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I-TASSER results for job id Rv2693c

[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
10.08 3 2qjyG HEM Rep, Mult 26,27,30,31,33,34,37,75,76,79,80,82,83,106,107,110
20.05 2 2aj4A MG Rep, Mult 39,88
30.05 2 4fbyZ CLA Rep, Mult 111,112,115
40.05 2 3zuxA TCH Rep, Mult 18,22,183,184,185,188
50.05 2 3ipoB PG0 Rep, Mult 180,181
60.03 1 2qjkJ HEM Rep, Mult 26,30,31,69,72,73,76,77,79,80,103,106,117
70.03 1 3zuxA NA Rep, Mult 80,175,176,177,178,179
80.03 1 2h8pC GOA Rep, Mult 86,91
90.03 1 1jb0M CLA Rep, Mult 43,47
100.03 1 1fp4B CA Rep, Mult 62,63
110.03 1 2qjkA HEM Rep, Mult 72,75,76,110,113,116,120,183,186,190
120.03 1 5d58A 78M Rep, Mult 22,162,173,178
130.03 1 1kfyB CE1 Rep, Mult 141,145

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
10.0602j2fA0.4543.500.0460.5831.14.19.2,1.14.99.6NA
20.0602ohyB0.4265.610.0710.7095.4.3.646
30.0602jjpA0.4165.590.0540.7091.14.-.-NA
40.0601fziA0.4234.260.0450.6011.14.13.25NA
50.0602v8tA0.4574.210.0500.6141.11.1.6179
60.0601uwkA0.4265.000.0630.6594.2.1.49NA
70.0601n40A0.4285.200.0470.6681.14.-.-NA
80.0603djlA0.4166.030.0690.7581.3.99.-NA
90.0602q9fA0.4245.180.0430.6641.14.13.98NA
100.0602uvnA0.4185.800.0360.6911.14.-.-NA
110.0601yrlA0.4335.310.0550.6911.1.1.86NA
120.0603b4xA0.4165.560.0270.6861.14.14.1144
130.0602wm4A0.4255.620.0570.7181.14.-.-NA
140.0602vuxB0.3974.020.0570.5381.17.4.1NA
150.0601xvgC0.4333.920.0830.5961.14.13.25NA
160.0601wyuB0.4125.390.0570.6771.4.4.2NA
170.0603cxhN0.4275.490.0470.7041.10.2.2NA
180.0601uzrB0.4413.880.0830.5961.17.4.1NA
190.0603hf1B0.4333.870.0620.5831.17.4.1NA

