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I-TASSER results for job id Rv1892

[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
10.09 5 3qvdA FE Rep, Mult 31,34,65
20.07 4 2q72A IXX Rep, Mult 16,19,35,36,39
30.04 2 2onk2 III Rep, Mult 18,19,21,22,23,24,25,26,27,28,32,33,35,70,74,75
40.04 2 4ryoA MPG Rep, Mult 37,54,61
50.04 2 3wmmD BCL Rep, Mult 48,54,58
60.02 1 1dxoA DQN Rep, Mult 48,84
70.02 1 3arcX CLA Rep, Mult 67,68,69,72,74
80.02 1 3gjdA BOG Rep, Mult 88,89,91,94
90.02 1 2y30A SM8 Rep, Mult 2,5,20,24,30,38,41,55,58,61,62
100.02 1 2bhwA CLA Rep, Mult 43,45
110.02 1 3rvzA PX4 Rep, Mult 47,48
120.02 1 3oa0B HP7 Rep, Mult 76,77
130.02 1 5hxcA MYC Rep, Mult 34,38,61
140.02 1 2etjA MG Rep, Mult 24,97
150.02 1 4bntD 36E Rep, Mult 51,55
160.02 1 4c72A M7U Rep, Mult 17,73,75
170.02 1 1zyrN STD Rep, Mult 36,39,40,45

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
10.0601jawA0.4724.090.0750.8353.4.11.9NA
20.0601hxgA0.4963.910.0290.8164.2.3.9,4.1.99.7NA
30.0601zumI0.4793.890.0830.7961.2.1.3NA
40.0602j5cB0.5013.880.0580.8254.2.3.-NA
50.0601bucA0.4973.490.0400.7671.3.99.2NA
60.0601g8kE0.5213.790.0470.8061.20.98.15
70.0601rx0A0.4933.430.0210.7381.3.99.-NA
80.0601obrA0.4923.670.0950.7673.4.17.18NA
90.0601ogyI0.5133.430.0720.7961.7.99.442
100.0602gksB0.5053.670.0830.8062.7.7.4,2.7.1.25NA
110.0601ynnJ0.3644.340.0690.6022.7.7.642,46,54
120.0601ynnD0.3364.430.0400.5922.7.7.67,43,51,70,74
130.0601fdiA0.5073.400.0720.7861.2.1.2NA
140.0601bxsA0.4924.650.0630.8741.2.1.36NA
150.0601q50A0.4754.110.0660.8355.3.1.9NA
160.0603cxhN0.4704.420.0500.8351.10.2.2NA
170.0602v45A0.5073.980.0570.8351.7.99.4NA
180.0602ix6A0.4474.130.0520.7091.3.3.6NA
190.0603iydD0.5124.090.0990.8452.7.7.6NA

