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I-TASSER results for job id Rv0692

[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 4 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
10.10 5 3ak1B EDO Rep, Mult 93,94,97
20.06 3 2axtH CLA Rep, Mult 90,91,94
30.04 2 1qpiA IMD Rep, Mult 46,47,49,50
40.04 2 3kllA MAL Rep, Mult 31,32,33,34,98,108
50.04 2 2bf0X CA Rep, Mult 97,100
60.04 2 3pfvA NA Rep, Mult 64,66,68,70,73,76
70.02 1 3u5zC 08T Rep, Mult 38,50
80.02 1 3iilA MG Rep, Mult 37,38
90.02 1 2dwlA NUC Rep, Mult 21,22,27,47,48,55,56
100.02 1 2hn2A CA Rep, Mult 84,88
110.02 1 4ej7B CA Rep, Mult 24,33
120.02 1 3eyxB ACT Rep, Mult 40,54
130.02 1 2cixA MAN Rep, Mult 59,67
140.02 1 3msuB OAA Rep, Mult 73,74,77,94,97
150.02 1 3gc9B ZN Rep, Mult 16,69,71

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
10.0602ib7D0.4604.890.0720.8622.3.1.9NA
20.0602q85A0.4534.190.0340.7711.1.1.158NA
30.0603k92A0.4474.560.1040.8441.4.1.295
40.0603il7A0.4444.470.0850.8072.3.1.180NA
50.0603gpyA0.4514.620.1010.8073.2.2.2347,79
60.0603cf4A0.4533.890.0590.7161.2.99.2NA
70.0601wogA0.4614.840.0880.8813.5.3.1172
80.0602i7vA0.4534.840.0460.8813.1.27.-NA
90.0601bw9A0.4264.750.0570.8171.4.1.2072
100.0601z1eA0.4594.520.0790.8532.3.1.95NA
110.0601u0uA0.4444.680.0780.8622.3.1.-NA
120.0603ffzA0.4504.930.0690.8813.4.24.69NA
130.0601e9iD0.4484.740.0500.8354.2.1.11NA
140.0601k3pA0.4614.190.1120.8172.3.3.1NA
150.0602irpA0.4574.220.0600.7524.2.1.109NA
160.0601gq7E0.4354.360.0780.7893.5.3.22NA
170.0602p0uA0.4564.750.0780.8532.3.1.74NA
180.0601iomA0.4534.780.0710.8624.1.3.7NA
190.0601vgmA0.4424.720.0510.8264.1.3.7NA

(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
00.070.4964.220.120.844yahX GO:0005886 GO:0006810 GO:0006865 GO:0016020 GO:0048473
10.070.4794.210.080.841xs5A GO:0005886 GO:0016020
20.070.4774.370.100.844gotA GO:0005886 GO:0006810 GO:0006865 GO:0016020
30.070.4674.200.110.834oteB GO:0046872
40.070.4424.720.050.831vgmA GO:0005737 GO:0006099 GO:0016020 GO:0016021 GO:0016740 GO:0016746 GO:0046912
50.070.4564.320.040.821o7xC GO:0003824 GO:0005737 GO:0006099 GO:0008152 GO:0016740 GO:0046912
60.060.4174.540.060.751x0aA GO:0000166 GO:0008152 GO:0016491 GO:0055114
70.060.4224.490.070.744ntlA GO:0046872
80.060.3014.720.060.534ryeA GO:0004175 GO:0004180 GO:0005887 GO:0006508 GO:0009002 GO:0009252 GO:0016787
90.060.4614.190.110.824g6bA GO:0003824 GO:0004108 GO:0005737 GO:0005829 GO:0006099 GO:0008152 GO:0016740 GO:0042802 GO:0046912
100.060.4474.240.020.811vgpA GO:0005737 GO:0006099 GO:0016740 GO:0016746 GO:0046912
110.060.4424.820.050.831aj8A GO:0003824 GO:0005737 GO:0006099 GO:0008152 GO:0016740 GO:0046912
120.060.3645.220.010.782ibpA GO:0005737 GO:0006099 GO:0016740 GO:0046912
130.060.4514.730.070.834xghA GO:0004108 GO:0005737 GO:0006099 GO:0016740 GO:0016746 GO:0046912
140.060.3354.700.010.592l2cA GO:0005549
150.060.4564.240.110.824e6yA GO:0004108 GO:0005737 GO:0006099 GO:0016020 GO:0016021 GO:0016740 GO:0016746 GO:0046912
160.060.4534.780.070.861iomA GO:0005737 GO:0016740 GO:0046912
170.060.4214.910.080.852h12B GO:0003824 GO:0004108 GO:0005737 GO:0006099 GO:0008152 GO:0016740 GO:0046912
180.060.3394.670.020.611t72A GO:0005315 GO:0005436 GO:0005737 GO:0005886 GO:0006810 GO:0006817 GO:0010629 GO:0015321 GO:0030643 GO:0035435 GO:0035725 GO:0042803 GO:0044341 GO:0045936 GO:0055085 GO:2000186


Consensus prediction of GO terms
 
Molecular Function GO:0046872 GO:0046912
GO-Score 0.07 0.07
Biological Processes GO:0048473 GO:0006099
GO-Score 0.07 0.07
Cellular Component GO:0071944
GO-Score 0.37

(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.