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I-TASSER results for job id Rv2798c

[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
10.25 77 2htnA HEM Rep, Mult 17,20,21,24,61,65,68,69,71,72
20.07 23 4ismA ZN Rep, Mult 16,67,70
30.05 18 2yjjI OFE Rep, Mult 31,34,50,54
40.04 16 2y02A 2CV Rep, Mult 27,30,53,57,60
50.04 16 2h7hA NUC Rep, Mult 49,50,53,54,56,61
60.03 9 1hjbA NUC Rep, Mult 52,53,56,57,59,60,63
70.03 9 3hahA CA Rep, Mult 37,38,40,42,46
80.03 12 1w5cB CLA Rep, Mult 9,74,77,80,81,84
90.02 6 1nf4G FEC Rep, Mult 20,27,28,31,35,54,61,65
100.02 8 3qblD 22B Rep, Mult 19,23,59,63,66,67,70
110.00 1 2frdB NAP Rep, Mult 5,8
120.00 1 4m1mA HG Rep, Mult 16,17,71
130.00 1 1h2aL F3S Rep, Mult 33,38
140.00 1 1i4d1 III Rep, Mult 21,24,27,28,31,32,34,35,36,38,39,54,57,61,64,65
150.00 2 1jccA ZN Rep, Mult 45,54

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
10.2542h8nA0.4731.570.0880.5183.5.1.9881,83,87
20.2071wt6B0.4681.740.1340.5182.7.11.185
30.1681cxzB0.5352.300.0410.6762.7.11.1321
40.1551urfA0.5382.400.1050.6762.7.11.1319,67
50.0661wu0A0.4802.680.1130.6483.6.3.14NA
60.0601mo7A0.2814.660.0590.5093.6.3.9NA
70.0602dq3A0.6003.600.0470.8986.1.1.1140
80.0603lssB0.6472.660.0580.8066.1.1.1143
90.0601ukwA0.5642.790.0480.7041.3.99.3NA
100.0601u7lA0.6133.060.0560.8803.6.3.14NA
110.0601dcnB0.5333.710.0650.8434.3.2.1NA
120.0601w27A0.5913.430.0490.8984.3.1.24NA
130.0602o6yA0.5013.300.0410.7044.3.1.-NA
140.0602iw5A0.6602.520.0890.8331.-.-.-NA
150.0602b5uA0.6832.540.0490.8803.1.-.-NA
160.0602ohyB0.5443.250.0770.7875.4.3.6NA
170.0601z0hB0.3214.800.0470.6483.4.24.69NA
180.0603b8eC0.5713.860.0750.9263.6.3.972
190.0601c3cA0.6002.850.0500.7684.3.2.2NA
200.0602e9fB0.6252.680.0690.7964.3.2.1NA
210.0603b8cB0.5633.810.0380.8333.6.3.6NA
220.0603b8eA0.5534.280.0760.9353.6.3.9NA
230.0601jswB0.5592.770.0480.7594.3.1.1NA
240.0601p49A0.5633.970.0670.9263.1.6.2NA

