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I-TASSER results for job id Rv3491

[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
10.04 2 3v8eA MG Rep, Mult 125,127,129
20.04 2 1umxL BPB Rep, Mult 11,14,15,18,19,50
30.04 2 2muvD 3LW Rep, Mult 3,10
40.04 2 1nnqA ZN Rep, Mult 58,80,124,155
50.04 2 1smyF MG Rep, Mult 7,8,146
60.04 2 4v1fA BQ1 Rep, Mult 17,18,21
70.04 2 3ir5B SF4 Rep, Mult 44,45,114,115,116,124,128,131
80.02 1 4n6hA OLA Rep, Mult 11,14,15,18
90.02 1 2ag4B OLA Rep, Mult 82,141,143
100.02 1 2a9cA MO Rep, Mult 80,81
110.02 1 2hj6L PS2 Rep, Mult 15,50
120.02 1 3pfdC IOD Rep, Mult 12,136
130.02 1 1q16B F3S Rep, Mult 35,36,37,40,54,58,59,71
140.02 1 1r27D F3S Rep, Mult 11,12,138,146,147,181
150.02 1 2wsc4 CLA Rep, Mult 156,158
160.02 1 3a44C ZN Rep, Mult 124,155
170.02 1 1dgjA FES Rep, Mult 44,45,46,50,111,112
180.02 1 2h8pC GOA Rep, Mult 38,40

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
10.0602gokA0.3945.530.0330.6883.5.2.7NA
20.0601xmeA0.3975.460.0500.6721.9.3.1NA
30.0602q01C0.3985.370.0880.6775.3.1.12137
40.0601jrpB0.4384.690.0430.6931.17.1.4111
50.0602gq1A0.3875.020.0750.6153.1.3.11NA
60.0602v3wA0.4075.220.0470.6674.1.1.7NA
70.0601y5nB0.4225.290.0610.7081.7.99.428,58
80.0601peuA0.4005.780.0430.7191.17.4.1NA
90.0602pfrA0.3985.890.0610.7602.3.1.559
100.0601ezfB0.3955.610.0650.6982.5.1.2116
110.0601jroB0.4364.810.0370.6981.1.1.204NA
120.0601t3qB0.4384.770.0580.7081.3.99.17NA
130.0601hm7B0.4035.840.0580.7344.2.3.7,4.6.1.5NA
140.0601d9qB0.3974.560.0580.6153.1.3.11140
150.0601hm7A0.3976.020.0640.7344.2.3.7,4.6.1.5NA
160.0601rm6A0.4335.050.0560.7241.3.99.20NA
170.0601ox0A0.3965.920.0490.7502.3.1.41138
180.0602pqtA0.3965.820.0490.7502.3.1.5NA
190.0602pffD0.3975.930.0560.7402.3.1.86NA

