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I-TASSER results for job id Rv1830

[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
10.16 7 1r8dA QNA Rep, Mult 66,67,68,79,82,103,104
20.15 7 1r8dA NUC Rep, Mult 77,79,80,83,84,98,103,121,126,127,128
30.04 2 1vf5S III Rep, Mult 169,170
40.04 2 2fkwD BCL Rep, Mult 154,157
50.02 1 3n1vF 3N1 Rep, Mult 114,117,118,121,130
60.02 1 1r8eA IMD Rep, Mult 171,175
70.02 1 1q060 III Rep, Mult 115,116,119,122,123,133,137,140,141,142,143,145,146,149,150,153,156,157,159,160,163,164,166,170,188,189,190
80.02 1 1r8d0 III Rep, Mult 122,123,124,149,153,156,157,159,160,163,164,166,167,170,171
90.02 1 1r8eA IMD Rep, Mult 196,198,209,212
100.02 1 1exjA P4P Rep, Mult 64,94,105
110.02 1 2q6qA CO Rep, Mult 164,168
120.02 1 2oa6D MG Rep, Mult 129,133,137

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
10.0601fpsA0.4265.320.0590.6842.5.1.1,2.5.1.107
20.0601gph10.4095.380.0550.6582.4.2.14124
30.0602vn0A0.4125.530.0760.6891.14.14.1NA
40.0602w90B0.4145.060.0680.6221.1.1.44NA
50.0601og2A0.3675.960.0510.6491.14.14.1NA
60.0603c46B0.4195.600.0330.6712.7.7.6NA
70.0601n6bA0.3795.760.1040.6491.14.14.1NA
80.0601hm7A0.3905.810.0410.6894.2.3.7,4.6.1.5NA
90.0601i1iP0.4124.240.0240.5733.4.24.16NA
100.0603cf4A0.4415.860.0720.7821.2.99.2NA
110.0601kqfA0.4035.960.0330.7161.2.1.2NA
120.0602z8kC0.3685.880.0640.6442.3.2.2NA
130.0601qmgA0.4235.430.0590.6801.1.1.86165
140.0602f89F0.4365.320.0530.7022.5.1.1,2.5.1.10NA
150.0601yrlA0.4105.220.0540.6491.1.1.86NA
160.0603jvpD0.4145.780.0560.7242.7.1.16NA
170.0602e0wB0.4165.930.0620.7162.3.2.2NA
180.0602h1nA0.4135.040.0320.6273.4.24.-NA
190.0601yrlC0.3855.590.0640.6441.1.1.86NA

(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
00.180.5232.010.200.583hh0A GO:0003677 GO:0006355
10.140.3773.220.100.483gp4A GO:0003677 GO:0006355
20.140.4713.450.140.613qaoA GO:0003677 GO:0006355
30.110.4722.560.180.554wlwA GO:0000986 GO:0001131 GO:0001204 GO:0003677 GO:0003700 GO:0005507 GO:0005737 GO:0006351 GO:0006355 GO:0045893 GO:0046872 GO:0071248
40.110.4361.950.190.481r8dA GO:0003677 GO:0005737 GO:0006351 GO:0006355
50.100.4283.110.130.524ua1B GO:0003677 GO:0006355 GO:0045340 GO:0046689
60.090.3642.690.250.442vz4A GO:0003677 GO:0006351 GO:0006355
70.090.4283.640.110.563d6yA GO:0003677 GO:0006351 GO:0006355
80.080.3182.140.200.354r4eB GO:0003677 GO:0006351 GO:0006355
90.060.4125.740.030.693iqmA GO:0000166 GO:0005524 GO:0005737 GO:0005829 GO:0005886 GO:0005887 GO:0006605 GO:0006810 GO:0006886 GO:0015031 GO:0015462 GO:0016020 GO:0017038 GO:0031522 GO:0043952 GO:0046872 GO:0065002
100.060.3883.020.110.483gpvB GO:0003677 GO:0006355
110.060.3685.940.030.632fsfB GO:0000166 GO:0005524 GO:0005737 GO:0005829 GO:0005886 GO:0005887 GO:0006605 GO:0006810 GO:0006886 GO:0015031 GO:0015462 GO:0016020 GO:0017038 GO:0031522 GO:0042802 GO:0043952 GO:0046872 GO:0061077 GO:0065002
120.060.2816.320.040.513enoA GO:0000166 GO:0002949 GO:0003824 GO:0004222 GO:0004674 GO:0004712 GO:0005506 GO:0005524 GO:0005737 GO:0006468 GO:0006508 GO:0008033 GO:0008152 GO:0008270 GO:0016301 GO:0016310 GO:0016740 GO:0016746 GO:0016747 GO:0046872 GO:0061711
130.060.3785.720.040.632fshA GO:0000166 GO:0005524 GO:0005737 GO:0005829 GO:0005886 GO:0005887 GO:0006605 GO:0006810 GO:0006886 GO:0015031 GO:0015462 GO:0016020 GO:0017038 GO:0031522 GO:0042802 GO:0043952 GO:0046872 GO:0061077 GO:0065002
140.060.3795.670.010.642vdaA GO:0000166 GO:0005524 GO:0005737 GO:0005829 GO:0005886 GO:0005887 GO:0006605 GO:0006810 GO:0006886 GO:0015031 GO:0015462 GO:0016020 GO:0017038 GO:0031522 GO:0042802 GO:0043952 GO:0046872 GO:0061077 GO:0065002
150.060.3066.270.060.552zskA GO:0006520 GO:0006807 GO:0008152 GO:0016855 GO:0036361
160.060.3385.380.060.553b6uB GO:0000166 GO:0003777 GO:0005524 GO:0005737 GO:0005813 GO:0005819 GO:0005829 GO:0005856 GO:0005873 GO:0005874 GO:0005876 GO:0005929 GO:0006890 GO:0007018 GO:0007052 GO:0007100 GO:0007368 GO:0008017 GO:0008089 GO:0008574 GO:0015630 GO:0016020 GO:0016939 GO:0017048 GO:0019886 GO:0030496 GO:0030990 GO:0032467 GO:0070062 GO:0072372 GO:0072383 GO:0090307 GO:0097542 GO:1904115
170.060.2975.130.050.472gqkA GO:0005507 GO:0005739 GO:0005743 GO:0006091 GO:0006825 GO:0006878 GO:0008535 GO:0030016 GO:0046872 GO:0072492
180.060.3172.170.200.354r24B GO:0003677 GO:0006355


Consensus prediction of GO terms
 
Molecular Function GO:0003677
GO-Score 0.52
Biological Processes GO:0006355
GO-Score 0.52
Cellular Component GO:0044424
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.