(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
00.100.5284.060.100.932q6hA GO:0005215 GO:0005328 GO:0005887 GO:0006810 GO:0006836 GO:0015293 GO:0016020 GO:0016021 GO:0055085
10.070.3565.240.060.755i6xA GO:0001666 GO:0005328 GO:0005335 GO:0005768 GO:0005829 GO:0005886 GO:0005887 GO:0006810 GO:0006836 GO:0006837 GO:0007268 GO:0007420 GO:0007584 GO:0007613 GO:0007623 GO:0008504 GO:0009636 GO:0010008 GO:0010033 GO:0010628 GO:0012505 GO:0015222 GO:0015293 GO:0015844 GO:0016020 GO:0016021 GO:0017022 GO:0017075 GO:0017137 GO:0019811 GO:0021794 GO:0021941 GO:0032227 GO:0032355 GO:0035176 GO:0042310 GO:0042493 GO:0042713 GO:0042803 GO:0043005 GO:0045121 GO:0045665 GO:0045787 GO:0046621 GO:0046872 GO:0048854 GO:0050998 GO:0051015 GO:0051259 GO:0051260 GO:0051610 GO:0055085 GO:0071300 GO:0071310 GO:0071321 GO:0098793
20.070.4423.880.100.714us3A GO:0005328 GO:0006810 GO:0006836 GO:0015293 GO:0016020 GO:0016021 GO:0055085
30.070.4923.840.010.774xp9C GO:0005328 GO:0005329 GO:0005330 GO:0005886 GO:0005887 GO:0006810 GO:0006836 GO:0015293 GO:0015872 GO:0016020 GO:0016021 GO:0019811 GO:0030431 GO:0042745 GO:0043005 GO:0046872 GO:0051583 GO:0055085 GO:0072488 GO:0098793 GO:0099509 GO:1990834
40.060.4054.160.010.671o9gA GO:0008168 GO:0008989 GO:0016740 GO:0031167 GO:0032259 GO:0046677
50.060.4464.220.040.785d6eA GO:0004177 GO:0005737 GO:0005829 GO:0005886 GO:0006508 GO:0008233 GO:0008235 GO:0016485 GO:0016787 GO:0018206 GO:0022400 GO:0031365 GO:0044822 GO:0046872 GO:0070006 GO:0070084
60.060.3853.980.040.612omdB GO:0005829 GO:0006777 GO:0016740 GO:0030366 GO:0032324
70.060.4073.660.010.642okcB GO:0003676 GO:0003677 GO:0006306 GO:0008168 GO:0008170 GO:0009007 GO:0009307 GO:0016740 GO:0032259 GO:0032775
80.060.3914.280.100.694ni9C GO:0001781 GO:0001878 GO:0002262 GO:0002384 GO:0002446 GO:0002548 GO:0002675 GO:0002690 GO:0005102 GO:0005125 GO:0005138 GO:0005576 GO:0005615 GO:0005737 GO:0005896 GO:0006469 GO:0006953 GO:0006954 GO:0006955 GO:0006959 GO:0007568 GO:0008083 GO:0008284 GO:0008285 GO:0008360 GO:0009408 GO:0009409 GO:0009611 GO:0009612 GO:0009617 GO:0009897 GO:0010574 GO:0010628 GO:0010888 GO:0010996 GO:0014070 GO:0016049 GO:0019221 GO:0030168 GO:0031000 GO:0031018 GO:0031175 GO:0031667 GO:0032494 GO:0032496 GO:0032722 GO:0032755 GO:0032868 GO:0032966 GO:0033138 GO:0033160 GO:0034097 GO:0035729 GO:0042060 GO:0042102 GO:0042110 GO:0042127 GO:0042493 GO:0042517 GO:0042593 GO:0042832 GO:0042981 GO:0043065 GO:0043066 GO:0043154 GO:0043200 GO:0043410 GO:0045079 GO:0045188 GO:0045429 GO:0045454 GO:0045599 GO:0045630 GO:0045666 GO:0045669 GO:0045721 GO:0045727 GO:0045740 GO:0045765 GO:0045893 GO:0045944 GO:0046427 GO:0046677 GO:0046716 GO:0046849 GO:0046888 GO:0048635 GO:0048661 GO:0050679 GO:0050710 GO:0050731 GO:0050829 GO:0050830 GO:0050871 GO:0051024 GO:0051091 GO:0051092 GO:0051384 GO:0051592 GO:0051602 GO:0051607 GO:0051897 GO:0051971 GO:0060445 GO:0060664 GO:0070091 GO:0070102 GO:0070301 GO:0070374 GO:0071222 GO:0071347 GO:0071356 GO:0071549 GO:0071864 GO:0072540 GO:1901215 GO:2000366 GO:2000676
90.060.3863.170.030.564mybA GO:0008299 GO:0016114 GO:0016740 GO:0016779 GO:0019288 GO:0050518
100.060.3614.710.040.703s8pB GO:0000780 GO:0005634 GO:0005694 GO:0006351 GO:0006355 GO:0007517 GO:0008168 GO:0016568 GO:0016571 GO:0016740 GO:0018024 GO:0032259 GO:0034773 GO:0042799
110.060.4554.230.080.801o0sA GO:0003824 GO:0004470 GO:0004471 GO:0005739 GO:0005759 GO:0006108 GO:0008152 GO:0008948 GO:0016491 GO:0046872 GO:0051287 GO:0055114
120.060.3973.790.030.624xz8A GO:0019013
130.060.3345.350.030.721t8tB GO:0000139 GO:0005794 GO:0006024 GO:0008146 GO:0008467 GO:0016020 GO:0016021 GO:0016740 GO:0033872
140.060.4594.630.070.823abaA GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
150.060.4214.470.010.761cpyA GO:0000324 GO:0004180 GO:0004185 GO:0005773 GO:0006508 GO:0007039 GO:0008233 GO:0016787 GO:0046938 GO:0051603
160.060.3513.800.000.581ijyA GO:0000122 GO:0001525 GO:0001934 GO:0004871 GO:0004888 GO:0004930 GO:0005102 GO:0005576 GO:0005794 GO:0005886 GO:0007165 GO:0007166 GO:0007186 GO:0007275 GO:0016020 GO:0016021 GO:0016055 GO:0017147 GO:0030165 GO:0031625 GO:0033077 GO:0035567 GO:0042813 GO:0043507 GO:0045944 GO:0060070 GO:1990851
170.060.5533.290.090.833s1sA GO:0003676 GO:0003677 GO:0006306 GO:0008168 GO:0008170 GO:0032259 GO:0046872
180.060.3245.120.020.634kl8S GO:0008901 GO:0009375 GO:0016491 GO:0033748 GO:0042597 GO:0046872 GO:0051536 GO:0051539 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0015370 GO:0005326
GO-Score 0.53 0.53
Biological Processes GO:0044765 GO:0044763
GO-Score 0.53 0.53
Cellular Component GO:0031226
GO-Score 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.