(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
00.070.4825.140.070.753mktA
10.070.4374.900.060.712e1qA GO:0001933 GO:0001937 GO:0003824 GO:0004854 GO:0004855 GO:0005506 GO:0005576 GO:0005615 GO:0005737 GO:0005777 GO:0005829 GO:0006195 GO:0006919 GO:0007595 GO:0009055 GO:0009115 GO:0010629 GO:0016491 GO:0016529 GO:0016614 GO:0016903 GO:0030856 GO:0042803 GO:0043546 GO:0045602 GO:0046872 GO:0050660 GO:0051536 GO:0051537 GO:0051898 GO:0055114 GO:1900745 GO:1900747 GO:2000379 GO:2001213
20.060.4344.900.070.714uhxA GO:0003824 GO:0004031 GO:0004854 GO:0005506 GO:0005737 GO:0005829 GO:0006954 GO:0009055 GO:0009115 GO:0016491 GO:0016614 GO:0042816 GO:0043546 GO:0046872 GO:0050660 GO:0051287 GO:0051536 GO:0051537 GO:0055114 GO:0070062 GO:0072593
30.060.4385.310.070.725c6pA GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
40.060.4395.290.070.714mlbB GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
50.060.4475.100.050.723vvpA GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
60.060.3835.840.040.721e6vA GO:0015948 GO:0016740 GO:0046872 GO:0050524
70.060.3566.210.070.672ckjA GO:0001933 GO:0001937 GO:0003824 GO:0004854 GO:0004855 GO:0005506 GO:0005576 GO:0005615 GO:0005737 GO:0005777 GO:0005829 GO:0006195 GO:0006919 GO:0007595 GO:0009055 GO:0009115 GO:0010629 GO:0016491 GO:0016529 GO:0016614 GO:0016903 GO:0030856 GO:0042803 GO:0043546 GO:0045602 GO:0046872 GO:0050660 GO:0051536 GO:0051537 GO:0051898 GO:0055114 GO:1900745 GO:1900747 GO:2000379 GO:2001213
80.060.3495.590.040.624lxfA GO:0003824 GO:0005975 GO:0046872
90.060.3595.450.050.644dwrB GO:0000394 GO:0003677 GO:0003972 GO:0004518 GO:0004519 GO:0006314 GO:0006396 GO:0008033 GO:0008452 GO:0016539 GO:0016787 GO:0016874 GO:0019002 GO:0030145 GO:0046872 GO:0090305
100.060.3545.880.050.651fo4A GO:0003824 GO:0004854 GO:0004855 GO:0005506 GO:0005576 GO:0005615 GO:0005737 GO:0005777 GO:0005829 GO:0009055 GO:0009115 GO:0016491 GO:0016614 GO:0016903 GO:0043546 GO:0046872 GO:0050660 GO:0051536 GO:0051537 GO:0055114
110.060.3556.060.050.651n63B GO:0005507 GO:0016491 GO:0018492 GO:0030151 GO:0046872 GO:0055114
120.060.4364.810.040.701jroB GO:0016491 GO:0030151 GO:0046872 GO:0055114
130.060.3295.990.010.623m84B GO:0000166 GO:0004641 GO:0005524 GO:0005737 GO:0006164 GO:0006189 GO:0016874
140.060.3735.270.040.611ffuB GO:0005507 GO:0016491 GO:0018492 GO:0030151 GO:0046872 GO:0055114
150.060.3315.320.040.563ax7A GO:0003824 GO:0004854 GO:0004855 GO:0005506 GO:0005576 GO:0005615 GO:0005737 GO:0005777 GO:0005829 GO:0009055 GO:0009115 GO:0016491 GO:0016614 GO:0016903 GO:0043546 GO:0046872 GO:0050660 GO:0051536 GO:0051537 GO:0055114
160.060.4335.050.060.721rm6A GO:0016491 GO:0018525 GO:0055114
170.060.3305.840.050.612ashA GO:0005737 GO:0006400 GO:0008033 GO:0008479 GO:0008616 GO:0016740 GO:0016757 GO:0046872
180.060.3085.360.050.522h0uA GO:0000166 GO:0016491 GO:0042802 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0050660 GO:0051537 GO:0043546 GO:0009055 GO:0004854 GO:0016614 GO:0005506 GO:0015238 GO:0015297 GO:0004031 GO:0042803 GO:0051287 GO:0004855
GO-Score 0.13 0.13 0.13 0.13 0.13 0.13 0.13 0.12 0.12 0.07 0.07 0.07 0.07
Biological Processes GO:0055114 GO:0009115 GO:0006855 GO:0006195 GO:0051898 GO:0006954 GO:0042816 GO:0001933 GO:2001213 GO:1900745 GO:0010629 GO:0001937 GO:1900747 GO:0006919 GO:0045602 GO:2000379 GO:0007595
GO-Score 0.13 0.13 0.12 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07
Cellular Component GO:0005829 GO:0016021 GO:0005777 GO:0070062 GO:0005615 GO:0016529
GO-Score 0.13 0.12 0.07 0.07 0.07 0.07

(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.