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I-TASSER results for job id Rv3821

[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
10.07 4 3a0bZ CLA Rep, Mult 187,190
20.05 3 1xvbD 3BR Rep, Mult 218,221,222,224
30.04 2 3wmoS BCL Rep, Mult 8,19
40.04 2 1xvgA BRJ Rep, Mult 13,14,17,79,82,83
50.04 2 1fz8D 2BM Rep, Mult 175,178,179,182
60.02 1 3wmnQ BCL Rep, Mult 8,19,23
70.02 1 3ojcA CA Rep, Mult 134,164
80.02 1 4n7wB MPG Rep, Mult 26,118,121,122,124,125,128,193
90.02 1 1xvgB BRJ Rep, Mult 9,10,14,79
100.02 1 4ryrA MPG Rep, Mult 130,224
110.02 1 1izlA CLA Rep, Mult 180,181
120.02 1 1mhy1 III Rep, Mult 14,15,18,19,21,22,25,26,114,118,121
130.02 1 2wscA CLA Rep, Mult 2,6
140.02 1 4brbB 78N Rep, Mult 91,95
150.02 1 4q54z CLA Rep, Mult 187,195
160.02 1 3ue8A 09M Rep, Mult 143,192
170.02 1 2y04A 2CV Rep, Mult 52,72,76
180.02 1 2aj4A MG Rep, Mult 41,114
190.02 1 1jb0M CLA Rep, Mult 79,83
200.02 1 2r9rB PGW Rep, Mult 206,221

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
10.0601s76D0.3495.290.0600.5482.7.7.6NA
20.0601gnxA0.3645.280.0470.5613.2.1.21NA
30.0601occA0.3775.230.0860.5821.9.3.115
40.0601ej6A0.3745.740.0590.6292.7.7.50NA
50.0602gl9C0.2485.400.0230.4053.5.1.26214
60.0601ygyA0.3725.400.0890.5871.1.1.9518
70.0602wyhA0.3665.950.0410.6253.2.1.24NA
80.0602o2rC0.3466.020.0590.6161.5.1.6NA
90.0601v5yA0.3684.980.0490.5401.6.99.-NA
100.0601ug9A0.3865.530.0760.6333.2.1.7070
110.0602rnpC0.3825.090.0560.5702.7.7.6NA
120.0601hrkA0.3715.400.0890.5914.99.1.1NA
130.0602occN0.3765.770.0430.6331.9.3.1148
140.0601o01C0.3775.500.0570.6031.2.1.3NA
150.0601cb8A0.3685.170.0390.5574.2.2.5NA
160.0602gl9D0.2404.970.0500.3633.5.1.2673
170.0601b8fA0.3696.040.0660.6544.3.1.3NA
180.0601g87B0.3885.780.0500.6503.2.1.4NA
190.0602de3B0.3664.980.0720.5653.13.1.33

(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
00.070.5793.760.050.764atvA GO:0005886 GO:0006810 GO:0006811 GO:0006814 GO:0006885 GO:0015081 GO:0015297 GO:0015491 GO:0015992 GO:0016020 GO:0016021 GO:0035725 GO:0055085 GO:0098655
10.060.4475.860.060.762innA GO:0006725 GO:0016491 GO:0046872 GO:0055114
20.060.4204.720.080.632f6hX GO:0000001 GO:0000011 GO:0000131 GO:0000132 GO:0000146 GO:0000166 GO:0000329 GO:0003774 GO:0003779 GO:0005516 GO:0005524 GO:0005934 GO:0005935 GO:0006810 GO:0007049 GO:0007107 GO:0007118 GO:0009826 GO:0015031 GO:0016192 GO:0016459 GO:0030050 GO:0030133 GO:0031941 GO:0031982 GO:0032432 GO:0043332 GO:0045033 GO:0048313 GO:0051015 GO:0051301 GO:0071563
30.060.3885.920.030.674zo6A GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
40.060.4165.600.060.682x41A GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0102483
50.060.3756.270.040.683abzB GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483
60.060.3396.270.040.614d0jA GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483
70.060.3796.230.060.694i8dB GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0102483
80.060.3766.380.050.703abzA GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483
90.060.3395.650.080.552oxnA GO:0004553 GO:0004563 GO:0005737 GO:0005975 GO:0007049 GO:0008152 GO:0008360 GO:0009252 GO:0009254 GO:0009273 GO:0016787 GO:0016798 GO:0046677 GO:0051301 GO:0071555
100.060.3386.090.040.595fjiA GO:0000272 GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483
110.060.3255.790.040.554kqxB GO:0000166 GO:0004455 GO:0008652 GO:0009082 GO:0009097 GO:0009099 GO:0016491 GO:0016853 GO:0046872 GO:0055114
120.060.3995.980.010.684iibA GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483
130.060.3515.740.070.594gnvB GO:0004553 GO:0004563 GO:0005737 GO:0005975 GO:0007049 GO:0008152 GO:0008360 GO:0009252 GO:0009254 GO:0016787 GO:0016798 GO:0051301 GO:0071555
140.060.3085.690.030.493dhiB GO:0004497 GO:0006725 GO:0016491 GO:0016709 GO:0019439 GO:0042203 GO:0055114
150.060.4515.420.040.741mhyD GO:0004497 GO:0006725 GO:0006730 GO:0015049 GO:0016491 GO:0046872 GO:0055114
160.060.4205.330.060.693dhiA GO:0004497 GO:0006725 GO:0016491 GO:0019439 GO:0042203 GO:0046872 GO:0055114
170.060.4325.580.100.731fziA GO:0004497 GO:0006725 GO:0006730 GO:0015049 GO:0015050 GO:0015947 GO:0016491 GO:0046872 GO:0055114
180.060.3735.840.030.625fjjA GO:0000272 GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0008422 GO:0016052 GO:0016787 GO:0016798 GO:0030245 GO:0102483


Consensus prediction of GO terms
 
Molecular Function GO:0015081 GO:0015491 GO:0016491 GO:0046872 GO:0005516 GO:0102483 GO:0000146 GO:0008422 GO:0051015 GO:0005524
GO-Score 0.07 0.07 0.07 0.07 0.06 0.06 0.06 0.06 0.06 0.06
Biological Processes GO:0005975 GO:0015992 GO:0035725 GO:0006885 GO:0055114 GO:0006725 GO:0015031 GO:0030050 GO:0007107 GO:0016192 GO:0000011 GO:0009826 GO:0000001 GO:0048313 GO:0007118 GO:0045033 GO:0000132
GO-Score 0.12 0.07 0.07 0.07 0.07 0.07 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06
Cellular Component GO:0005886 GO:0016021 GO:0032432 GO:0071563 GO:0031941 GO:0000329 GO:0016459 GO:0005934 GO:0000131 GO:0043332 GO:0005935 GO:0030133
GO-Score 0.07 0.07 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06

(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.