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I-TASSER results for job id Rv2699c

[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
10.20 10 1x4lA ZN Rep, Mult 73,76,95,98
20.14 7 2uxqA MG Rep, Mult 15,19
30.10 5 1sl8A CA Rep, Mult 37,39,41,44,63
40.06 3 3iqeD CA Rep, Mult 18,22

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
10.0602q80A0.4484.140.0310.7502.5.1.29,2.5.1.10,2.5.1.120
20.0601wndA0.4564.350.1120.8001.2.1.1977
30.0603eqoA0.4474.480.0650.8403.2.1.58NA
40.0601hm7A0.4504.410.0420.7704.2.3.7,4.6.1.5NA
50.0601dmuA0.4424.420.0540.7803.1.21.4NA
60.0602f89F0.4464.190.0310.7702.5.1.1,2.5.1.1047
70.0601m21A0.4574.670.0530.7803.5.1.-NA
80.0601xjjA0.4554.240.0560.7901.17.4.1NA
90.0601zumI0.4444.410.0820.7901.2.1.3NA
100.0601uxvA0.4384.420.0710.7901.2.1.957
110.0601wnbA0.4554.430.1110.8101.2.1.19,1.2.1.895
120.0601o01C0.4004.920.0110.7401.2.1.358
130.0602j6lB0.4314.510.0300.7701.2.1.31,1.2.1.3NA
140.0602wj2A0.4414.620.0640.7703.5.1.9960
150.0602gl9C0.2924.160.0220.5003.5.1.26NA
160.0601bxsA0.4364.620.0710.8101.2.1.36NA
170.0602z4yB0.4004.170.0210.7002.5.1.29NA
180.0602azjA0.4464.180.0310.7602.5.1.19
190.0602ftzA0.4474.170.0210.7302.5.1.10NA

(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
00.200.4844.330.060.871el4A GO:0005509 GO:0008218 GO:0046872
10.130.3085.040.080.572aaoA GO:0000166 GO:0004672 GO:0004674 GO:0004683 GO:0005509 GO:0005516 GO:0005524 GO:0005634 GO:0005777 GO:0005778 GO:0005886 GO:0006468 GO:0009738 GO:0009931 GO:0016020 GO:0016301 GO:0016310 GO:0016740 GO:0018105 GO:0035556 GO:0046777 GO:0046872
20.120.2984.990.090.613kf9A GO:0005509 GO:0007049 GO:0007067 GO:0046872 GO:0051301
30.110.3314.100.100.565palA GO:0005509 GO:0046872
40.090.3483.940.090.562kn2A GO:0005509 GO:0046872
50.070.4904.110.020.844nqgA GO:0005509 GO:0008218 GO:0046872
60.070.4914.200.050.871jf0A GO:0005509 GO:0008218 GO:0046872
70.070.4934.120.070.863kpxA
80.070.4584.630.040.832hpsA GO:0005509 GO:0046872
90.070.4044.420.070.781nyaA GO:0005509 GO:0046872
100.060.3634.390.050.631v1fA GO:0004723 GO:0005509 GO:0005513 GO:0005634 GO:0005737 GO:0005886 GO:0005955 GO:0006470 GO:0016020 GO:0030007 GO:0042539 GO:0046872
110.060.3424.860.020.713qfhD GO:0004252 GO:0006508 GO:0008233 GO:0016787
120.060.2964.650.040.554n5xA GO:0003735 GO:0005347 GO:0005509 GO:0005739 GO:0005743 GO:0006412 GO:0006810 GO:0006839 GO:0010941 GO:0015867 GO:0016020 GO:0016021 GO:0034599 GO:0046872 GO:0055085 GO:0071277
130.060.4044.190.040.752l2eA GO:0005509 GO:0005634 GO:0005737 GO:0005829 GO:0005886 GO:0010515 GO:0016020 GO:0030435 GO:0042327 GO:0043950 GO:0046872 GO:0071277 GO:0090281 GO:0098744
140.060.3604.430.070.651uhnA GO:0005509 GO:0005773 GO:0005774 GO:0009705 GO:0016020 GO:0019722 GO:0022626 GO:0046872 GO:0055075
150.060.3974.070.080.682r2iA GO:0001750 GO:0005509 GO:0005886 GO:0007601 GO:0007602 GO:0008048 GO:0030249 GO:0031282 GO:0031284 GO:0046872 GO:0050896 GO:0071277
160.060.3804.220.070.682lhiA GO:0000131 GO:0000742 GO:0000754 GO:0004721 GO:0004723 GO:0005509 GO:0005516 GO:0005737 GO:0005816 GO:0005823 GO:0005856 GO:0005934 GO:0005935 GO:0005955 GO:0006470 GO:0006607 GO:0006661 GO:0006873 GO:0006897 GO:0006898 GO:0007010 GO:0007114 GO:0016237 GO:0016787 GO:0031505 GO:0042144 GO:0042991 GO:0043332 GO:0046872 GO:0048306 GO:0051300 GO:1903525
170.060.3854.600.060.733cs1A GO:0005509 GO:0005929 GO:0031514 GO:0042995 GO:0046872
180.060.3564.580.040.652ggzA GO:0005509 GO:0007165 GO:0007601 GO:0008048 GO:0022400 GO:0031282 GO:0031284 GO:0046872 GO:0097381


Consensus prediction of GO terms
 
Molecular Function GO:0005509
GO-Score 0.51
Biological Processes GO:0044237
GO-Score 0.34
Cellular Component GO:0005886 GO:0005634 GO:0005778
GO-Score 0.13 0.13 0.13

(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.