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I-TASSER results for job id Rv0397

[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
10.08 2 2q6qA CO Rep, Mult 84,88
20.08 2 2voyK III Rep, Mult 73,77,80,81,88
30.04 1 3ar3A PTY Rep, Mult 68,72,75,76
40.04 1 1cq1A CA Rep, Mult 9,22,23
50.04 1 3hdbA CA Rep, Mult 2,3
60.04 1 2vk6A MG Rep, Mult 14,15
70.04 1 2zfzC ARG Rep, Mult 7,15
80.04 1 2wsc2 CLA Rep, Mult 37,85
90.04 1 2o011 CLA Rep, Mult 81,82,86
100.04 1 2x2eA MG Rep, Mult 34,45
110.04 1 1c9uA CA Rep, Mult 9,22,23,103
120.04 1 5it9G MG Rep, Mult 12,69

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
10.0603mebA0.4833.580.0550.6802.6.1.1NA
20.0603b8eA0.4734.730.0500.8203.6.3.9NA
30.0601aamA0.4543.850.0380.6722.6.1.1NA
40.0603c46B0.4924.460.0260.8202.7.7.635
50.0603ikmD0.4784.100.0500.7212.7.7.7NA
60.0601eulA0.4554.220.0490.7543.6.3.8NA
70.0602inrA0.4654.210.0180.6725.99.1.-NA
80.0603bcbA0.4664.320.0590.7622.9.1.271
90.0607aatA0.4703.660.0180.6722.6.1.1NA
100.0603mosA0.4764.810.0730.8612.2.1.1NA
110.0603ii0C0.4763.570.0450.6642.6.1.1NA
120.0602z67A0.4674.380.0400.7622.9.1.-NA
130.0601ykdA0.4764.970.0830.7874.6.1.110
140.0601mc0A0.3904.430.0270.6643.1.4.17NA
150.0601s0kA0.4354.480.0210.7543.2.1.18NA
160.0601w27A0.4704.610.0600.7954.3.1.24NA
170.0601yaaA0.4813.770.0550.6802.6.1.1NA
180.0601aklA0.4714.900.0520.8443.4.24.40NA
190.0602rgrA0.4644.130.0460.6975.99.1.3NA

