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I-TASSER results for job id Rv2307D

[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
10.09 9 1t85A UUU Rep, Mult 19,20,30,40,41,44,45,46,49,50
20.06 6 2z97A 7HE Rep, Mult 15,21,22,23,25,27
30.05 5 2qbnA HEM Rep, Mult 16,22,30,39,54,55
40.04 4 3q2wA MAN Rep, Mult 30,40
50.04 4 1nx0B III Rep, Mult 1,5
60.03 3 1dz4B HEM Rep, Mult 20,21,24,28,39,51
70.03 3 2zawA 6HE Rep, Mult 15,16,23,32,33,34,39
80.02 2 1usyF HIS Rep, Mult 5,9
90.02 2 1iwjA HEM Rep, Mult 4,5,16,17,20,29,30,39,41
100.02 2 2gcpA MG Rep, Mult 3,14
110.01 1 1mpwA TMH Rep, Mult 25,29,40
120.01 1 1le9A NUC Rep, Mult 12,13,16,17
130.01 1 3p6oA ETG Rep, Mult 14,15,41,46
140.01 1 3fxrA SO4 Rep, Mult 1,2,3,54,56
150.01 1 1w77A CU Rep, Mult 48,58
160.01 1 1vkxA NUC Rep, Mult 12,13
170.01 1 1akdA CAM Rep, Mult 9,36,39
180.01 1 2nxfA ZN Rep, Mult 4,8

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
10.0602a4kB0.3993.810.0910.8671.1.1.100NA
20.0601w6jA0.4293.450.1330.9005.4.99.7NA
30.0601px8A0.3784.320.0350.9173.2.1.37NA
40.0601zd1A0.4263.760.0360.7502.8.2.-NA
50.0602a4kA0.4313.690.1270.8501.1.1.100NA
60.0603eolA0.3973.750.0190.8504.1.3.1NA
70.0601e5eA0.4343.690.0730.8504.4.1.11NA
80.0602cb1A0.4334.000.0890.8834.2.99.10NA
90.0601bsgA0.4283.970.0730.9003.5.2.6NA
100.0601e6vA0.4263.920.0180.9002.8.4.1NA
110.0601f89A0.4323.610.0580.8333.5.-.-NA
120.0601xkyA0.4183.920.0370.8674.2.1.52NA
130.0603cogD0.4373.670.0360.8504.4.1.1NA
140.0603eolB0.3863.870.0180.8834.1.3.1NA
150.0601ut9A0.4303.810.0360.9003.2.1.4NA
160.0604matA0.4263.400.0930.7833.4.11.18NA
170.0601cb7B0.4313.810.0190.8505.4.99.1NA
180.0601fo2A0.4253.950.0330.8673.2.1.113NA
190.0601y4iA0.4343.890.0730.8674.4.1.11NA

