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I-TASSER results for job id Rv1066

[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
10.29 6 1qxnA PS5 Rep, Mult 37,85,88,89,90,111,112,113
20.18 4 3ilmA MN Rep, Mult 42,47,124
30.03 1 3icsB ADP Rep, Mult 36,37,42,54,55,85,86
40.03 1 1eu1A O Rep, Mult 112,113,114
50.03 1 2yv5A GDP Rep, Mult 56,57,90,91,92,93
60.03 1 3icrB COA Rep, Mult 1,6,9,10,13,87,88,89,92
70.03 1 3hixA MN Rep, Mult 129,131
80.03 1 3hixA MN Rep, Mult 44,128,130

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
10.2833d1pA0.6882.500.1270.8242.8.1.133
20.1601cwsA0.6862.430.0980.8323.1.3.4859,85,111
30.1423f4aB0.6692.520.1440.8093.1.3.1695
40.1262gwfC0.6392.810.1110.8173.1.2.15NA
50.0601fdiA0.5374.420.1510.8931.2.1.2NA
60.0601okgA0.7063.520.1520.9542.8.1.2NA
70.0603ictA0.7042.280.1910.8241.8.1.1483
80.0601ti2A0.5334.220.0630.8701.97.1.2NA
90.0601dmrA0.5344.180.0710.8551.7.2.386,88
100.0602oucB0.6433.290.1170.8473.1.3.16,3.1.3.4887
110.0601gn0A0.6782.140.2450.7862.8.1.136,51,94,98
120.0603ippB0.7422.790.1630.9392.8.1.1111
130.0602nyaF0.5224.570.0560.8701.7.99.4NA
140.0602e7zA0.5224.210.0980.8174.2.1.71NA
150.0601tmoA0.5244.300.0650.8471.7.2.3NA
160.0602hgsA0.5304.110.0960.8176.3.2.3NA
170.0601j8fA0.5234.130.0950.8173.5.1.-NA
180.0601h0hA0.5204.400.0890.8471.2.1.2NA
190.0602jtqA0.5771.670.2260.6412.8.1.151,85,88,111
200.0602ivfA0.5194.350.0640.8471.17.99.235,36
210.0601e1eB0.4534.790.0770.8013.2.1.21NA
220.0601hfeL0.5254.310.0940.8781.12.7.2NA
230.0601c25A0.6902.530.1070.8403.1.3.4850

(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
00.340.7122.620.210.892eg4A GO:0004792 GO:0016740 GO:0046872
10.300.7422.900.170.953p3aA GO:0004792 GO:0016740
20.270.6782.140.240.791gn0A GO:0004792 GO:0005737 GO:0006071 GO:0016740
30.250.7022.480.120.843d1pA GO:0004792 GO:0005739 GO:0016740
40.250.6692.420.260.793i2vA GO:0000166 GO:0002098 GO:0002143 GO:0003824 GO:0004792 GO:0005524 GO:0005737 GO:0005829 GO:0006777 GO:0008033 GO:0008152 GO:0008641 GO:0016740 GO:0016779 GO:0016783 GO:0018117 GO:0018192 GO:0032324 GO:0032447 GO:0034227 GO:0042292 GO:0046872 GO:0061604 GO:0061605 GO:0070733
50.230.6442.600.190.802moiA GO:0004792 GO:0005886 GO:0005887 GO:0016020 GO:0016021
60.230.7442.510.160.921h4kX GO:0004792 GO:0005737 GO:0016740
70.210.6802.740.180.851urhA GO:0004792 GO:0005737 GO:0005829 GO:0016740 GO:0016784 GO:0046677
80.190.7153.400.150.951okgA GO:0005829 GO:0016740 GO:0016784 GO:0019343 GO:0019499
90.170.7542.900.190.953hzuA GO:0004792 GO:0005618 GO:0005829 GO:0005886 GO:0016740
100.170.6902.530.110.841c25A GO:0000079 GO:0000082 GO:0000086 GO:0004721 GO:0004725 GO:0005622 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0006260 GO:0006470 GO:0007049 GO:0007067 GO:0008283 GO:0009314 GO:0016787 GO:0019901 GO:0034644 GO:0035335 GO:0051301 GO:0051726
110.170.7602.860.200.953aaxB GO:0004792 GO:0005618 GO:0005829 GO:0005886 GO:0016740
120.160.6142.520.140.743g5jA GO:0016785 GO:0043828 GO:0070329
130.150.7672.780.170.971orbA GO:0003723 GO:0004792 GO:0005615 GO:0005739 GO:0005743 GO:0005759 GO:0008097 GO:0016740 GO:0030855 GO:0035928 GO:0051029 GO:0070062
140.140.7493.070.120.963utnX GO:0002098 GO:0002143 GO:0004792 GO:0005737 GO:0005739 GO:0016740
150.140.7672.000.270.863tp9A GO:0046872
160.130.7062.410.200.851yt8A GO:0004792 GO:0016740
170.120.7422.790.160.943ippB GO:0004792 GO:0016740 GO:0016783 GO:0042597
180.120.7263.050.150.944jgtA GO:0001822 GO:0001889 GO:0004792 GO:0005737 GO:0005739 GO:0005829 GO:0009440 GO:0009636 GO:0016740 GO:0016784 GO:0019346 GO:0021510 GO:0030054 GO:0042802 GO:0043005 GO:0045202 GO:0070062 GO:0070814
190.120.7492.920.190.951uarA GO:0004792 GO:0016740
200.110.7352.360.180.863ictA GO:0000166 GO:0003756 GO:0005623 GO:0016491 GO:0045454 GO:0050451 GO:0050660 GO:0050661 GO:0055114
210.100.5771.670.230.642jtqA GO:0004792 GO:0016740 GO:0030288 GO:0042597
220.100.5203.910.140.791t3kA GO:0004721 GO:0004725 GO:0005634 GO:0005739 GO:0006468 GO:0006470 GO:0007049 GO:0007067 GO:0009507 GO:0016491 GO:0016787 GO:0035335 GO:0046685 GO:0046872 GO:0051301 GO:0055114
230.060.3105.340.070.601o8oB GO:0000166 GO:0003824 GO:0005524 GO:0005829 GO:0006777 GO:0008152 GO:0009734 GO:0016740 GO:0018315 GO:0030151 GO:0032324 GO:0046872 GO:0061598 GO:0061599


Consensus prediction of GO terms
 
Molecular Function GO:0004792 GO:0046872 GO:0016877 GO:0070566 GO:0032550 GO:0032559 GO:0035639
GO-Score 0.81 0.50 0.50 0.50 0.50 0.50 0.50
Biological Processes GO:0019400 GO:0018307 GO:0098822 GO:0046039 GO:0009108 GO:1901362 GO:0002098 GO:0090407 GO:0018130 GO:0019720 GO:1901566 GO:0044711 GO:0032446 GO:0018175
GO-Score 0.53 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50
Cellular Component GO:0044444 GO:0043231
GO-Score 0.50 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.