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I-TASSER results for job id Rv0030

[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
10.22 18 1n1qA FEO Rep, Mult 95,99
20.05 4 2w6dB CPL Rep, Mult 46,47,48,49,50,91,92,95
30.04 3 2h9dD CA Rep, Mult 80,83
40.03 2 2qtsC MAL Rep, Mult 97,100,101,104
50.03 2 3prqX CLA Rep, Mult 85,92
60.02 2 2ckjA FES Rep, Mult 49,50,51,53,86,87,88,89
70.02 2 2w6dA GDP Rep, Mult 44,45,46,47,94
80.01 1 3au2A CA Rep, Mult 16,18
90.01 1 3i0oA MG Rep, Mult 58,65
100.01 1 4ehtA ACT Rep, Mult 31,61,62,63
110.01 1 4n6hA OLA Rep, Mult 88,91,92,95
120.01 1 2ckjB FES Rep, Mult 48,56,57,58,61,63,89,95
130.01 1 1pug0 III Rep, Mult 61,63,66,67,68,70,73,78,81,82,85,86,89,90
140.01 1 2nsfA ZN Rep, Mult 65,69
150.01 1 1smyF MG Rep, Mult 51,52
160.01 1 3fqnA MG Rep, Mult 42,93

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
10.0601fo4A0.5733.710.0500.8901.17.1.4NA
20.0601t9kD0.4904.260.0790.8175.3.1.23NA
30.0601flcD0.5303.250.0670.7613.1.1.5344
40.0601b65A0.4883.490.0650.6883.4.11.946,58
50.0602np0A0.5124.110.0960.8073.4.24.69103
60.0603b9jC0.3765.070.0100.7711.17.3.2,1.17.1.4NA
70.0602pflA0.4983.920.0280.8262.3.1.5447,90
80.0602ckjA0.4384.960.0710.8171.17.1.4,1.17.3.2NA
90.0601q8iA0.5233.970.0610.8172.7.7.795
100.0603ikmC0.4993.420.0580.7802.7.7.7NA
110.0603g61A0.5493.980.0410.8073.6.3.4441
120.0601g5iD0.5243.800.0670.8352.7.7.744
130.0602e1qA0.5083.920.1080.8261.17.3.2,1.17.1.4NA
140.0601iv8A0.4874.200.0470.8175.4.99.15NA
150.0603b8eC0.5434.030.0200.8623.6.3.9NA
160.0601clqA0.5394.040.0830.8622.7.7.792
170.0603ikmB0.3894.860.0480.7612.7.7.7NA
180.0601up8A0.4723.980.0560.7431.11.1.18NA
190.0603b9jJ0.3514.740.0650.6791.17.1.4,1.17.3.2NA

(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
00.240.6781.980.120.781pugA GO:0003677 GO:0005737 GO:0005829 GO:0009295 GO:0043590
10.210.6352.180.110.771j8bA GO:0003677 GO:0005737 GO:0009295 GO:0043590
20.200.6692.220.140.833f42A GO:0003677 GO:0005737 GO:0009295 GO:0043590
30.160.5952.630.170.751ybxB GO:0003677 GO:0005737 GO:0009295 GO:0043590
40.070.4804.470.050.874uhxA 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
50.070.4384.960.070.822ckjA 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
60.070.4724.550.060.853a3yA GO:0000166 GO:0005391 GO:0005524 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0010248 GO:0016020 GO:0016021 GO:0016787 GO:0046872 GO:0090662
70.070.4664.330.080.823w5bA GO:0000166 GO:0005388 GO:0005509 GO:0005524 GO:0005783 GO:0005789 GO:0005793 GO:0006810 GO:0006811 GO:0006816 GO:0006942 GO:0016020 GO:0016021 GO:0016529 GO:0016787 GO:0031448 GO:0031673 GO:0031674 GO:0033017 GO:0045988 GO:0046872 GO:0048471 GO:0070588
80.070.4854.410.080.863b8eA GO:0000166 GO:0002028 GO:0005391 GO:0005524 GO:0005886 GO:0005890 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0006883 GO:0010107 GO:0010248 GO:0015991 GO:0016020 GO:0016021 GO:0016787 GO:0030007 GO:0030955 GO:0031402 GO:0036376 GO:0042383 GO:0043231 GO:0046872 GO:0051117 GO:0086009 GO:0090662 GO:1990573
90.070.4933.550.020.761mhsA GO:0000166 GO:0005524 GO:0005886 GO:0005887 GO:0006754 GO:0006810 GO:0006811 GO:0008553 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0043231 GO:0046872 GO:0051453 GO:1902600
100.070.4763.770.060.744bbjA GO:0000166 GO:0005886 GO:0006812 GO:0016020 GO:0016021 GO:0016787 GO:0019829 GO:0046872 GO:0098655
110.070.4944.560.030.873ixzA GO:0000166 GO:0000287 GO:0005391 GO:0005524 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0006883 GO:0008900 GO:0010107 GO:0010248 GO:0015991 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030007 GO:0036376 GO:0043231 GO:0046872
120.070.5053.670.070.753j09A GO:0000166 GO:0005507 GO:0005524 GO:0005886 GO:0006810 GO:0006811 GO:0006812 GO:0006825 GO:0016020 GO:0016021 GO:0016787 GO:0019829 GO:0030001 GO:0046872 GO:0098655
130.070.4652.790.040.631ffuB GO:0005507 GO:0016491 GO:0018492 GO:0030151 GO:0046872 GO:0055114
140.070.4682.830.060.621t3qB GO:0016491 GO:0055114
150.070.4454.280.070.783b8cA GO:0000166 GO:0000287 GO:0005524 GO:0005886 GO:0005887 GO:0006754 GO:0006810 GO:0006811 GO:0008553 GO:0015991 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0046872 GO:0051453
160.060.4112.560.110.511n63B GO:0005507 GO:0016491 GO:0018492 GO:0030151 GO:0046872 GO:0055114
170.060.4363.390.060.623fahA GO:0009055 GO:0016491 GO:0033727 GO:0046872 GO:0051536 GO:0051537 GO:0055114
180.060.3194.930.080.611t3qC GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0050660 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0003677
GO-Score 0.59
Biological Processes GO:0009115 GO:0072593 GO:0006954 GO:0055114 GO:0042816
GO-Score 0.07 0.07 0.07 0.07 0.07
Cellular Component GO:0043590 GO:0044444
GO-Score 0.59 0.57

(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.