(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
00.170.7361.640.110.813zifN GO:0019012 GO:0031423
10.070.5064.610.040.803lfvA GO:0000166 GO:0003824 GO:0004112 GO:0004114 GO:0005829 GO:0007165 GO:0008081 GO:0008152 GO:0010613 GO:0016787 GO:0030553 GO:0030823 GO:0042130 GO:0043406 GO:0046068 GO:0046069 GO:0046872 GO:0047555 GO:0055118 GO:0055119 GO:0060282
20.070.4934.740.070.843nopC GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0005524 GO:0005622 GO:0006355 GO:0007165 GO:0009584 GO:0009881 GO:0016301 GO:0016310 GO:0016740 GO:0018106 GO:0018298 GO:0023014 GO:0050896
30.070.4924.540.070.773zq5A GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0005524 GO:0005622 GO:0006355 GO:0007165 GO:0009584 GO:0009585 GO:0009639 GO:0009881 GO:0009883 GO:0016301 GO:0016310 GO:0016740 GO:0018106 GO:0018298 GO:0023014 GO:0042802 GO:0046777 GO:0050896
40.070.4834.570.030.764r6lA GO:0000155 GO:0000160 GO:0005622 GO:0006355 GO:0007165 GO:0009584 GO:0009881 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0018298 GO:0023014
50.070.4744.650.030.764bwiA GO:0006355 GO:0009584 GO:0009585 GO:0009881 GO:0009883 GO:0018298 GO:0050896
60.070.4654.710.040.774r70A GO:0000155 GO:0000160 GO:0005622 GO:0006355 GO:0007165 GO:0009584 GO:0009881 GO:0016301 GO:0016310 GO:0018298 GO:0023014
70.070.4644.980.050.794ourB GO:0000155 GO:0000160 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0006325 GO:0006351 GO:0006355 GO:0007165 GO:0009409 GO:0009584 GO:0009585 GO:0009630 GO:0009638 GO:0009640 GO:0009649 GO:0009687 GO:0009867 GO:0009881 GO:0009883 GO:0010017 GO:0010018 GO:0010029 GO:0010148 GO:0010161 GO:0010202 GO:0010218 GO:0010244 GO:0010374 GO:0010617 GO:0015979 GO:0016604 GO:0016607 GO:0017006 GO:0017012 GO:0018298 GO:0023014 GO:0031347 GO:0031516 GO:0031517 GO:0042802 GO:0042803 GO:0050896 GO:2000028
80.070.4784.890.050.804gw9A GO:0006355 GO:0007165 GO:0009584 GO:0009881 GO:0018298
90.070.4444.810.040.774q0jA GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0005524 GO:0005622 GO:0006355 GO:0007165 GO:0009584 GO:0009881 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0018106 GO:0018298 GO:0023014 GO:0050896
100.070.4654.790.100.805akpB GO:0006355 GO:0007165 GO:0009584 GO:0009881 GO:0018298
110.070.4644.370.050.703ibjB GO:0000122 GO:0000166 GO:0004112 GO:0004114 GO:0004115 GO:0004118 GO:0005262 GO:0005634 GO:0005737 GO:0005739 GO:0005759 GO:0005783 GO:0005794 GO:0005829 GO:0005886 GO:0006198 GO:0006626 GO:0007165 GO:0008081 GO:0008144 GO:0008152 GO:0016020 GO:0016787 GO:0019933 GO:0019934 GO:0030224 GO:0030552 GO:0030553 GO:0030818 GO:0030911 GO:0033159 GO:0035690 GO:0036006 GO:0042734 GO:0042803 GO:0043116 GO:0043117 GO:0045121 GO:0046069 GO:0046872 GO:0047555 GO:0048471 GO:0050729 GO:0061028 GO:0070588 GO:0071260 GO:0071321 GO:0071560 GO:0097011
120.070.4974.220.060.753ibjA GO:0000122 GO:0000166 GO:0004112 GO:0004114 GO:0004115 GO:0004118 GO:0005262 GO:0005634 GO:0005737 GO:0005739 GO:0005759 GO:0005783 GO:0005794 GO:0005829 GO:0005886 GO:0006198 GO:0006626 GO:0007165 GO:0008081 GO:0008144 GO:0008152 GO:0016020 GO:0016787 GO:0019933 GO:0019934 GO:0030224 GO:0030552 GO:0030553 GO:0030818 GO:0030911 GO:0033159 GO:0035690 GO:0036006 GO:0042734 GO:0042803 GO:0043116 GO:0043117 GO:0045121 GO:0046069 GO:0046872 GO:0047555 GO:0048471 GO:0050729 GO:0061028 GO:0070588 GO:0071260 GO:0071321 GO:0071560 GO:0097011
130.070.4764.970.080.791ykdA GO:0000166 GO:0004016 GO:0005622 GO:0006171 GO:0009190 GO:0016829 GO:0016849 GO:0035556
140.060.4304.530.080.644ourA GO:0000155 GO:0000160 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0006325 GO:0006351 GO:0006355 GO:0007165 GO:0009409 GO:0009584 GO:0009585 GO:0009630 GO:0009638 GO:0009640 GO:0009649 GO:0009687 GO:0009867 GO:0009881 GO:0009883 GO:0010017 GO:0010018 GO:0010029 GO:0010148 GO:0010161 GO:0010202 GO:0010218 GO:0010244 GO:0010374 GO:0010617 GO:0015979 GO:0016604 GO:0016607 GO:0017006 GO:0017012 GO:0018298 GO:0023014 GO:0031347 GO:0031516 GO:0031517 GO:0042802 GO:0042803 GO:0050896 GO:2000028
150.060.4453.900.040.634mcwB GO:0000166 GO:0016787 GO:0046872
160.060.3634.540.040.624ekzA GO:0000302 GO:0003756 GO:0004656 GO:0005178 GO:0005576 GO:0005783 GO:0005788 GO:0005793 GO:0005886 GO:0005925 GO:0006457 GO:0009897 GO:0016020 GO:0016222 GO:0016853 GO:0018401 GO:0019899 GO:0031012 GO:0034663 GO:0034976 GO:0042158 GO:0042470 GO:0044822 GO:0045454 GO:0046598 GO:0046982 GO:0070062 GO:0071456 GO:1902175
170.060.3884.500.050.574fofA GO:0004871 GO:0007165 GO:0016020 GO:0016021 GO:0018298
180.060.3615.070.030.685djqA GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0005887 GO:0006119 GO:0009055 GO:0009060 GO:0015078 GO:0015990 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0016705 GO:0019411 GO:0019646 GO:0019825 GO:0020037 GO:0045154 GO:0045278 GO:0046872 GO:0055114 GO:0070069 GO:0070469 GO:0070470 GO:1902600


Consensus prediction of GO terms
 
Molecular Function GO:1901265 GO:0004673 GO:0038023 GO:0036094 GO:0005515
GO-Score 0.37 0.37 0.37 0.37 0.34
Biological Processes GO:0006468 GO:0044710 GO:0009583 GO:0035556 GO:1903506 GO:0010468 GO:2000112 GO:0006351
GO-Score 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37
Cellular Component GO:0044464
GO-Score 0.30

(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.