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I-TASSER results for job id Rv1828

[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
10.27 14 4r4eB NUC Rep, Mult 14,15,31,34,46,50,51,52
20.08 4 2zhgA NUC Rep, Mult 29,31,32,35,36,69,75,76
30.04 2 3o8oD F6P Rep, Mult 33,34,53,60,63
40.02 1 3gp4A MED Rep, Mult 124,128
50.02 1 1taqA ZN Rep, Mult 3,8,17,20
60.02 1 5ktqA DCP Rep, Mult 80,84,88
70.02 1 2ktqA DCT Rep, Mult 34,36,62,67
80.02 1 1q05A CU1 Rep, Mult 128,141

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
10.0602e1qA0.3526.800.0580.6801.17.3.2,1.17.1.4NA
20.0601bxrA0.4216.380.0530.7616.3.5.530
30.0601h19A0.4125.970.0400.6883.3.2.6NA
40.0601n2cB0.3326.290.0690.5911.18.6.1NA
50.0601y11A0.4145.150.0640.6194.6.1.1NA
60.0601hrdA0.3486.370.0450.6191.4.1.222,56,77
70.0602r8oB0.4015.890.0650.6682.2.1.1NA
80.0601itzB0.3396.450.0670.6272.2.1.1NA
90.0602g25A0.3095.790.0770.5301.2.4.1NA
100.0602gtqA0.4166.050.0670.7253.4.11.2NA
110.0601bgxT0.4246.270.0620.7612.7.7.7149
120.0603ebgA0.4186.230.0500.7373.4.11.-NA
130.0603b9jJ0.2886.130.0380.5061.17.1.4,1.17.3.238
140.0602amoA0.3836.150.0570.6641.14.13.39NA
150.0602p8uA0.4006.270.0650.7252.3.3.1057
160.0601l8aA0.3665.810.0720.6111.2.4.1NA
170.0602ckjA0.3126.620.0180.5951.17.1.4,1.17.3.2NA
180.0602v4wD0.4006.150.0510.7132.3.3.10221
190.0601fp4B0.3326.390.0450.6031.18.6.1NA

