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I-TASSER results for job id Rv1535

[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 6 3a0bX CLA Rep, Mult 49,52,53,56
20.08 5 2axtH CLA Rep, Mult 57,61
30.08 5 2bufD ADP Rep, Mult 6,9,11,43,48,49,52
40.06 4 4dr5F MG Rep, Mult 66,70
50.05 3 1ai0B IPH Rep, Mult 63,64,67
60.05 3 2j5tA GLU Rep, Mult 47,52,53,68,71,72
70.03 2 2we5A ADP Rep, Mult 10,11,41,42,43,48,49,52
80.02 1 3ak3D EDO Rep, Mult 56,59
90.02 1 5l8gK CA Rep, Mult 51,54
100.02 1 1h6dA NDP Rep, Mult 24,25,27,28,29,30,31

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
10.0601gs5A0.4763.210.1110.7952.7.2.8NA
20.0601k8cB0.4064.270.0960.8721.1.1.2151
30.0602j5tD0.4573.650.0740.8332.7.2.1146
40.0603lerA0.4524.000.0810.8594.2.1.5212,36
50.0602j4lH0.2884.770.0450.6672.7.4.2256
60.0601jqnA0.4794.010.0570.8724.1.1.31NA
70.0602j4lF0.3964.250.0770.8082.7.4.2253
80.0602ap9A0.4683.550.1670.8462.7.2.8NA
90.0602rd5B0.4773.290.1230.8332.7.2.8NA
100.0603d2pB0.4733.360.1090.8082.3.1.131,52
110.0602ehhA0.4583.710.0420.8334.2.1.522
120.0602yyjA0.4534.000.0970.8211.14.13.3NA
130.0602v5hB0.4623.550.1790.8462.7.2.8NA
140.0602i2xA0.4503.930.0800.8722.1.1.90NA
150.0602j62A0.3903.390.0700.6283.2.1.5211
160.0603e96B0.4534.120.1330.8854.2.1.52NA
170.0603i9v10.4683.940.1330.8331.6.99.5NA
180.0602bufK0.4843.220.1290.7952.7.2.8NA
190.0603g0sA0.4564.120.0400.8854.2.1.52NA

(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
00.070.4753.230.130.782bufC GO:0000166 GO:0003991 GO:0005524 GO:0005737 GO:0006526 GO:0006561 GO:0008652 GO:0016301 GO:0016310 GO:0016740 GO:0034618
10.070.5183.370.110.854jz7C GO:0000166 GO:0005829 GO:0006525 GO:0008804 GO:0016301 GO:0016310 GO:0016740 GO:0019546
20.070.4843.220.130.792bufK GO:0000166 GO:0003991 GO:0005524 GO:0005737 GO:0006526 GO:0006561 GO:0008652 GO:0016301 GO:0016310 GO:0016740 GO:0034618
30.070.5123.320.140.831e19A GO:0000166 GO:0005524 GO:0005737 GO:0006525 GO:0008804 GO:0016301 GO:0016310 GO:0016740
40.070.4913.700.140.862we4A GO:0000166 GO:0005524 GO:0005737 GO:0006525 GO:0008804 GO:0016301 GO:0016310 GO:0016740 GO:0035975
50.070.4223.920.100.833k9dA GO:0004029 GO:0008152 GO:0016491 GO:0016620 GO:0055114
60.070.4773.510.140.813kzfD GO:0000166 GO:0005829 GO:0006525 GO:0008804 GO:0016301 GO:0016310 GO:0016740 GO:0019546
70.070.4394.500.100.902bmuB GO:0000166 GO:0005524 GO:0005737 GO:0006221 GO:0009041 GO:0016301 GO:0016310 GO:0016740 GO:0033862 GO:0044210 GO:0046872 GO:0046939
80.070.4623.550.180.852v5hB GO:0000166 GO:0003991 GO:0005524 GO:0005737 GO:0006526 GO:0006561 GO:0008652 GO:0016301 GO:0016310 GO:0016740 GO:0042802
90.060.3173.760.050.584wd0A GO:0000105 GO:0000162 GO:0003824 GO:0003949 GO:0004640 GO:0005737 GO:0008152 GO:0008652 GO:0016853
100.060.4183.750.070.744q1tB GO:0000166 GO:0003723 GO:0004349 GO:0005524 GO:0005737 GO:0006561 GO:0008652 GO:0016301 GO:0016310 GO:0016740 GO:0055129
110.060.3804.450.090.815fjjA GO:0000272 GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0008422 GO:0016052 GO:0016787 GO:0016798 GO:0030245 GO:0102483
120.060.3734.000.060.734dxbA GO:0005215 GO:0005363 GO:0006810 GO:0006974 GO:0008643 GO:0008800 GO:0015768 GO:0016787 GO:0030288 GO:0030655 GO:0034289 GO:0042597 GO:0042956 GO:0043190 GO:0046677 GO:0055052 GO:0060326 GO:1901982 GO:1990060
130.060.3694.130.030.721q9uA GO:0046872
140.060.3505.140.040.812zjlA GO:0001540 GO:0004175 GO:0004190 GO:0005768 GO:0005770 GO:0005771 GO:0005783 GO:0005788 GO:0005794 GO:0005802 GO:0005886 GO:0005887 GO:0006508 GO:0006509 GO:0008233 GO:0008798 GO:0009986 GO:0010008 GO:0016020 GO:0016021 GO:0016787 GO:0019899 GO:0030163 GO:0030424 GO:0030659 GO:0031410 GO:0044267 GO:0045121 GO:0050435 GO:0070931
150.060.3764.460.070.814iibA GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483
160.060.3294.000.070.645djqC GO:0005886 GO:0006119 GO:0006811 GO:0009055 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0046872 GO:0055114 GO:0070069 GO:0070469
170.060.4733.260.130.782btyA GO:0000166 GO:0003824 GO:0003991 GO:0005524 GO:0005737 GO:0006526 GO:0006561 GO:0008152 GO:0008652 GO:0016301 GO:0016310 GO:0016740 GO:0034618
180.060.3254.780.030.714jooA GO:0001540 GO:0004175 GO:0004190 GO:0005768 GO:0005770 GO:0005771 GO:0005783 GO:0005788 GO:0005794 GO:0005802 GO:0005886 GO:0005887 GO:0006508 GO:0006509 GO:0008233 GO:0008798 GO:0009986 GO:0010008 GO:0016020 GO:0016021 GO:0016787 GO:0019899 GO:0030163 GO:0030424 GO:0030659 GO:0031410 GO:0044267 GO:0045121 GO:0050435 GO:0070931


Consensus prediction of GO terms
 
Molecular Function GO:0032559 GO:0035639 GO:0032550 GO:0016774
GO-Score 0.49 0.49 0.49 0.37
Biological Processes GO:0006796 GO:0009064 GO:0006520
GO-Score 0.59 0.37 0.37
Cellular Component GO:0044424
GO-Score 0.49

(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.