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I-TASSER results for job id Rv2709

[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
10.10 5 1knyA APC Rep, Mult 44,48
20.10 5 2zfeA XE Rep, Mult 65,66,69,78,81,82
30.04 2 2axtl UNK Rep, Mult 60,63
40.04 2 2hi8X BR Rep, Mult 97,98,99,102
50.04 2 2axtH CLA Rep, Mult 53,56
60.02 1 3jv2A III Rep, Mult 50,80,81,82,86
70.02 1 4ywqA ZN Rep, Mult 42,80
80.02 1 2wpnB SBY Rep, Mult 15,52
90.02 1 3lw52 CLA Rep, Mult 83,87
100.02 1 4amiA 2CV Rep, Mult 30,34
110.02 1 3hd7F GGG Rep, Mult 48,51
120.02 1 2r9vA MG Rep, Mult 35,112
130.02 1 1jb0K CLA Rep, Mult 89,94
140.02 1 2ql2C NUC Rep, Mult 46,50

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
10.0602pffA0.4295.010.0750.7502.3.1.41,2.3.1.86NA
20.0601alkA0.4215.230.0500.7303.1.3.1NA
30.0603evhA0.4214.790.1250.7034.2.2.3NA
40.0603czkA0.4394.740.1090.7373.2.1.48NA
50.0602a4zA0.3954.670.0080.6762.7.1.153NA
60.0603hhsB0.4305.280.0350.7771.14.18.1NA
70.0603fr8B0.4344.530.0410.6821.1.1.86NA
80.0602gtqA0.4264.970.0530.7033.4.11.2NA
90.0602fp0B0.3995.020.0840.7033.2.1.143NA
100.0603c5wA0.4154.740.0620.6823.1.3.1641
110.0602cw7A0.4424.980.0580.7632.7.7.7NA
120.0601t3tA0.4295.320.0570.7846.3.5.314
130.0601qmgA0.4314.550.0470.6821.1.1.86NA
140.0601ujkB0.3934.320.0530.6013.4.23.4666,96
150.0601ultA0.4344.140.0690.6356.2.1.373
160.0602pflA0.4324.830.0440.7572.3.1.5456,80
170.0601ajbA0.4215.230.0500.7303.1.3.1NA
180.0601h16A0.4204.970.0370.7372.3.1.54NA
190.0602pffD0.4305.200.0440.7702.3.1.8634

