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I-TASSER results for job id Rv2840c

[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 12 4up0A ZN Rep, Mult 4,7,47,52
20.12 5 3h1cR III Rep, Mult 45,47,53
30.09 2 1g2rA SO4 Rep, Mult 2,18,43,45
40.02 1 1ibk4 III Rep, Mult 15,72,76,83,85,86,87,88
50.02 1 1ibk9 III Rep, Mult 18,19,44,46,56,57,58,59,60,61,62,63,70,74

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
10.0601e1yA0.3754.670.0330.7172.4.1.1NA
20.0601wdeA0.4774.040.1020.7982.1.1.985,69
30.0602jg6A0.4823.620.0810.7273.2.2.20NA
40.0601r6lA0.4733.780.1000.7782.7.7.56NA
50.0601udoA0.5093.690.0940.8182.7.7.56NA
60.0603gpbA0.4234.420.1200.7982.4.1.1NA
70.0602wodA0.5033.710.0580.7583.2.2.2464
80.0602qllA0.4804.330.0710.7682.4.1.1NA
90.0601qi9B0.4834.270.0570.8181.11.1.10NA
100.0603cdjA0.5383.390.0960.8082.7.7.834
110.0601s9cD0.4904.440.0520.8494.2.1.107NA
120.0601fa9A0.3764.740.0650.7272.4.1.1NA
130.0602pffB0.4764.420.0820.8492.3.1.8625
140.0601z1lA0.3334.420.0200.6263.1.4.17NA
150.0603fy4A0.4844.450.0210.7884.1.99.1345
160.0602a96B0.4804.030.0630.7683.1.3.247
170.0602zuwC0.4863.980.0670.7682.4.1.211NA
180.0602nztA0.4663.990.1000.7272.7.1.1NA
190.0601dinA0.4744.070.1070.8493.1.1.457

