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I-TASSER results for job id Rv2433c

[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
10.13 5 2iypB UUU Rep, Mult 67,70,71,73
20.06 2 3ze3D 78M Rep, Mult 36,39,43,47
30.05 2 4amiA 2CV Rep, Mult 64,68
40.05 2 5d56B 78M Rep, Mult 33,36,40
50.03 1 3kziX CLA Rep, Mult 34,37
60.03 1 3wmoP BCL Rep, Mult 49,50
70.03 1 2jkvA NAP Rep, Mult 32,72,73,77
80.03 1 1gk9B EDO Rep, Mult 52,63,64,65
90.03 1 3c9iA XE Rep, Mult 49,66
100.03 1 3rkoN LFA Rep, Mult 40,41,44,63,64,67
110.03 1 3a3yB CLR Rep, Mult 66,70
120.03 1 3se1A MG Rep, Mult 42,45

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
10.1623h36A0.5092.800.0960.6882.7.7.815,39
20.0661r6rB0.4523.740.0790.7602.1.1.56,2.7.7.4812,31,34
30.0602o36A0.5693.420.0950.8653.4.24.1537
40.0601tiwA0.5833.230.0940.8441.5.1.12,1.5.99.86
50.0602pulA0.5593.960.0830.9062.7.1.100NA
60.0601s4bP0.5683.430.0950.8653.4.24.1577
70.0601bwkA0.5423.730.1460.8851.6.99.1NA
80.0602uxwA0.5523.990.0990.9271.3.99.-46
90.0603lomA0.5572.710.0420.7502.5.1.1067
100.0601rh9A0.5513.850.0820.8543.2.1.78NA
110.0602f6dA0.5642.910.1260.7603.2.1.369
120.0602iz1B0.5873.950.0000.9271.1.1.4465
130.0601yi8A0.5553.240.1230.8336.1.1.2NA
140.0603fwnA0.5663.730.0440.8961.1.1.4465
150.0603hhsB0.5763.630.0470.8961.14.18.1NA
160.0601jtnA0.3394.600.0540.5213.2.1.17NA
170.0601pgjA0.5504.030.0430.8961.1.1.4437
180.0601vbgA0.5544.280.0890.9172.7.9.1NA
190.0602i2xA0.5543.620.0110.8962.1.1.9068
200.0602w90B0.5913.790.0000.9271.1.1.4465
210.0602v8tA0.5583.710.0220.8541.11.1.6NA

(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
00.190.6762.490.100.892n39A GO:0000166 GO:0003677 GO:0004003 GO:0004386 GO:0005524 GO:0005634 GO:0005737 GO:0006338 GO:0006351 GO:0006355 GO:0006357 GO:0016568 GO:0016787 GO:0032508 GO:0035064 GO:0043923
10.070.6403.340.070.933zheB GO:0000184 GO:0005634 GO:0005737
20.070.5493.980.040.864d8mA GO:0009405 GO:0030435
30.070.6303.670.060.951ciyA GO:0005102 GO:0006952 GO:0009405 GO:0030435
40.070.6253.620.070.944w8jA GO:0005102 GO:0006952 GO:0009405 GO:0030435
50.070.5103.700.050.812c9kA GO:0005102 GO:0006952 GO:0009405 GO:0030435
60.070.5493.960.100.894moaA GO:0005102 GO:0006952 GO:0009405 GO:0030435
70.070.5254.150.050.851ji6A GO:0005102 GO:0006952 GO:0009405 GO:0030435
80.070.5703.430.080.811i5pA GO:0005102 GO:0006952 GO:0009405 GO:0030435
90.070.5054.270.080.891dlcA GO:0005102 GO:0006952 GO:0009405 GO:0030435
100.070.5473.370.040.813eb7A GO:0005102 GO:0006952 GO:0009405 GO:0030435
110.070.5213.750.080.824um2A GO:0000184 GO:0000333 GO:0000723 GO:0000781 GO:0003677 GO:0004518 GO:0004519 GO:0004521 GO:0005634 GO:0005694 GO:0005697 GO:0005730 GO:0005737 GO:0005829 GO:0006406 GO:0016787 GO:0032210 GO:0035145 GO:0035303 GO:0042162 GO:0043021 GO:0046872 GO:0070034 GO:0070182 GO:0090305 GO:0090502 GO:1904354
120.070.4884.030.070.801ya0B GO:0000184 GO:0005634 GO:0005737 GO:0005829 GO:0006406 GO:0035303 GO:0042162 GO:0045111 GO:0051721
130.070.3954.320.030.721t5cA GO:0000166 GO:0000278 GO:0000775 GO:0000776 GO:0000777 GO:0000779 GO:0000940 GO:0003777 GO:0005524 GO:0005634 GO:0005694 GO:0005737 GO:0005819 GO:0005829 GO:0005856 GO:0005871 GO:0005874 GO:0006890 GO:0007018 GO:0007049 GO:0007059 GO:0007062 GO:0007067 GO:0007079 GO:0007080 GO:0007275 GO:0008017 GO:0015630 GO:0016020 GO:0016887 GO:0019886 GO:0030071 GO:0030496 GO:0043515 GO:0045860 GO:0051301 GO:0051315 GO:0051382 GO:1990023
140.070.4443.570.090.703n9sA GO:0003824 GO:0004332 GO:0005975 GO:0006096 GO:0008270 GO:0016829 GO:0016832 GO:0030388 GO:0046872
150.070.5043.910.060.802c0mC GO:0000268 GO:0005052 GO:0005622 GO:0005737 GO:0005777 GO:0005778 GO:0005782 GO:0005829 GO:0006625 GO:0006810 GO:0008022 GO:0015031 GO:0016020 GO:0016558 GO:0016560 GO:0016561 GO:0019899 GO:0031267 GO:0043234 GO:0045046 GO:0047485 GO:0051262 GO:1901094
160.060.4473.530.040.694eqfA GO:0000268 GO:0005052 GO:0005737 GO:0005778 GO:0005829 GO:0016020 GO:0016560 GO:0030425 GO:0031267 GO:0042391 GO:0043235 GO:0043949 GO:0045185
170.060.4273.840.050.672iewA GO:0000122 GO:0000166 GO:0000821 GO:0000823 GO:0000824 GO:0000825 GO:0000827 GO:0005524 GO:0005634 GO:0006351 GO:0006355 GO:0006525 GO:0008440 GO:0016236 GO:0016301 GO:0016310 GO:0016740 GO:0030674 GO:0032958 GO:0035004 GO:0045944 GO:0046854 GO:0046872 GO:0050821
180.060.4143.650.060.642vyiA GO:0005737 GO:0005829 GO:0016020 GO:0016032 GO:1903071 GO:1904288


Consensus prediction of GO terms
 
Molecular Function GO:0008094 GO:0032559 GO:0042393 GO:0032550 GO:0003676 GO:0035639 GO:0003678 GO:0008026
GO-Score 0.38 0.38 0.38 0.38 0.38 0.38 0.38 0.38
Biological Processes GO:0006355 GO:0050434 GO:0043921 GO:0006325 GO:0006366 GO:0032392 GO:0030154 GO:0048646 GO:0043934
GO-Score 0.38 0.38 0.38 0.38 0.38 0.38 0.37 0.37 0.37
Cellular Component GO:0043231
GO-Score 0.50

(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.