(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
00.070.4463.550.170.784up8A GO:0000049 GO:0000166 GO:0003676 GO:0004812 GO:0004824 GO:0005524 GO:0005737 GO:0006418 GO:0006430
10.060.3423.880.050.754dpgB GO:0000049 GO:0000166 GO:0003676 GO:0004812 GO:0004824 GO:0005524 GO:0005576 GO:0005634 GO:0005737 GO:0005739 GO:0005759 GO:0005829 GO:0005886 GO:0006412 GO:0006418 GO:0006430 GO:0008033 GO:0015630 GO:0015966 GO:0016020 GO:0016032 GO:0016597 GO:0016874 GO:0017101 GO:0046872
20.060.3753.810.040.784up7A GO:0000049 GO:0000166 GO:0003676 GO:0004812 GO:0004824 GO:0005524 GO:0005737 GO:0006418 GO:0006430
30.060.4023.690.060.751asyA GO:0000166 GO:0003676 GO:0003723 GO:0004812 GO:0004815 GO:0005524 GO:0005634 GO:0005737 GO:0006412 GO:0006418 GO:0006422 GO:0016874
40.060.4603.780.090.922yikA GO:0000272 GO:0003824 GO:0004553 GO:0005975 GO:0016787 GO:0046872
50.060.3783.420.020.753kfuC GO:0000166 GO:0003676 GO:0004812 GO:0004815 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006422 GO:0016874 GO:0050560
60.060.3324.200.040.774pe5C GO:0004872 GO:0004970 GO:0004972 GO:0005102 GO:0005216 GO:0005234 GO:0005886 GO:0006810 GO:0006811 GO:0007611 GO:0010942 GO:0014069 GO:0014070 GO:0014075 GO:0016020 GO:0016021 GO:0016594 GO:0016595 GO:0017146 GO:0019899 GO:0022843 GO:0030054 GO:0032590 GO:0034220 GO:0034765 GO:0035235 GO:0035254 GO:0042165 GO:0043025 GO:0043083 GO:0043195 GO:0043197 GO:0044307 GO:0045202 GO:0045211 GO:0046982 GO:0046983 GO:0048511 GO:0051262 GO:0051592 GO:0060076 GO:0060992 GO:0071287 GO:2000463
70.060.3913.750.090.823a5yA GO:0000166 GO:0004812 GO:0004824 GO:0005524 GO:0005737 GO:0005829 GO:0006418 GO:0006430 GO:0016874 GO:0016880 GO:0043687 GO:0052868 GO:0071915 GO:0072581
80.060.3823.740.050.801b8aA GO:0000166 GO:0003676 GO:0004812 GO:0004815 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006422 GO:0016874 GO:0046872
90.060.3424.250.030.801ia7A GO:0000272 GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0046872
100.060.3733.800.070.823i7fA GO:0000166 GO:0004812 GO:0004815 GO:0005524 GO:0005737 GO:0006418 GO:0006422
110.060.3723.720.130.785a9zAI GO:0003723 GO:0005622 GO:0005840 GO:0006412 GO:0019843 GO:0030529 GO:0042254 GO:0070180
120.060.3623.810.050.722cxfA GO:0005737 GO:0007015 GO:0007275 GO:0007399 GO:0012505 GO:0016020 GO:0030027 GO:0030054 GO:0030154 GO:0030175 GO:0030335 GO:0030424 GO:0030425 GO:0030426 GO:0042995 GO:0043025 GO:0043204 GO:0045773 GO:0050770 GO:0050771 GO:0050772 GO:0071437 GO:0090316 GO:2000114
130.060.3824.490.100.874dodA GO:0000272 GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798 GO:0030245 GO:0030246 GO:0030248 GO:0046872
140.060.3663.360.040.751n9wA GO:0000166 GO:0003676 GO:0004812 GO:0004815 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006422 GO:0016874 GO:0050560
150.060.3603.830.060.773m4qB GO:0000166 GO:0003676 GO:0004812 GO:0004816 GO:0005524 GO:0005737 GO:0006418 GO:0006421
160.060.3513.390.050.654piaA GO:0004040 GO:0016020 GO:0016021
170.060.3344.520.040.855fxkA GO:0004872 GO:0004970 GO:0004972 GO:0005102 GO:0005216 GO:0005234 GO:0005886 GO:0006810 GO:0006811 GO:0007611 GO:0010942 GO:0014069 GO:0014070 GO:0014075 GO:0016020 GO:0016021 GO:0016594 GO:0016595 GO:0017146 GO:0019899 GO:0022843 GO:0030054 GO:0032590 GO:0034220 GO:0034765 GO:0035235 GO:0035254 GO:0042165 GO:0043025 GO:0043083 GO:0043195 GO:0043197 GO:0044307 GO:0045202 GO:0045211 GO:0046982 GO:0046983 GO:0048511 GO:0051262 GO:0051592 GO:0060076 GO:0060992 GO:0071287 GO:2000463
180.060.3664.320.070.834cj1A GO:0000272 GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798 GO:0030245


Consensus prediction of GO terms
 
Molecular Function GO:0032559 GO:0035639 GO:0032550 GO:0016876 GO:0003723
GO-Score 0.47 0.47 0.47 0.47 0.36
Biological Processes GO:0043039 GO:0006412
GO-Score 0.47 0.47
Cellular Component GO:0044424
GO-Score 0.47

(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.