(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
00.190.6652.990.090.824uvmA GO:0005215 GO:0006810 GO:0006857 GO:0015197 GO:0015833 GO:0016020 GO:0016021
10.170.6372.950.080.782xutA GO:0005215 GO:0006810 GO:0006857 GO:0015197 GO:0015833 GO:0016020 GO:0016021
20.130.6543.900.080.893o7qA GO:0005886 GO:0005887 GO:0005975 GO:0006004 GO:0006810 GO:0008643 GO:0015150 GO:0015293 GO:0015517 GO:0015518 GO:0015535 GO:0015751 GO:0015756 GO:0015757 GO:0016020 GO:0016021 GO:0055085
30.120.6433.570.090.844yb9D GO:0003044 GO:0005215 GO:0005353 GO:0005886 GO:0005887 GO:0006810 GO:0008643 GO:0009750 GO:0015755 GO:0016020 GO:0016021 GO:0016324 GO:0022857 GO:0022891 GO:0042383 GO:0055085 GO:0070061 GO:0071332 GO:1990539
40.110.6793.850.110.904ybqB GO:0003044 GO:0005215 GO:0005353 GO:0005355 GO:0005886 GO:0005887 GO:0006810 GO:0008643 GO:0015755 GO:0015758 GO:0016020 GO:0016021 GO:0016324 GO:0022857 GO:0022891 GO:0042383 GO:0055085 GO:0070061 GO:0071332 GO:1904659 GO:1990539
50.100.6453.570.110.864gbyA GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0008643 GO:0015293 GO:0015519 GO:0015753 GO:0016020 GO:0016021 GO:0022857 GO:0022891 GO:0055085
60.100.6623.810.110.894zw9A GO:0005215 GO:0005355 GO:0005536 GO:0005886 GO:0005887 GO:0005975 GO:0006810 GO:0008643 GO:0015758 GO:0016020 GO:0016021 GO:0019852 GO:0022857 GO:0022891 GO:0033300 GO:0055056 GO:0055085 GO:0070062 GO:0070837 GO:1904659
70.100.6703.240.090.854xnjA GO:0005215 GO:0006810 GO:0006857 GO:0015197 GO:0015833 GO:0016020 GO:0016021 GO:0042802
80.100.6653.800.090.874oh3A GO:0005215 GO:0005886 GO:0006810 GO:0006857 GO:0009414 GO:0009635 GO:0009734 GO:0010167 GO:0015112 GO:0015293 GO:0015706 GO:0016020 GO:0016021 GO:0042128 GO:0055085
90.090.6593.870.090.874oh3B GO:0005215 GO:0005886 GO:0006810 GO:0006857 GO:0009414 GO:0009635 GO:0009734 GO:0010167 GO:0015112 GO:0015293 GO:0015706 GO:0016020 GO:0016021 GO:0042128 GO:0055085
100.090.6483.300.090.834ikvA GO:0005215 GO:0006810 GO:0006857 GO:0015197 GO:0015833 GO:0016020 GO:0016021
110.090.6493.660.090.855a2nA GO:0005215 GO:0005886 GO:0006810 GO:0006857 GO:0009414 GO:0009635 GO:0009734 GO:0010167 GO:0015112 GO:0015293 GO:0015706 GO:0016020 GO:0016021 GO:0042128 GO:0055085
120.080.6164.010.060.874tpgA GO:0005215 GO:0005427 GO:0006810 GO:0006857 GO:0015197 GO:0015833 GO:0016020 GO:0016021 GO:0035672 GO:0042802
130.080.6433.080.070.804q65A GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006857 GO:0015031 GO:0015197 GO:0015333 GO:0015833 GO:0015992 GO:0016020 GO:0016021 GO:0042936 GO:0042938
140.080.6592.980.120.834ldsA GO:0005215 GO:0006810 GO:0016020 GO:0016021 GO:0022857 GO:0022891 GO:0055085
150.080.6433.660.090.845eqgA GO:0000139 GO:0001939 GO:0005215 GO:0005355 GO:0005622 GO:0005737 GO:0005829 GO:0005886 GO:0005887 GO:0005901 GO:0005911 GO:0005989 GO:0006461 GO:0006810 GO:0006970 GO:0008643 GO:0015758 GO:0016020 GO:0016021 GO:0016323 GO:0016324 GO:0019852 GO:0019900 GO:0022857 GO:0022891 GO:0030496 GO:0030864 GO:0031982 GO:0033300 GO:0042149 GO:0042470 GO:0042802 GO:0042908 GO:0042910 GO:0043621 GO:0045121 GO:0050796 GO:0055056 GO:0055085 GO:0070062 GO:0070837 GO:0072562 GO:1904659
160.070.6472.980.100.804ja4A GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0008643 GO:0015293 GO:0015519 GO:0015753 GO:0016020 GO:0016021 GO:0022857 GO:0022891 GO:0055085
170.070.6103.730.070.824zp0A GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015385 GO:0015386 GO:0016020 GO:0016021 GO:0030641 GO:0035725 GO:0046677 GO:0055085 GO:0071805
180.070.6573.580.060.852cfpA GO:0005351 GO:0005886 GO:0005887 GO:0006810 GO:0008643 GO:0015293 GO:0015528 GO:0015767 GO:0015992 GO:0016020 GO:0016021 GO:0030395 GO:0055085


Consensus prediction of GO terms
 
Molecular Function GO:0048029 GO:0015149 GO:0015197
GO-Score 0.43 0.43 0.32
Biological Processes GO:0098704 GO:0003073 GO:0032445 GO:0009750 GO:0035428 GO:0071331 GO:0006857
GO-Score 0.43 0.43 0.43 0.43 0.43 0.43 0.32
Cellular Component GO:0098590 GO:0045177 GO:0005887
GO-Score 0.43 0.43 0.31

(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.