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I-TASSER results for job id Rv1590

[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
10.19 11 2vjeB ZN Rep, Mult 44,47,64,65
20.11 6 3raeD NUC Rep, Mult 71,72
30.07 4 1ofzA FUL Rep, Mult 65,67,68,69,73
40.07 4 1iucA FUL Rep, Mult 19,37,38,55,61
50.02 1 2cvxA DGT Rep, Mult 1,2,18,56
60.02 1 1zzdA III Rep, Mult 20,21,44,62
70.02 1 2ajrA MG Rep, Mult 33,37,39

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
10.0601gt7A0.4504.240.0270.8734.1.2.19NA
20.0601wyeA0.4423.990.0810.8482.7.1.45NA
30.0603dr2A0.4493.920.0280.8613.1.1.17NA
40.0603e7wA0.4154.320.0640.8616.1.1.1350
50.0602cu0A0.4383.840.1030.8101.1.1.205NA
60.0602z7bA0.4264.140.0810.8104.1.1.51NA
70.0601k9yA0.4394.000.0550.7853.1.3.7NA
80.0601utwF0.4454.060.0560.8863.2.1.2670
90.0602jg1A0.4513.830.0630.8352.7.1.144NA
100.0601zyzA0.4554.260.0530.8611.17.4.1NA
110.0602o6yA0.4383.610.0450.7474.3.1.-NA
120.0601oygA0.3973.820.0430.7972.4.1.10NA
130.0603cqdB0.4543.690.0380.8352.7.1.11NA
140.0603ec3A0.4444.050.0700.8355.3.4.1NA
150.0601e5eA0.4393.900.0270.8104.4.1.11NA
160.0601ebfA0.4243.740.0430.7591.1.1.3NA
170.0602wghB0.4304.230.0420.8611.17.4.1NA
180.0603ie7A0.4694.020.0250.8612.7.1.-NA
190.0603go6A0.4303.970.0770.8352.7.1.1537

(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
00.100.4363.940.180.851gqtB GO:0000166 GO:0004747 GO:0005524 GO:0005737 GO:0005829 GO:0005975 GO:0006014 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019303 GO:0046835 GO:0046872
10.070.4893.790.010.914nn2A GO:0000775 GO:0000776 GO:0000777 GO:0003677 GO:0005634 GO:0005654 GO:0005694 GO:0005730 GO:0006351 GO:0006355 GO:0008270 GO:0015631 GO:0019899 GO:0042393 GO:0042826 GO:0043021 GO:0044822 GO:0046872 GO:0051219 GO:0097110
20.070.4763.810.030.823pl2A GO:0008865 GO:0016301 GO:0016310 GO:0016740 GO:0046835
30.070.4493.740.100.843kzhA GO:0016301 GO:0016310 GO:0016740
40.070.3204.420.060.622qcvA GO:0000166 GO:0005524 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019310 GO:0047590
50.070.4553.580.080.822c49A GO:0004747 GO:0006014 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0046835
60.070.3284.460.060.633n1cA GO:0000166 GO:0000287 GO:0003872 GO:0005524 GO:0005829 GO:0005975 GO:0006096 GO:0006974 GO:0009024 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0042802 GO:0046872 GO:0061615
70.070.4744.020.110.862irpA GO:0005737 GO:0008270 GO:0008652 GO:0009086 GO:0016829 GO:0019284 GO:0019509 GO:0046570 GO:0046872
80.070.3314.220.030.653ljsB GO:0000166 GO:0005524 GO:0016301 GO:0016310 GO:0016740 GO:0016773
90.070.4423.990.080.851wyeA GO:0000166 GO:0008673 GO:0016301 GO:0016310 GO:0016740 GO:0046835
100.070.3634.720.060.734m6rA GO:0005737 GO:0006915 GO:0008270 GO:0008652 GO:0009086 GO:0016829 GO:0019284 GO:0019509 GO:0042802 GO:0043066 GO:0046570 GO:0046872 GO:0070372
110.070.3094.800.010.651vm7A GO:0004747 GO:0005524 GO:0005737 GO:0006014 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019303 GO:0046835
120.070.4684.030.030.853q1yA GO:0000166 GO:0005524 GO:0005975 GO:0005988 GO:0009024 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:2001059
130.070.4463.310.030.783in1A GO:0004747 GO:0006014 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0046835
140.070.3134.540.090.634gm6C GO:0016301 GO:0016310 GO:0016740
150.070.4454.190.030.852opiB GO:0008738 GO:0016829
160.070.4663.870.090.852f02A GO:0000166 GO:0005524 GO:0005975 GO:0005988 GO:0009024 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019512 GO:2001059
170.070.3644.040.040.711pvtA GO:0005829 GO:0008994 GO:0016829 GO:0016832 GO:0019323
180.070.4314.270.080.852fk5A


Consensus prediction of GO terms
 
Molecular Function GO:0016772 GO:0043169 GO:0032550 GO:0032559 GO:0035639
GO-Score 0.54 0.33 0.33 0.33 0.33
Biological Processes GO:0006796 GO:0044262
GO-Score 0.54 0.33
Cellular Component GO:0005829 GO:0005730 GO:0000777 GO:0005654
GO-Score 0.10 0.07 0.07 0.07

(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.