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I-TASSER results for job id Rv1081c

[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 4 4il9A UNL Rep, Mult 39,43,46
20.04 2 2ckjA FES Rep, Mult 93,94,95,97,119,120,121
30.04 2 3aefC EPH Rep, Mult 41,44,130
40.02 1 2is1B NUC Rep, Mult 13,14
50.02 1 3pddA CA Rep, Mult 79,81,83
60.02 1 2vvdA CA Rep, Mult 65,67
70.02 1 3mflB DHY Rep, Mult 9,13
80.02 1 4xk8L CLA Rep, Mult 46,50
90.02 1 3u14A FRU Rep, Mult 122,123
100.02 1 2hi8X BR Rep, Mult 41,62,63
110.02 1 2ff4B III Rep, Mult 100,121
120.02 1 5klgA 6UC Rep, Mult 40,43
130.02 1 1wygA CA Rep, Mult 77,78,79,81,108,109
140.02 1 1fo4A FES Rep, Mult 75,86,87,89,101,102,103,116
150.02 1 2ckjC FES Rep, Mult 12,13,14,16,35,37,38
160.02 1 2h8pC GOA Rep, Mult 60,61
170.02 1 4fe1F CLA Rep, Mult 30,34
180.02 1 3eubS FES Rep, Mult 47,55,56,57,58,76
190.02 1 2x2vH DPV Rep, Mult 32,40
200.02 1 1lnyA MG Rep, Mult 79,99

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
10.0601ezfB0.4944.290.0440.7712.5.1.2182
20.0601bk4A0.4784.570.0570.7643.1.3.11NA
30.0603bpsA0.4014.890.0830.7083.4.21.-NA
40.0602oa6D0.4744.170.0420.7154.2.3.9NA
50.0601r58A0.4815.150.0430.8263.4.11.18NA
60.0603fmrB0.4914.690.0900.7993.4.11.1896
70.0603kb9A0.4844.810.0370.7784.2.3.37NA
80.0602j5cB0.4884.690.1000.7854.2.3.-NA
90.0601ftaA0.4864.770.0730.7993.1.3.11NA
100.0603h8eA0.4774.910.0650.7923.4.11.135
110.0601z11A0.4794.230.0340.7221.14.14.1NA
120.0603b9jC0.5114.960.0700.8891.17.3.2,1.17.1.4NA
130.0601spiA0.4714.660.0620.7713.1.3.11NA
140.0601fsaA0.4824.720.0760.7923.1.3.11NA
150.0601t3qB0.4984.860.0560.8611.3.99.17NA
160.0603g4dA0.4974.460.0420.7714.2.3.13NA
170.0603b9jJ0.3635.200.0440.6741.17.1.4,1.17.3.284
180.0601ffuB0.5105.160.0850.8751.2.99.2NA
190.0602hb6B0.4934.660.0790.8263.4.11.1NA

(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
00.070.4974.460.040.773g4dA GO:0000287 GO:0008152 GO:0010333 GO:0016114 GO:0016829 GO:0046872 GO:0047461
10.070.4994.910.070.823s9vB GO:0000287 GO:0003824 GO:0008152 GO:0009507 GO:0009536 GO:0010333 GO:0016829 GO:0016853 GO:0046872 GO:0050554 GO:0050559
20.070.4904.610.050.782ongA GO:0000287 GO:0008152 GO:0010333 GO:0016829 GO:0046872
30.070.4954.500.060.773pybB GO:0000287 GO:0008152 GO:0009507 GO:0009536 GO:0009686 GO:0009740 GO:0009905 GO:0010333 GO:0016829 GO:0016853
40.070.4924.300.080.764gaxA GO:0000287 GO:0008152 GO:0010333 GO:0016829 GO:0034006 GO:0046872
50.070.4994.420.040.775c05B GO:0000287 GO:0008152 GO:0010333 GO:0016829 GO:0046872
60.070.4884.690.100.782j5cB GO:0000287 GO:0008152 GO:0010333 GO:0016829 GO:0046872
70.070.5014.400.060.775dhiA GO:0000287 GO:0005737 GO:0008152 GO:0010333 GO:0016114 GO:0016829 GO:0046872
80.060.3985.250.030.741vkhA GO:0004061 GO:0006569 GO:0008152 GO:0009435 GO:0016787 GO:0019441 GO:0030307 GO:0034354
90.060.3824.960.100.674rifB GO:0016740
100.060.3584.370.030.542p0uA GO:0003824 GO:0008152 GO:0009058 GO:0016740 GO:0016746 GO:0016747
110.060.3544.720.070.573on7B GO:0016491 GO:0046872 GO:0051213 GO:0055114
120.060.3214.890.070.524gc3A GO:0000105 GO:0003677 GO:0003824 GO:0003887 GO:0004401 GO:0006260 GO:0008652 GO:0016311 GO:0016787 GO:0071897
130.060.3694.340.070.581r5aA GO:0016740 GO:0046872
140.060.5124.480.080.803saeA GO:0000287 GO:0005737 GO:0008152 GO:0010333 GO:0016829 GO:0046872 GO:0052681
150.060.3614.310.010.562ab6A GO:0004364 GO:0005102 GO:0005737 GO:0005829 GO:0006749 GO:0008152 GO:0010880 GO:0010881 GO:0014809 GO:0016529 GO:0016740 GO:0018916 GO:0019899 GO:0042178 GO:0042803 GO:0043295 GO:0055119 GO:0060315 GO:0060316 GO:0070062 GO:0070458 GO:0071313 GO:1901687
160.060.3704.760.040.651y4uB GO:0000166 GO:0005524 GO:0005737 GO:0005829 GO:0005886 GO:0006457 GO:0006950 GO:0006974 GO:0009408 GO:0016020 GO:0016887 GO:0042623 GO:0042802 GO:0051082
170.060.3604.690.040.604v06A GO:0004497 GO:0004510 GO:0005506 GO:0005829 GO:0007623 GO:0008152 GO:0009072 GO:0014823 GO:0016491 GO:0016597 GO:0016714 GO:0031667 GO:0042427 GO:0043005 GO:0043627 GO:0046219 GO:0046872 GO:0051384 GO:0051592 GO:0055114 GO:0071285
180.060.4484.460.040.723t3zA GO:0000139 GO:0004497 GO:0005506 GO:0005739 GO:0005783 GO:0005789 GO:0006641 GO:0006805 GO:0008202 GO:0008392 GO:0008395 GO:0010193 GO:0010243 GO:0016020 GO:0016098 GO:0016491 GO:0016705 GO:0016709 GO:0016712 GO:0017144 GO:0018885 GO:0018910 GO:0019373 GO:0019825 GO:0019899 GO:0020037 GO:0031090 GO:0031227 GO:0042197 GO:0042493 GO:0043231 GO:0045471 GO:0046483 GO:0046872 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0016838 GO:0046872
GO-Score 0.58 0.58
Biological Processes GO:0009686 GO:0009740
GO-Score 0.07 0.07
Cellular Component GO:0009507
GO-Score 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.