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I-TASSER results for job id Rv0540

[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 3 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
10.19 6 1w55A C Rep, Mult 11,12,13,59,87,88,89,90,93,112,113,191
20.12 4 3st8A MG Rep, Mult 113,193
30.06 2 2y6pA CTP Rep, Mult 11,12,13,20,23,88,89,90,93,113,193
40.04 1 3cgxA IMD Rep, Mult 21,37,113
50.03 1 2ycmA 30A Rep, Mult 90,91,110,135,136,147,161,183
60.03 1 1yp2A PMB Rep, Mult 8,10,109,110,111,147
70.03 1 4y7uA MG Rep, Mult 23,191,193

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
10.3871wvcA0.6304.260.0910.8822.7.7.3323
20.3781i52A0.6383.890.1840.8502.7.7.60,2.7.7.-23
30.3621vpaA0.6583.670.0900.8502.7.7.6023
40.1101hm8A0.6564.110.1200.8912.7.7.2323
50.0973dk5A0.6934.010.1500.9232.3.1.15723
60.0823jtjA0.6304.050.1550.8322.7.7.3823
70.0782px7A0.6103.370.1990.7732.7.7.6045,47
80.0671eziA0.5893.840.1000.7732.7.7.43114,191
90.0671qwjB0.6003.830.1210.7772.7.7.43114,191
100.0671vicA0.6294.140.1220.8412.7.7.38NA
110.0672j0aA0.5974.200.0750.8462.4.1.222143
120.0662d0jC0.5733.770.0630.7772.4.1.135NA
130.0662d0jA0.5743.770.0790.7772.4.1.135NA
140.0651mc3A0.6154.440.0890.8682.7.7.2424
150.0602yqjA0.6753.990.0910.9232.7.7.2312,22,24,146
160.0603k8dA0.6303.740.1700.8232.7.7.3823
170.0603hl3A0.6453.890.0860.8642.7.7.2423
180.0602ggoA0.6544.020.0960.8862.7.7.2423
190.0601h7tA0.6424.110.1360.8552.7.7.38190,193
200.0601jv3A0.6684.030.0870.9092.7.7.2312,62,85,87
210.0603f1cB0.6563.560.1110.8412.7.7.6012,118,143,197
220.0602ux8A0.6174.260.0660.8552.7.7.923
230.0602oefA0.6304.540.1230.9092.7.7.9NA
240.0601ll0B0.6104.000.0850.8362.4.1.186187
250.0602pa4B0.6694.080.1350.9142.7.7.923
260.0602vsiB0.6363.630.1410.8232.7.7.60NA
270.0601h7eA0.6424.110.1310.8552.7.7.38NA
280.0602oi6B0.6904.050.1120.9182.3.1.157,2.7.7.23NA
290.0601vgwB0.6343.370.1240.8042.7.7.60188