(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
00.070.4794.180.060.752iw3B GO:0000166 GO:0001933 GO:0003723 GO:0003746 GO:0005524 GO:0005737 GO:0005840 GO:0006412 GO:0006414 GO:0006415 GO:0006469 GO:0010494 GO:0016887 GO:0019843 GO:0022626 GO:0042788
10.070.4384.230.090.684g3aB GO:0000022 GO:0000070 GO:0000775 GO:0000776 GO:0000922 GO:0005525 GO:0005634 GO:0005737 GO:0005813 GO:0005815 GO:0005819 GO:0005827 GO:0005856 GO:0005874 GO:0005875 GO:0005876 GO:0007049 GO:0007051 GO:0007052 GO:0007067 GO:0007275 GO:0007282 GO:0007411 GO:0008017 GO:0016325 GO:0019827 GO:0030154 GO:0030426 GO:0030723 GO:0031116 GO:0032154 GO:0035099 GO:0035371 GO:0040001 GO:0042995 GO:0045169 GO:0045172 GO:0046580 GO:0046602 GO:0048477 GO:0051225 GO:0051301 GO:0051315 GO:0090307
20.060.4794.040.080.724a0cA GO:0000151 GO:0005634 GO:0005654 GO:0005737 GO:0005794 GO:0010265 GO:0016020 GO:0016567 GO:0017025 GO:0030154 GO:0031461 GO:0043086 GO:0045893 GO:0045899 GO:0070062
30.060.3834.600.010.634ohwA GO:0000166 GO:0005524 GO:0005634 GO:0005849 GO:0006378 GO:0006379 GO:0006388 GO:0006397 GO:0031124 GO:0046939 GO:0051736
40.060.4224.400.050.714ol0B GO:0004872 GO:0005634 GO:0005737 GO:0006810 GO:0008139 GO:0008565 GO:0015031 GO:0031965 GO:0035048 GO:0042802 GO:0043231
50.060.4064.210.060.615f9hG GO:0000166 GO:0002230 GO:0002376 GO:0003676 GO:0003690 GO:0003723 GO:0003725 GO:0003727 GO:0004386 GO:0005524 GO:0005737 GO:0005829 GO:0005856 GO:0005886 GO:0005923 GO:0008270 GO:0009597 GO:0009615 GO:0010628 GO:0015629 GO:0016020 GO:0016032 GO:0016787 GO:0016817 GO:0030054 GO:0030334 GO:0032480 GO:0032587 GO:0032725 GO:0032727 GO:0032728 GO:0032755 GO:0032757 GO:0034344 GO:0039528 GO:0039529 GO:0042802 GO:0042993 GO:0042995 GO:0043330 GO:0045087 GO:0045944 GO:0046872 GO:0051091 GO:0051607
60.060.4044.090.060.615f9fI GO:0000166 GO:0002230 GO:0002376 GO:0003676 GO:0003690 GO:0003723 GO:0003725 GO:0003727 GO:0004386 GO:0005524 GO:0005737 GO:0005829 GO:0005856 GO:0005886 GO:0005923 GO:0008270 GO:0009597 GO:0009615 GO:0010628 GO:0015629 GO:0016020 GO:0016032 GO:0016787 GO:0016817 GO:0030054 GO:0030334 GO:0032480 GO:0032587 GO:0032725 GO:0032727 GO:0032728 GO:0032755 GO:0032757 GO:0034344 GO:0039528 GO:0039529 GO:0042802 GO:0042993 GO:0042995 GO:0043330 GO:0045087 GO:0045944 GO:0046872 GO:0051091 GO:0051607
70.060.3874.630.100.663tuzC GO:0000166 GO:0003333 GO:0005524 GO:0005886 GO:0006810 GO:0006865 GO:0009276 GO:0015424 GO:0015821 GO:0016020 GO:0016787 GO:0016887 GO:0042626 GO:0043190 GO:0048473 GO:0048474 GO:0055085
80.060.3484.940.040.631oc5A GO:0000272 GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0016162 GO:0016787 GO:0016798 GO:0030245 GO:0030248
90.060.3205.700.090.621ji0A GO:0000166 GO:0005524 GO:0015658 GO:0015803 GO:0016887
100.060.4044.410.040.664mmhA GO:0015021 GO:0016829 GO:0030200 GO:0042597
110.060.3854.530.030.612ykgA GO:0000166 GO:0002230 GO:0002376 GO:0003676 GO:0003690 GO:0003723 GO:0003725 GO:0003727 GO:0004386 GO:0005524 GO:0005737 GO:0005829 GO:0005856 GO:0005886 GO:0005923 GO:0008270 GO:0009597 GO:0009615 GO:0010628 GO:0015629 GO:0016020 GO:0016032 GO:0016787 GO:0016817 GO:0030054 GO:0030334 GO:0032480 GO:0032587 GO:0032725 GO:0032727 GO:0032728 GO:0032755 GO:0032757 GO:0034344 GO:0039528 GO:0039529 GO:0042802 GO:0042993 GO:0042995 GO:0043330 GO:0045087 GO:0045944 GO:0046872 GO:0051091 GO:0051607
120.060.3804.850.060.655dn8A GO:0000027 GO:0000166 GO:0003924 GO:0005525 GO:0005737 GO:0042254 GO:0043022
130.060.3974.800.060.661w63A GO:0005737 GO:0005794 GO:0005802 GO:0005829 GO:0006810 GO:0006886 GO:0008565 GO:0015031 GO:0016020 GO:0016192 GO:0017137 GO:0019894 GO:0030117 GO:0030131 GO:0030136 GO:0030665 GO:0030742 GO:0031410 GO:0035646 GO:0043231 GO:0043323 GO:0045954 GO:0048471 GO:0055037 GO:0090160
140.060.4274.560.060.704c0qA GO:0004872 GO:0005634 GO:0005737 GO:0006810 GO:0008139 GO:0008565 GO:0015031 GO:0031965 GO:0035048 GO:0042802 GO:0043231
150.060.3114.980.050.531mkyA GO:0000027 GO:0000166 GO:0003924 GO:0005525 GO:0005737 GO:0042254 GO:0043022
160.060.3495.070.070.643pihA GO:0000166 GO:0003677 GO:0003824 GO:0004518 GO:0005524 GO:0005737 GO:0006281 GO:0006289 GO:0006974 GO:0008270 GO:0009380 GO:0009381 GO:0009432 GO:0016887 GO:0046872 GO:0090305
170.060.3285.200.110.613b5xA GO:0000166 GO:0005319 GO:0005524 GO:0005886 GO:0006810 GO:0006869 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0034040 GO:0042626 GO:0043190 GO:0055085
180.060.3614.940.080.642d62A GO:0000166 GO:0005215 GO:0005524 GO:0006810 GO:0016820 GO:0016887 GO:0043190 GO:0055085


Consensus prediction of GO terms
 
Molecular Function GO:0005524 GO:0019843 GO:0016887 GO:0003746 GO:0004872 GO:0042802 GO:0005525 GO:0008565 GO:0017025 GO:0008017 GO:0051736 GO:0008139
GO-Score 0.13 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07
Biological Processes GO:0006469 GO:0006414 GO:0006415 GO:0040001 GO:0006388 GO:0035099 GO:0031116 GO:0046580 GO:0006379 GO:0046602 GO:0016325 GO:0000022 GO:0016567 GO:0007411 GO:0051315 GO:0006378 GO:0010265 GO:0030723 GO:0007282 GO:0035048 GO:0045899 GO:0046939 GO:0019827 GO:0090307
GO-Score 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07
Cellular Component GO:0043231
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.