0007186 GO:0007187 GO:0007188 GO:0007197 GO:0007207 GO:0007213 GO:0007271 GO:0007399 GO:0008016 GO:0008144 GO:0008152 GO:0009253 GO:0009615 GO:0016020 GO:0016021 GO:0016787 GO:0016798 GO:0016907 GO:0016998 GO:0019076 GO:0019835 GO:0030054 GO:0030425 GO:0030430 GO:0032279 GO:0032280 GO:0042742 GO:0043025 GO:0043679 GO:0045202 GO:0045211
210.060.3915.200.070.624axsA GO:0006525 GO:0008804 GO:0016301 GO:0016310 GO:0016740
220.060.2875.980.070.503rzeA GO:0003796 GO:0003824 GO:0004871 GO:0004930 GO:0004969 GO:0005654 GO:0005737 GO:0005886 GO:0005887 GO:0006954 GO:0007165 GO:0007186 GO:0007200 GO:0007613 GO:0008152 GO:0008542 GO:0009253 GO:0016020 GO:0016021 GO:0016787 GO:0016798 GO:0016998 GO:0019076 GO:0019229 GO:0019835 GO:0030430 GO:0032962 GO:0042742 GO:0043114 GO:0045907 GO:0048016 GO:0048167 GO:0048245 GO:0050804 GO:0071420


Consensus prediction of GO terms
 
Molecular Function GO:0004622 GO:0042802 GO:0016290 GO:0008233 GO:0004064
GO-Score 0.59 0.36 0.36 0.36 0.35
Biological Processes GO:0006508 GO:0006629
GO-Score 0.36 0.36
Cellular Component GO:0030288 GO:0005576 GO:0016021
GO-Score 0.36 0.35 0.31

(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.