(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
00.320.7662.110.140.862i5eA GO:0000166 GO:0005525 GO:0009108 GO:0016740 GO:0016779 GO:0043814
10.250.6313.950.140.852wawA
20.160.5913.630.110.761e5kA GO:0000166 GO:0000287 GO:0003824 GO:0005525 GO:0005737 GO:0006777 GO:0016740 GO:0019720 GO:0046872 GO:0061603 GO:0070568 GO:1902758
30.120.6934.010.150.923dk5A GO:0000287 GO:0000902 GO:0003824 GO:0003977 GO:0005737 GO:0006048 GO:0008152 GO:0008360 GO:0009103 GO:0009245 GO:0009252 GO:0016740 GO:0016746 GO:0016779 GO:0019134 GO:0046872 GO:0071555
40.110.6634.030.090.903fwwA GO:0000287 GO:0000902 GO:0003824 GO:0003977 GO:0005737 GO:0006048 GO:0008152 GO:0008360 GO:0009103 GO:0009245 GO:0009252 GO:0016740 GO:0016746 GO:0016779 GO:0019134 GO:0046872 GO:0071555
50.110.7044.030.140.953d8vA GO:0000287 GO:0000902 GO:0003824 GO:0003977 GO:0005737 GO:0006048 GO:0008152 GO:0008360 GO:0009103 GO:0009245 GO:0009252 GO:0016740 GO:0016746 GO:0016779 GO:0019134 GO:0040007 GO:0046872 GO:0070569 GO:0071555
60.110.6904.050.110.922oi6B GO:0000287 GO:0000902 GO:0003824 GO:0003977 GO:0005737 GO:0005829 GO:0006048 GO:0008152 GO:0008360 GO:0009103 GO:0009245 GO:0009252 GO:0016740 GO:0016746 GO:0016779 GO:0019134 GO:0042802 GO:0046872 GO:0071555
70.100.6694.080.140.912pa4B GO:0003983 GO:0009058 GO:0016740 GO:0016779
80.100.6634.020.100.904e1kA GO:0000287 GO:0000902 GO:0003824 GO:0003977 GO:0005737 GO:0006048 GO:0008152 GO:0008360 GO:0009103 GO:0009245 GO:0009252 GO:0016740 GO:0016746 GO:0016779 GO:0019134 GO:0046872 GO:0071555
90.100.6463.720.150.854zdqA GO:0003824 GO:0008299 GO:0016114 GO:0016740 GO:0016779 GO:0019288 GO:0050518
100.100.6463.800.160.852xwlB GO:0000166 GO:0003824 GO:0008299 GO:0016114 GO:0016740 GO:0016779 GO:0019288 GO:0050518
110.090.6763.970.100.934bqhA GO:0003977 GO:0005829 GO:0006011 GO:0006048 GO:0008152 GO:0016740 GO:0016779 GO:0070569
120.090.6583.670.090.851vpaA GO:0003824 GO:0008299 GO:0016114 GO:0016740 GO:0016779 GO:0019288 GO:0050518
130.090.6383.890.180.851i52A GO:0000287 GO:0003824 GO:0005829 GO:0008299 GO:0016114 GO:0016740 GO:0016779 GO:0019288 GO:0042802 GO:0050518
140.090.6783.970.100.922yqcA GO:0003977 GO:0005737 GO:0006048 GO:0008152 GO:0016740 GO:0016779 GO:0070569
150.090.6513.930.090.895idsA GO:0008879 GO:0009058 GO:0016740 GO:0016779 GO:0045226 GO:0046872
160.090.6223.830.150.822we9B GO:0046872
170.080.6033.200.120.752e8bA GO:0000166 GO:0003824 GO:0005525 GO:0005737 GO:0006777 GO:0016740 GO:0019720 GO:0046872 GO:0061603 GO:0070568
180.080.6313.610.130.823tqdA GO:0005737 GO:0005829 GO:0008690 GO:0009103 GO:0016740 GO:0016779 GO:0019294 GO:0033468
190.080.6544.020.100.892ggoA GO:0000166 GO:0003977 GO:0009058 GO:0016740 GO:0016779 GO:0019134
200.080.6564.110.120.891hm8A GO:0000287 GO:0000902 GO:0003824 GO:0003977 GO:0005737 GO:0006048 GO:0008152 GO:0008360 GO:0009058 GO:0009103 GO:0009245 GO:0009252 GO:0016740 GO:0016746 GO:0016779 GO:0019134 GO:0046872 GO:0071555
210.070.6174.260.070.852ux8A GO:0003983 GO:0006011 GO:0009058 GO:0016740 GO:0016779
220.070.6524.020.090.894jd0A GO:0009058 GO:0016740 GO:0016779
230.070.6224.370.100.882ux8G GO:0003983 GO:0006011 GO:0009058 GO:0016740 GO:0016779
240.070.5543.680.150.713d5nA


Consensus prediction of GO terms
 
Molecular Function GO:0070569 GO:0008080 GO:0005525 GO:0000287 GO:0043814
GO-Score 0.44 0.44 0.43 0.35 0.32
Biological Processes GO:1901271 GO:0000270 GO:0006024 GO:0008654 GO:0009226 GO:0046349 GO:0008653 GO:0006047 GO:0046493 GO:0022604 GO:0009247 GO:0045229 GO:0009273 GO:0044038 GO:0065008 GO:0033692 GO:1902757 GO:0009165 GO:0009108
GO-Score 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.33 0.33 0.32
Cellular Component GO:0005737
GO-Score 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.