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I-TASSER results for job id Rv3839

[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
10.14 10 4qvbA F42 Rep, Mult 31,36,39,40,51,52,56,57,58,61,132
20.06 4 4ybnB FAD Rep, Mult 73,81,83,84,85,87,143,145
30.06 4 3gasB HEM Rep, Mult 52,53,55,56,58,125,126,129,132
40.03 2 3swjA HEM Rep, Mult 173,176,181,184,246
50.03 2 2iab0 III Rep, Mult 24,26,28,29,30,31,32,34,35,36,38,65,67,69,70,71,83,85,145
60.03 2 2ig6B FMN Rep, Mult 206,211,213
70.01 1 2gpjA CA Rep, Mult 176,180,181
80.01 1 2zhcA MG Rep, Mult 207,210
90.01 1 3rbxA CA Rep, Mult 46,97
100.01 1 3sahB MG Rep, Mult 30,164
110.01 1 2ou5A FMN Rep, Mult 71,85,87,143,145
120.01 1 1l0zA BR Rep, Mult 11,12,153
130.01 1 1dxeA MG Rep, Mult 138,157
140.01 1 2h1iC CA Rep, Mult 164,167
150.01 1 3lu2B ZN Rep, Mult 181,183
160.01 1 3dp2D 4BE Rep, Mult 228,230
170.01 1 5bncB MG Rep, Mult 54,130,133
180.01 1 1p6bA ZN Rep, Mult 176,207

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
10.0601jnwA0.4283.600.0780.5231.4.3.5NA
20.0601f7uA0.3955.870.0400.6516.1.1.19176
30.0601ci0A0.4363.690.0470.5351.4.3.5NA
40.0601qhoA0.3895.840.0640.6433.2.1.13316
50.0601ffyA0.3816.240.0250.6436.1.1.5181
60.0602vgkD0.3896.300.0330.6703.4.16.4NA
70.0601tz7A0.4025.840.0540.6592.4.1.25NA
80.0602aaaA0.3795.760.0500.6243.2.1.1NA
90.0601jxaA0.4035.940.0870.6782.6.1.16NA
100.0601a47A0.3806.020.0420.6362.4.1.1916
110.0603gm8A0.3806.640.0330.7053.2.1.-13
120.0601x1nA0.4045.610.0560.6432.4.1.25NA
130.0602vf4X0.2856.810.0950.5432.6.1.1667
140.0601cygA0.3825.800.0780.6392.4.1.1969
150.0601e1cA0.3836.020.0470.6365.4.99.2181
160.0601ug9A0.3946.190.0530.6943.2.1.70NA
170.0603c8zB0.3855.680.0920.6326.1.1.16NA
180.0601cgtA0.3855.930.0390.6432.4.1.19NA
190.0602taaA0.3825.770.0560.6323.2.1.1198

(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
00.400.7592.810.160.904n7rC GO:0006783 GO:0009507 GO:0009534 GO:0009536 GO:0009570 GO:0009767 GO:0009791 GO:0010181 GO:0015995 GO:0016491 GO:0033014 GO:0043234 GO:0043495 GO:0055114 GO:0070455
10.400.9071.090.170.935bncA GO:0010181 GO:0016491 GO:0055114
20.130.5253.450.100.633dnhA GO:0010181 GO:0016491 GO:0055114
30.100.5152.140.130.561xhnA GO:0003714 GO:0005576 GO:0005615 GO:0005667 GO:0006355 GO:0006357 GO:0007275 GO:0008134 GO:0008283 GO:0010181 GO:0016491 GO:0040008 GO:0055114 GO:0070062 GO:1903507
40.100.4412.910.060.523tgvA GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
50.090.5403.630.080.662arzA GO:0010181 GO:0016491 GO:0055114
60.090.4282.990.100.504qvbB GO:0004733 GO:0010181 GO:0016491 GO:0030170 GO:0042803 GO:0042816 GO:0042823 GO:0055114
70.060.4512.890.070.521rfeA GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
80.060.4312.350.060.481vl7A GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
90.060.2656.330.040.484r1iA GO:0015558 GO:0016020 GO:0016021 GO:1902604
100.060.2495.930.040.413szmC GO:0005654 GO:0005737 GO:0005815 GO:0005856 GO:0021987 GO:0042802 GO:0071850
110.060.2566.260.050.453gn6C GO:0046872
120.060.2996.190.070.523aq0C GO:0004659 GO:0005739 GO:0006744 GO:0008299 GO:0009507 GO:0009536 GO:0009793 GO:0016740 GO:0046872 GO:0050347 GO:0052924
130.060.2676.330.040.471gpzA GO:0002376 GO:0004252 GO:0005509 GO:0005576 GO:0006508 GO:0006955 GO:0006956 GO:0006958 GO:0008233 GO:0008236 GO:0016787 GO:0045087 GO:0070062 GO:0072562
140.060.2125.940.030.363tu4K GO:0000781 GO:0000784 GO:0001308 GO:0003677 GO:0003682 GO:0003690 GO:0003697 GO:0005634 GO:0005677 GO:0005720 GO:0005724 GO:0005730 GO:0006351 GO:0006355 GO:0030466 GO:0031491 GO:0031493 GO:0031507 GO:0042802 GO:0070481
150.060.2335.150.090.361lj9A GO:0003677 GO:0003700 GO:0006351 GO:0006355
160.060.2355.780.060.382fvuB GO:0000781 GO:0000784 GO:0001308 GO:0003677 GO:0003682 GO:0003690 GO:0003697 GO:0005634 GO:0005677 GO:0005720 GO:0005724 GO:0005730 GO:0006351 GO:0006355 GO:0030466 GO:0031491 GO:0031493 GO:0031507 GO:0042802 GO:0070481
170.060.2124.840.070.303my2A GO:0005886 GO:0005887 GO:0015221 GO:0015920 GO:0016020 GO:0016021 GO:0017089 GO:0030288 GO:0042802 GO:0043165 GO:0046836
180.060.1574.290.030.214r2zA GO:0005886 GO:0006810 GO:0015879 GO:0016020 GO:0030165 GO:0031526 GO:0034767 GO:0044070 GO:0070062 GO:0090002 GO:0090314


Consensus prediction of GO terms
 
Molecular Function GO:0010181 GO:0016491 GO:0043495
GO-Score 0.75 0.75 0.40
Biological Processes GO:0009791 GO:0009767 GO:0070455 GO:0015995
GO-Score 0.40 0.40 0.40 0.40
Cellular Component GO:0009570 GO:0043234 GO:0009534
GO-Score 0.40 0.40 0.40

(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.