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I-TASSER results for job id Rv2510c

[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
10.60 28 1gkiD ADP Rep, Mult 61,62,63,64,65,66,67,68,414
20.03 2 1gkiA ADP Rep, Mult 54,322
30.02 1 4ag5A MG Rep, Mult 67,90

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
10.0602a4zA0.3447.210.0510.5422.7.1.153NA
20.0601n1hA0.3657.730.0290.6142.7.7.48NA
30.0602nyaA0.3507.060.0450.5401.7.99.4NA
40.0601uaaA0.3906.440.0600.5673.6.4.12NA
50.0601jqnA0.3457.380.0600.5504.1.1.31349
60.0602v45A0.3677.400.0600.5931.7.99.4NA
70.0601w36C0.3496.580.0400.5163.1.11.5NA
80.0602r7oA0.3617.430.0560.5892.7.7.48NA
90.0601w36B0.3716.810.0450.5523.1.11.583
100.0601ti2A0.3707.240.0380.5851.97.1.2NA
110.0602qf7A0.3437.210.0570.5486.4.1.1NA
120.0601pjrA0.3697.010.0320.5653.6.4.12NA
130.0602nyaF0.3486.940.0410.5311.7.99.4NA
140.0601h0hA0.3697.570.0540.6121.2.1.2NA
150.0602vsfA0.3666.010.0700.5083.6.4.12360
160.0603pjrA0.3996.770.0680.5933.6.4.12NA
170.0601t3tA0.3457.390.0460.5576.3.5.3NA
180.0603crvA0.3625.850.0770.4923.6.4.1263,298,300
190.0602qf7B0.3447.210.0630.5486.4.1.1NA

(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
00.300.6671.720.160.694d2iA GO:0000166 GO:0004386 GO:0005524 GO:0006281 GO:0006974 GO:0016787
10.210.5274.660.130.651e9sA GO:0000166 GO:0016020 GO:0016021
20.190.2576.170.060.371pujA GO:0000166 GO:0003723 GO:0003924 GO:0005525 GO:0005737 GO:0016787 GO:0042254
30.170.5263.940.140.624ag6B GO:0000166
40.090.2937.130.060.472iusD GO:0000166 GO:0000920 GO:0003677 GO:0005524 GO:0005886 GO:0005887 GO:0006970 GO:0007049 GO:0007059 GO:0009651 GO:0015616 GO:0016020 GO:0016021 GO:0016887 GO:0033676 GO:0042802 GO:0043085 GO:0043565 GO:0045893 GO:0051301 GO:0071236
50.060.3893.850.150.452iutA GO:0000166 GO:0003677 GO:0005524 GO:0005886 GO:0007049 GO:0007059 GO:0016020 GO:0016021 GO:0051301 GO:0071236
60.060.3733.950.140.444ag5D GO:0000166
70.060.3357.280.040.544l22A GO:0004645 GO:0005975 GO:0008184 GO:0016740 GO:0016757 GO:0030170
80.060.3084.100.100.372w0mA GO:0000150 GO:0000400 GO:0000730 GO:0003690 GO:0003697 GO:0004520 GO:0005524 GO:0006312 GO:0008094 GO:0010212 GO:0042148 GO:0046872
90.060.2875.410.070.382qbyA GO:0000166 GO:0003677 GO:0005524 GO:0006260
100.060.2955.180.110.382pjzA GO:0005524 GO:0016887
110.060.2917.620.060.483h71B GO:0004308 GO:0005576 GO:0005618 GO:0005737 GO:0005975 GO:0006689 GO:0008152 GO:0009313 GO:0016020 GO:0016787 GO:0016798 GO:0043231 GO:0052794 GO:0052795 GO:0052796
120.060.2526.060.070.354delA GO:0003824 GO:0004332 GO:0005576 GO:0005618 GO:0005829 GO:0005886 GO:0005975 GO:0006094 GO:0006096 GO:0008270 GO:0016829 GO:0016832 GO:0046872
130.060.2684.210.130.324ag6D GO:0000166
140.060.2266.510.030.344mo2B GO:0000166 GO:0008767 GO:0016853
150.060.2557.230.040.412cmlA GO:0004308 GO:0005975 GO:0008152 GO:0016020 GO:0016021 GO:0016787 GO:0016798 GO:0019012 GO:0020002 GO:0033644 GO:0046872 GO:0052794 GO:0052795 GO:0052796 GO:0055036
160.060.2356.720.040.352vugA GO:0000166
170.060.2126.070.040.303h3dY GO:0000288 GO:0000900 GO:0001709 GO:0003723 GO:0003730 GO:0005635 GO:0005737 GO:0006417 GO:0007067 GO:0007268 GO:0007275 GO:0007280 GO:0007281 GO:0007616 GO:0008258 GO:0008582 GO:0008595 GO:0016441 GO:0016477 GO:0017148 GO:0031594 GO:0042059 GO:0042078 GO:0045727 GO:0045786 GO:0045892 GO:0048149 GO:0048477 GO:0048813 GO:0050804 GO:0060213 GO:0061176 GO:0061177 GO:0097482
180.060.1985.330.070.263gdhA GO:0000387 GO:0001510 GO:0005615 GO:0005634 GO:0005654 GO:0005730 GO:0005737 GO:0005829 GO:0006351 GO:0006355 GO:0008168 GO:0008173 GO:0009452 GO:0015030 GO:0016740 GO:0022613 GO:0030532 GO:0032259 GO:0036261 GO:0044255 GO:0071164 GO:0071167


Consensus prediction of GO terms
 
Molecular Function GO:0017111 GO:0032561 GO:0003676 GO:0005524
GO-Score 0.59 0.37 0.37 0.36
Biological Processes GO:0033554 GO:0006259 GO:0022613
GO-Score 0.59 0.59 0.37
Cellular Component GO:0031224 GO:0044424
GO-Score 0.45 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.