(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
00.240.7412.020.150.822dg6A GO:0003677 GO:0006355
10.070.3716.030.070.664av6A GO:0000287 GO:0004427 GO:0005509 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006814 GO:0009678 GO:0015081 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030955 GO:0035725 GO:0042803 GO:0046872
20.060.4426.350.050.794av3B GO:0000287 GO:0004427 GO:0005509 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006814 GO:0009678 GO:0015081 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030955 GO:0035725 GO:0042803 GO:0046872
30.060.4575.680.060.762cse1 GO:0000166 GO:0001172 GO:0003723 GO:0003968 GO:0016740 GO:0016779 GO:0019012 GO:0019013 GO:0019028 GO:0019079 GO:0032774
40.060.4565.990.040.774a01A GO:0004427 GO:0005773 GO:0005774 GO:0006810 GO:0006811 GO:0009678 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0046872 GO:0055085
50.060.4155.650.050.663r3jA GO:0004354 GO:0006520 GO:0006537 GO:0016491 GO:0016639 GO:0020011 GO:0055114
60.060.3603.400.170.453gp4A GO:0003677 GO:0006355
70.060.3566.060.050.634zchA GO:0002376 GO:0005102 GO:0005125 GO:0005164 GO:0005576 GO:0005615 GO:0005654 GO:0005737 GO:0005829 GO:0005886 GO:0006955 GO:0007165 GO:0008283 GO:0008284 GO:0016020 GO:0016021 GO:0030890 GO:0033209 GO:0043488 GO:0048298 GO:0048471 GO:0070062
80.060.3276.140.040.573lstA GO:0008168 GO:0008171 GO:0032259
90.060.3935.820.080.644bhtA GO:0004354 GO:0005737 GO:0005829 GO:0006520 GO:0006537 GO:0016491 GO:0016639 GO:0042802 GO:0055114
100.060.3466.560.060.642wbeC GO:0000166 GO:0000278 GO:0000922 GO:0001578 GO:0003774 GO:0003777 GO:0005524 GO:0005634 GO:0005737 GO:0005783 GO:0005794 GO:0005813 GO:0005818 GO:0005819 GO:0005856 GO:0005871 GO:0005873 GO:0005874 GO:0005875 GO:0007018 GO:0007030 GO:0007049 GO:0007052 GO:0007059 GO:0007067 GO:0007100 GO:0008017 GO:0008574 GO:0009306 GO:0022008 GO:0031535 GO:0042998 GO:0045169 GO:0045478 GO:0048085 GO:0051289 GO:0051298 GO:0051299 GO:0051301 GO:0072686 GO:0090307 GO:0097431 GO:1990498
110.060.3016.310.040.551ainA GO:0000733 GO:0001533 GO:0001780 GO:0001891 GO:0002250 GO:0002376 GO:0002548 GO:0002685 GO:0003697 GO:0003727 GO:0004386 GO:0004859 GO:0005102 GO:0005198 GO:0005509 GO:0005543 GO:0005544 GO:0005576 GO:0005615 GO:0005634 GO:0005654 GO:0005737 GO:0005768 GO:0005769 GO:0005886 GO:0005913 GO:0005925 GO:0005929 GO:0006909 GO:0006954 GO:0007165 GO:0007166 GO:0007187 GO:0008360 GO:0009725 GO:0009986 GO:0010008 GO:0010165 GO:0014070 GO:0014839 GO:0016020 GO:0016023 GO:0016323 GO:0016324 GO:0016328 GO:0018149 GO:0019834 GO:0019898 GO:0030073 GO:0030216 GO:0030659 GO:0030674 GO:0030850 GO:0031018 GO:0031232 GO:0031313 GO:0031340 GO:0031394 GO:0031410 GO:0031514 GO:0031532 GO:0031901 GO:0031960 GO:0031966 GO:0031982 GO:0032355 GO:0032508 GO:0032652 GO:0032743 GO:0033031 GO:0033676 GO:0036292 GO:0036310 GO:0042063 GO:0042102 GO:0042127 GO:0042383 GO:0042493 GO:0042629 GO:0042803 GO:0042995 GO:0043065 GO:0043066 GO:0043234 GO:0043434 GO:0044849 GO:0045087 GO:0045627 GO:0045629 GO:0045920 GO:0046632 GO:0046872 GO:0046883 GO:0048306 GO:0050482 GO:0050709 GO:0050727 GO:0051384 GO:0070062 GO:0070301 GO:0070365 GO:0070459 GO:0070555 GO:0071385 GO:0071621 GO:0090303 GO:0097350 GO:0098641 GO:1900087 GO:1900138 GO:2000483
120.060.3125.590.060.492qtqA GO:0003677 GO:0006351 GO:0006355
130.060.3285.470.040.534kzxB GO:0003735 GO:0005622 GO:0005634 GO:0005737 GO:0005840 GO:0006412 GO:0022627 GO:0030154 GO:0030529
140.060.3162.580.180.364wlwA GO:0000986 GO:0001131 GO:0001204 GO:0003677 GO:0003700 GO:0005507 GO:0005737 GO:0006351 GO:0006355 GO:0045893 GO:0046872 GO:0071248
150.060.3043.010.100.354ua1B GO:0003677 GO:0006355 GO:0045340 GO:0046689
160.060.2924.530.040.413k3cA GO:0000155 GO:0000160 GO:0000287 GO:0003824 GO:0004035 GO:0005622 GO:0006355 GO:0016311 GO:0016791 GO:0023014 GO:0030145
170.060.3035.570.050.501p2fA GO:0000160 GO:0003677 GO:0005622 GO:0006351 GO:0006355 GO:0046872
180.060.2776.390.030.494qrzA GO:0005215 GO:0006810


Consensus prediction of GO terms
 
Molecular Function GO:0003676 GO:0015405 GO:0016462 GO:0043169
GO-Score 0.48 0.36 0.36 0.36
Biological Processes GO:0010468 GO:2000112 GO:1903506 GO:0006351 GO:0006818 GO:0015672
GO-Score 0.48 0.48 0.48 0.48 0.36 0.36
Cellular Component GO:0005887 GO:0019013 GO:0005774
GO-Score 0.13 0.07 0.06

(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.