(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
00.070.5223.850.060.821e3pA GO:0000175 GO:0000287 GO:0003676 GO:0003723 GO:0004654 GO:0005737 GO:0006396 GO:0006402 GO:0016740 GO:0016779 GO:0046872 GO:0090503
10.070.5383.390.100.813cdjA GO:0000175 GO:0000287 GO:0003676 GO:0003723 GO:0004654 GO:0005737 GO:0005829 GO:0006396 GO:0006402 GO:0009408 GO:0016020 GO:0016740 GO:0016779 GO:0035438 GO:0042802 GO:0046872 GO:0090503
20.070.5143.800.110.822br2P GO:0000175 GO:0000177 GO:0000178 GO:0004518 GO:0004527 GO:0005737 GO:0006401 GO:0016075 GO:0016787 GO:0016896 GO:0090305 GO:0090503
30.070.5013.790.060.801oyrA GO:0000049 GO:0004549 GO:0006364 GO:0008033 GO:0009022 GO:0016075 GO:0016740 GO:0016779 GO:0031125 GO:0090501
40.070.4963.790.100.803dd6A GO:0000049 GO:0004540 GO:0004549 GO:0008033 GO:0009022 GO:0016740 GO:0016779 GO:0090501
50.070.5073.940.090.815c0wB GO:0000176 GO:0000177 GO:0000178 GO:0000467 GO:0003723 GO:0005634 GO:0005730 GO:0005737 GO:0006364 GO:0016075 GO:0034427 GO:0034473 GO:0034475 GO:0034476 GO:0070478 GO:0070481 GO:0070651 GO:0071028 GO:0071038 GO:0071039 GO:0071042 GO:0071051
60.070.5033.960.050.812pnzB GO:0000178 GO:0005737 GO:0006401
70.070.5243.650.080.824aidA GO:0000175 GO:0000287 GO:0003676 GO:0003723 GO:0004654 GO:0005737 GO:0006396 GO:0006402 GO:0016740 GO:0016779 GO:0046872 GO:0090503
80.070.4793.840.120.792nn6B GO:0000175 GO:0000176 GO:0000177 GO:0000178 GO:0000460 GO:0000956 GO:0003723 GO:0004532 GO:0005634 GO:0005654 GO:0005730 GO:0005737 GO:0005829 GO:0006364 GO:0016075 GO:0017091 GO:0030307 GO:0031125 GO:0034427 GO:0034475 GO:0035327 GO:0043488 GO:0043928 GO:0045006 GO:0051607 GO:0071028 GO:0071044 GO:0071051 GO:0090503
90.070.5313.500.110.823cdiA GO:0000175 GO:0000287 GO:0003676 GO:0003723 GO:0004654 GO:0005737 GO:0005829 GO:0006396 GO:0006402 GO:0009408 GO:0016020 GO:0016740 GO:0016779 GO:0035438 GO:0042802 GO:0046872 GO:0090503
100.070.4984.040.060.832nn6D GO:0000175 GO:0000176 GO:0000177 GO:0000178 GO:0003723 GO:0004532 GO:0005634 GO:0005654 GO:0005730 GO:0005737 GO:0005829 GO:0006364 GO:0016075 GO:0031125 GO:0034427 GO:0034475 GO:0035327 GO:0043488 GO:0043928 GO:0045006 GO:0051607 GO:0071028 GO:0071051 GO:0090503
110.070.5093.770.090.813krnA
120.070.5083.670.100.821udnA GO:0000049 GO:0004549 GO:0008033 GO:0009022 GO:0016075 GO:0016740 GO:0016779 GO:0090501
130.070.5303.690.040.833u1kC GO:0000175 GO:0000957 GO:0000958 GO:0000962 GO:0000964 GO:0000965 GO:0003676 GO:0003723 GO:0004518 GO:0004527 GO:0004654 GO:0005737 GO:0005739 GO:0005758 GO:0006396 GO:0006397 GO:0006401 GO:0006402 GO:0006810 GO:0008266 GO:0016020 GO:0016740 GO:0016779 GO:0016787 GO:0034046 GO:0034599 GO:0035198 GO:0035458 GO:0035927 GO:0035928 GO:0043457 GO:0043631 GO:0044822 GO:0045025 GO:0045926 GO:0051260 GO:0061014 GO:0070207 GO:0070584 GO:0071042 GO:0071850 GO:0090305 GO:0090503 GO:0097222 GO:2000627 GO:2000772
140.070.4734.310.110.822wnrB GO:0000175 GO:0000178 GO:0004518 GO:0004527 GO:0005737 GO:0006401 GO:0016787 GO:0016896 GO:0090305 GO:0090503
150.070.5053.830.090.813hkmB GO:0000176 GO:0000177 GO:0000178 GO:0003677 GO:0003690 GO:0003723 GO:0003727 GO:0004518 GO:0004527 GO:0004536 GO:0004540 GO:0005634 GO:0005730 GO:0006259 GO:0006364 GO:0016075 GO:0016787 GO:0031125 GO:0034427 GO:0034475 GO:0042802 GO:0071028 GO:0071051 GO:0090305 GO:0090501
160.070.5063.850.100.813m85I GO:0000178 GO:0005737 GO:0006401
170.070.4963.820.070.802wp8B GO:0000176 GO:0000177 GO:0000178 GO:0000467 GO:0003723 GO:0005634 GO:0005730 GO:0005737 GO:0006364 GO:0016075 GO:0034427 GO:0034473 GO:0034475 GO:0034476 GO:0070478 GO:0070481 GO:0070651 GO:0071028 GO:0071038 GO:0071039 GO:0071042 GO:0071051
180.070.4764.050.030.812pnzA GO:0000175 GO:0000178 GO:0004518 GO:0004527 GO:0005737 GO:0006401 GO:0016787 GO:0016896 GO:0090305 GO:0090503


Consensus prediction of GO terms
 
Molecular Function GO:0016772 GO:0016896 GO:0008408
GO-Score 0.48 0.37 0.37
Biological Processes GO:0090501
GO-Score 0.37
Cellular Component GO:0044424
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.