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I-TASSER results for job id Rv3108

[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
10.10 5 1jrzA HEM Rep, Mult 11,12,17,19,20,73,74,75
20.10 5 3f1fW MG Rep, Mult 76,78
30.06 3 3ildA MG Rep, Mult 93,95
40.06 3 3q2wA MAN Rep, Mult 90,101
50.04 2 2jlrA MN Rep, Mult 8,94,95
60.04 2 1c3oB GLN Rep, Mult 73,76
70.02 1 1yp6A PRZ Rep, Mult 5,63,86,105,107,125
80.02 1 3zwuA CA Rep, Mult 95,113
90.02 1 2chhA UNX Rep, Mult 86,88,105
100.02 1 3t6cA MG Rep, Mult 95,108,123
110.02 1 1e39A NA Rep, Mult 1,2,4,15,16,17,18

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
10.0601qo8D0.4444.650.0620.7601.3.99.14,33
20.0601lj1A0.4255.010.0520.7531.3.99.143
30.0601qw6A0.4044.760.0530.6711.14.13.3919
40.0601g8mA0.4074.950.0770.7333.5.4.10,2.1.2.3NA
50.0601fokA0.4363.930.0480.6643.1.21.4NA
60.0601d0cA0.4064.770.0530.6711.14.13.39NA
70.0601rsrB0.4325.100.0230.7401.17.4.1NA
80.0603eqvA0.4154.960.1090.7123.4.16.4NA
90.0601h0nA0.4135.140.0220.7401.17.4.1NA
100.0601vs1D0.4054.860.0630.7122.5.1.54NA
110.0603etcB0.4125.290.0770.7476.2.1.-NA
120.0602iukA0.4555.220.0350.8081.13.11.12NA
130.0601p4rA0.4054.690.0430.7192.1.2.3,3.5.4.10NA
140.0601ei1A0.4164.750.0360.7265.99.1.39
150.0602iukB0.3555.140.0430.6641.13.11.124,8
160.0601yiqA0.4064.900.0450.7401.1.99.-NA
170.0601jk0A0.4134.850.0230.7061.17.4.1NA
180.0601uzrB0.4185.100.0380.7191.17.4.1NA
190.0601e39A0.4315.020.0600.7671.3.99.1NA

(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
00.070.4584.700.030.772bteA GO:0000166 GO:0002161 GO:0004812 GO:0004823 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006429 GO:0006450 GO:0016874 GO:0046872
10.070.4364.530.050.723zgzD GO:0000166 GO:0002161 GO:0004812 GO:0004823 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006429 GO:0006450 GO:0016874
20.060.3355.820.060.701gaxA GO:0000166 GO:0002161 GO:0004812 GO:0004832 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006438 GO:0006450 GO:0016874 GO:0046872
30.060.4434.790.020.763ziuA GO:0000166 GO:0004812 GO:0004823 GO:0005524 GO:0006418 GO:0006429 GO:0016874
40.060.3055.650.060.601obhA GO:0000166 GO:0002161 GO:0004812 GO:0004823 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006429 GO:0006450 GO:0016874 GO:0046872
50.060.3565.570.060.691a8hA GO:0000049 GO:0000166 GO:0003723 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006431 GO:0016874 GO:0046872
60.060.3695.370.030.695ah5A GO:0000166 GO:0002161 GO:0004812 GO:0004823 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006429 GO:0006450 GO:0016874
70.060.3605.920.070.771ileA GO:0000166 GO:0002161 GO:0004812 GO:0004822 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006428 GO:0006450 GO:0008270 GO:0016874 GO:0046872
80.060.4055.140.030.753kflA GO:0000166 GO:0000287 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006431 GO:0016874
90.060.3904.890.070.684dlpC GO:0000166 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006431 GO:0016874
100.060.3215.240.020.581irxB GO:0000049 GO:0000166 GO:0004812 GO:0004824 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006430 GO:0016874 GO:0046872
110.060.3635.110.060.641pg0A GO:0000049 GO:0000166 GO:0003723 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006431 GO:0008270 GO:0016020 GO:0016874 GO:0046872
120.060.3485.340.030.661rqgA GO:0000049 GO:0000166 GO:0003723 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006431 GO:0016874 GO:0046872
130.060.3505.060.060.631pfuA GO:0000049 GO:0000166 GO:0003723 GO:0004812 GO:0004825 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006431 GO:0008270 GO:0016020 GO:0016874 GO:0046872
140.060.3385.700.030.673tqoA GO:0000166 GO:0004812 GO:0004817 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006423 GO:0008270 GO:0016874 GO:0046872
150.060.3464.490.050.553o0aB GO:0000166 GO:0002161 GO:0004812 GO:0004823 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006429 GO:0006450 GO:0016874
160.060.3265.510.050.604xkzA GO:0000166 GO:0002161 GO:0004812 GO:0004832 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006438 GO:0006450 GO:0016874
170.060.3405.440.040.641wp9A GO:0000166 GO:0003676 GO:0003677 GO:0004386 GO:0004518 GO:0005524 GO:0006259 GO:0006281 GO:0046872 GO:0090305
180.060.3794.730.040.644k5rB GO:0000166 GO:0016491 GO:0055114 GO:0071949


Consensus prediction of GO terms
 
Molecular Function GO:0016876 GO:0035639 GO:0032550 GO:0032559 GO:0052689 GO:0043169
GO-Score 0.57 0.57 0.57 0.57 0.47 0.36
Biological Processes GO:0043039 GO:0006448 GO:0065008
GO-Score 0.57 0.47 0.47
Cellular Component GO:0044424
GO-Score 0.47

(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.