(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
00.300.7811.420.090.872vrzA GO:0005576 GO:0009405
10.220.5772.650.090.753k9aA
20.200.6171.930.060.733wfvA GO:0005198 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0020002 GO:0033644 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036
30.180.5402.710.070.733p30A
40.180.5631.650.090.661jq0A GO:0005198 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036
50.170.7682.840.040.972efkA GO:0001891 GO:0005086 GO:0005096 GO:0005654 GO:0005737 GO:0005764 GO:0005794 GO:0005802 GO:0005829 GO:0005856 GO:0005886 GO:0005938 GO:0006897 GO:0007154 GO:0007165 GO:0008289 GO:0016020 GO:0016192 GO:0030036 GO:0042802 GO:0042995 GO:0043231 GO:0043547 GO:0048471 GO:0051056 GO:0070062
60.170.4701.500.060.523q8tB GO:0000045 GO:0000407 GO:0000910 GO:0001666 GO:0005634 GO:0005737 GO:0005739 GO:0005768 GO:0005776 GO:0005783 GO:0005789 GO:0005794 GO:0005802 GO:0006897 GO:0006914 GO:0006915 GO:0006995 GO:0007040 GO:0007049 GO:0007080 GO:0008285 GO:0010008 GO:0010508 GO:0016020 GO:0016023 GO:0016236 GO:0016239 GO:0019898 GO:0030425 GO:0031410 GO:0031625 GO:0031966 GO:0032258 GO:0032465 GO:0032801 GO:0033197 GO:0034271 GO:0034272 GO:0035032 GO:0042149 GO:0042493 GO:0043066 GO:0043234 GO:0043548 GO:0043652 GO:0044804 GO:0045324 GO:0045335 GO:0048666 GO:0050435 GO:0050790 GO:0051301 GO:0051607 GO:0051707 GO:0060548 GO:0071275 GO:0071364 GO:0098779 GO:1902425 GO:1903599 GO:2000378
70.170.5853.000.030.842ezoA GO:0005198 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0020002 GO:0033644 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036
80.160.6463.440.060.953i2wA GO:0000281 GO:0005543 GO:0005768 GO:0005829 GO:0005886 GO:0007053 GO:0007112 GO:0007269 GO:0008289 GO:0030100 GO:0030496 GO:0032154 GO:0036090 GO:0045211 GO:0045887 GO:0048488 GO:0061024 GO:0071212
90.160.6513.420.060.943i2wB GO:0000281 GO:0005543 GO:0005768 GO:0005829 GO:0005886 GO:0007053 GO:0007112 GO:0007269 GO:0008289 GO:0030100 GO:0030496 GO:0032154 GO:0036090 GO:0045211 GO:0045887 GO:0048488 GO:0061024 GO:0071212
100.140.6042.490.050.791qbzA GO:0005198 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0020002 GO:0033644 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036
110.130.6783.390.020.943syvC GO:0005654 GO:0005737 GO:0005768 GO:0005802 GO:0005886 GO:0006897 GO:0008092 GO:0008289 GO:0016020 GO:0019855 GO:0045806 GO:0051044 GO:0051926 GO:0070062 GO:0097320
120.120.6773.200.060.922eflA GO:0005086 GO:0005737 GO:0005764 GO:0005802 GO:0005856 GO:0005886 GO:0005905 GO:0005938 GO:0006897 GO:0008289 GO:0016020 GO:0016023 GO:0016192 GO:0031410 GO:0042802 GO:0043547
130.120.6493.400.090.943m3wB GO:0005654 GO:0005737 GO:0005768 GO:0005802 GO:0005886 GO:0006897 GO:0008092 GO:0008289 GO:0016020 GO:0019855 GO:0045806 GO:0051044 GO:0051926 GO:0070062 GO:0097320
140.110.7471.890.100.882ch7A GO:0004871 GO:0005886 GO:0006935 GO:0007165 GO:0016020 GO:0016021
150.110.6513.380.100.943haiA GO:0005543 GO:0005737 GO:0005768 GO:0005829 GO:0005886 GO:0006897 GO:0007015 GO:0008092 GO:0008289 GO:0016020 GO:0030054 GO:0030100 GO:0030137 GO:0030659 GO:0031410 GO:0032587 GO:0042995 GO:0043005 GO:0043209 GO:0043679 GO:0045202 GO:0045806 GO:0048471 GO:0048488 GO:0048666 GO:0048812 GO:0072657 GO:0090002 GO:0097320 GO:1900006
160.100.6862.980.070.873syvB GO:0005654 GO:0005737 GO:0005768 GO:0005802 GO:0005886 GO:0006897 GO:0008092 GO:0008289 GO:0016020 GO:0019855 GO:0045806 GO:0051044 GO:0051926 GO:0070062 GO:0097320
170.090.6103.320.060.882v0oA GO:0001786 GO:0005546 GO:0005886 GO:0005905 GO:0006897 GO:0010324 GO:0016020 GO:0030136 GO:0035091 GO:0048268 GO:0072583 GO:0072659
180.090.6382.910.070.894wpeA GO:0000142 GO:0000144 GO:0000281 GO:0000917 GO:0005737 GO:0005856 GO:0005935 GO:0007049 GO:0007067 GO:0008092 GO:0044697 GO:0051301 GO:0090339
190.070.6453.390.070.943qniA GO:0005543 GO:0005737 GO:0005768 GO:0005829 GO:0005886 GO:0006897 GO:0007015 GO:0008092 GO:0008289 GO:0016020 GO:0030054 GO:0030100 GO:0030137 GO:0030659 GO:0031410 GO:0032587 GO:0042995 GO:0043005 GO:0043209 GO:0043679 GO:0045202 GO:0045806 GO:0048471 GO:0048488 GO:0048666 GO:0048812 GO:0072657 GO:0090002 GO:0097320 GO:1900006
200.060.3754.100.050.582eabA GO:0003824 GO:0016020 GO:0016021 GO:0046872
210.060.2853.940.030.394h1zB GO:0003824 GO:0008152 GO:0009063 GO:0046872
220.060.2835.000.030.561j6uA GO:0000166 GO:0005524 GO:0005737 GO:0007049 GO:0008360 GO:0008763 GO:0009058 GO:0009252 GO:0016874 GO:0051301 GO:0071555
230.060.3004.250.070.494gvpA GO:0000160 GO:0003677 GO:0005737 GO:0006351 GO:0006355 GO:0046677
240.060.2214.210.010.312ox1A GO:0003824 GO:0003855 GO:0008652 GO:0009073 GO:0009423 GO:0016829


Consensus prediction of GO terms
 
Molecular Function GO:0005198
GO-Score 0.35
Biological Processes GO:0039663 GO:0019062
GO-Score 0.35 0.35
Cellular Component GO:0016021 GO:0019031 GO:0055036 GO:0044175
GO-Score 0.35 0.35 0.35 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.