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I-TASSER results for job id Rv1061

[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
10.62 23 1ofeA ONL Rep, Mult 2,81,82,94,105,106,107,108,133,134
20.04 2 1ecfB PIN Rep, Mult 52,53,70,92
30.02 1 1te50 III Rep, Mult 47,48,49,50,53,54,68,90,98,99,125,126,127,128,129,146

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
10.3911ecfB0.7822.740.1780.9022.4.2.14106,107
20.2881gmsG0.6902.370.1970.7672.6.1.16171,186,245
30.0602pnqB0.3925.470.0710.5823.1.3.43NA
40.0601w7cA0.3946.230.0430.6761.4.3.1325
50.0601gph10.7941.840.2080.8542.4.2.14123
60.0601ct9A0.6012.890.1350.6936.3.5.4NA
70.0601rf4B0.3895.910.0740.6312.5.1.1998,180
80.0601ayyD0.3423.830.0940.4433.5.1.26NA
90.0601ofdA0.7213.680.1250.8811.4.7.1NA
100.0601iq8A0.4126.450.0460.7142.4.2.29NA
110.0601vncA0.3966.450.0550.6721.11.1.10NA
120.0601moqA0.2776.480.0370.4842.6.1.1656
130.0602d0vA0.3916.110.0390.6451.1.99.8NA
140.0603gbdA0.3886.260.0470.6555.4.99.11186
150.0601llwA0.7173.670.1250.8811.4.7.1NA
160.0601jxaA0.6942.570.1880.7802.6.1.16NA
170.0603c17B0.4624.430.0600.6343.4.19.510
180.0601pg3B0.3906.130.0470.6416.2.1.16,59
190.0601ea0A0.7193.610.1370.8781.4.1.13NA
200.0602a8iA0.4774.620.0680.6653.4.25.-NA
210.0601w6sC0.3856.300.0310.6521.1.99.8NA

(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
00.380.7822.740.180.901ecfB GO:0000287 GO:0004044 GO:0005737 GO:0005829 GO:0006164 GO:0006189 GO:0006541 GO:0009113 GO:0009116 GO:0016740 GO:0016757 GO:0042802 GO:0046872
10.310.6612.790.280.764zfkB GO:0006541 GO:0016787 GO:0016811 GO:0052699 GO:0052704
20.300.6322.770.200.723mdnD GO:0006541 GO:0016740
30.200.6012.890.140.691ct9A GO:0000166 GO:0004066 GO:0004071 GO:0005524 GO:0005737 GO:0005829 GO:0006529 GO:0006541 GO:0008652 GO:0009063 GO:0016597 GO:0016874 GO:0042802 GO:0042803 GO:0070981
40.180.7202.890.200.831te5A
50.150.7941.840.210.851gph1 GO:0000287 GO:0003824 GO:0004044 GO:0006164 GO:0006189 GO:0006541 GO:0008152 GO:0009113 GO:0009116 GO:0016740 GO:0016757 GO:0046872 GO:0051536 GO:0051539
60.100.6982.590.190.784amvA GO:0004360 GO:0005737 GO:0005829 GO:0005975 GO:0006002 GO:0006048 GO:0006541 GO:0008483 GO:0016740 GO:0030246 GO:1901137
70.060.3316.320.070.562hdwA GO:0016787
80.060.3166.370.060.552ekcB GO:0000162 GO:0003824 GO:0004834 GO:0005737 GO:0006568 GO:0008152 GO:0008652 GO:0009073 GO:0009507 GO:0016829 GO:0030170
90.060.2956.710.060.523dahC GO:0000166 GO:0000287 GO:0004749 GO:0005524 GO:0005737 GO:0006015 GO:0009156 GO:0009165 GO:0016301 GO:0016310 GO:0016740 GO:0044249 GO:0046872
100.060.3006.050.040.502avnA GO:0008152 GO:0008168 GO:0016740 GO:0032259
110.060.2216.090.060.374gsnB GO:0016740
120.060.2856.290.090.483zmkB GO:0016740
130.060.3576.090.070.594dozA GO:0000166 GO:0003723 GO:0005737 GO:0046872 GO:0051607
140.060.2746.480.070.494ohcD GO:0000287 GO:0004588 GO:0006221 GO:0009116 GO:0016740 GO:0016757 GO:0044205
150.060.2756.740.040.503mbiA GO:0000166 GO:0000287 GO:0004749 GO:0005524 GO:0005737 GO:0006015 GO:0009116 GO:0009156 GO:0009165 GO:0016301 GO:0016310 GO:0016740 GO:0046872
160.060.2826.420.040.484ojqB GO:0000166 GO:0001172 GO:0003723 GO:0003968 GO:0004197 GO:0004252 GO:0004386 GO:0005198 GO:0005524 GO:0006508 GO:0008026 GO:0008236 GO:0008270 GO:0016020 GO:0016021 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0017111 GO:0019012 GO:0019028 GO:0019031 GO:0019079 GO:0019087 GO:0039694 GO:0046872
170.060.2936.430.050.512e4gA GO:0000166 GO:0016491 GO:0055114
180.060.2726.520.020.484tz7A GO:0016301 GO:0016307 GO:0016310 GO:0046488 GO:0046854
190.060.2726.390.050.481lh0A GO:0000287 GO:0004588 GO:0006221 GO:0009116 GO:0016740 GO:0016757 GO:0044205
200.060.2436.220.070.421u9yA GO:0000166 GO:0000287 GO:0004749 GO:0005524 GO:0005737 GO:0006015 GO:0009116 GO:0009156 GO:0009165 GO:0016301 GO:0016310 GO:0016740 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0042802 GO:0031406 GO:0032559 GO:0035639 GO:0046983 GO:0016211 GO:0032550 GO:0016884 GO:0000287 GO:0004044 GO:0016811
GO-Score 0.50 0.39 0.39 0.39 0.39 0.39 0.39 0.39 0.38 0.38 0.31
Biological Processes GO:0006541 GO:0070982 GO:0008652 GO:0009067 GO:0006189 GO:0009116 GO:0009113 GO:0052704
GO-Score 0.76 0.39 0.39 0.39 0.38 0.38 0.38 0.31
Cellular Component GO:0005829
GO-Score 0.50

(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.