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I-TASSER results for job id Rv0025

[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 6 2q7rB 3CS Rep, Mult 42,43,101,105,108,109,112
20.06 4 3omiC TRD Rep, Mult 38,41,45
30.06 4 2q7mB 2CS Rep, Mult 49,51,52,53,55,56,84
40.05 3 4m70Q III Rep, Mult 13,78,81,82,85,86,89
50.05 3 4dmzB MG Rep, Mult 111,114,115
60.03 2 2q7rA 3CS Rep, Mult 20,21,23,24,25,27
70.03 2 5hxcA MYC Rep, Mult 54,58,79
80.03 2 3de8C CA Rep, Mult 28,30
90.02 1 3fyiA DMU Rep, Mult 48,50,82,86,89
100.02 1 2pnoC GSH Rep, Mult 87,90,91,94,104,107
110.02 1 1vdfB CL Rep, Mult 19,22
120.02 1 3zukB CA Rep, Mult 99,101
130.02 1 2uuhA GSH Rep, Mult 50,54,57,58,111,115
140.02 1 2np5C NDS Rep, Mult 61,62,64,76
150.02 1 3wmnU CRT Rep, Mult 82,93

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
10.1053gm1B0.5973.060.1120.8082.7.10.256
20.0661i5nD0.5413.470.1030.7922.7.13.318,20,51
30.0603c20B0.5823.720.0440.8672.7.2.429,34,93
40.0603czoB0.5733.920.0640.8834.3.1.3NA
50.0602occN0.5853.660.0500.9001.9.3.1NA
60.0601occA0.6183.690.0260.9501.9.3.1NA
70.0603dwwA0.6153.410.0720.9085.3.99.384
80.0602hc8A0.2634.780.0970.4503.6.3.-NA
90.0601fbvA0.6104.030.0510.9426.3.2.1989
100.0602bl2A0.6603.180.0690.9673.6.3.1493,95
110.0602h8aA0.6033.090.0580.8582.5.1.1834,40,100
120.0601pn0C0.5673.350.0300.8251.14.13.724,44
130.0601m56A0.6193.620.0260.9331.9.3.1NA
140.0602rf7D0.5753.710.0520.8421.7.2.2NA
150.0601mhsA0.5673.930.0960.8753.6.3.6NA
160.0601eulA0.5154.170.0740.8423.6.3.8NA
170.0602pnoL0.6442.960.0450.9174.4.1.20111
180.0601y2mB0.5753.640.0890.8584.3.1.24NA
190.0603b8cB0.5813.700.0830.8923.6.3.6NA
200.0601k04A0.5932.920.1140.7922.7.10.2106
210.0601xmeA0.6153.770.0420.9501.9.3.1NA

(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
00.290.7013.070.070.981r0dA GO:0003779 GO:0005543 GO:0005737 GO:0005856 GO:0005905 GO:0006897 GO:0006898 GO:0006915 GO:0012505 GO:0016020 GO:0030136 GO:0030276 GO:0030665 GO:0031410 GO:0035091 GO:0043231 GO:0048471 GO:0072583
10.240.7222.690.070.973ay5A GO:0005634 GO:0005654 GO:0005737 GO:0007049 GO:0051726
20.140.6872.930.120.942jswA GO:0001726 GO:0003779 GO:0005178 GO:0005200 GO:0005737 GO:0005815 GO:0005856 GO:0005886 GO:0005925 GO:0007016 GO:0007044 GO:0007155 GO:0009986 GO:0016020 GO:0017166 GO:0030054 GO:0030274 GO:0030866 GO:0032403 GO:0032587 GO:0042995 GO:0051015 GO:0070062 GO:0070527
30.090.6683.130.110.934wvmA GO:0005576 GO:0019835 GO:0044179
40.090.6712.820.050.924wvmB GO:0005576 GO:0019835 GO:0044179
50.070.5773.820.060.895flzB GO:0000226 GO:0000922 GO:0000923 GO:0000928 GO:0005200 GO:0005634 GO:0005737 GO:0005813 GO:0005815 GO:0005816 GO:0005822 GO:0005824 GO:0005856 GO:0005874 GO:0007020 GO:0007126 GO:0030472 GO:0031122 GO:0043015 GO:0051011 GO:0051298 GO:0051415 GO:0090307
60.070.5923.680.090.933ripA GO:0000226 GO:0000922 GO:0000923 GO:0000930 GO:0005200 GO:0005737 GO:0005813 GO:0005815 GO:0005816 GO:0005829 GO:0005856 GO:0005874 GO:0006461 GO:0007020 GO:0007126 GO:0008274 GO:0015630 GO:0016020 GO:0031122 GO:0043015 GO:0044732 GO:0051011 GO:0051298 GO:0051415 GO:0055037 GO:0090307
70.060.4214.520.040.744u8gA GO:0016491 GO:0055114
80.060.4044.120.070.622htmC GO:0003824 GO:0005737 GO:0009228 GO:0009229 GO:0016740 GO:0016783
90.060.3764.620.080.633v7pA GO:0009234 GO:0016787 GO:0016810 GO:0046872
100.060.5553.460.120.825ic0A GO:0001726 GO:0003779 GO:0005178 GO:0005200 GO:0005737 GO:0005815 GO:0005856 GO:0005886 GO:0005925 GO:0007016 GO:0007044 GO:0007155 GO:0009986 GO:0016020 GO:0017166 GO:0030054 GO:0030274 GO:0030866 GO:0032403 GO:0032587 GO:0042995 GO:0051015 GO:0070062 GO:0070527
110.060.3613.500.060.534kpqB GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0019064 GO:0019065 GO:0020002 GO:0033644 GO:0039654 GO:0039663 GO:0046718 GO:0046789 GO:0055036 GO:0075509 GO:0075512
120.060.4493.570.030.662p5oB GO:0000166 GO:0003676 GO:0003677 GO:0003887 GO:0004518 GO:0004527 GO:0006260 GO:0008408 GO:0016740 GO:0016779 GO:0016787 GO:0039693 GO:0071897 GO:0090305
130.060.3684.790.060.653k53D GO:0005525 GO:0015093 GO:0015684 GO:0016020 GO:0016021 GO:1903874
140.060.2854.830.020.524b8eA GO:0002376 GO:0004842 GO:0005654 GO:0005737 GO:0006513 GO:0008270 GO:0016567 GO:0016740 GO:0016874 GO:0016881 GO:0036503 GO:0042787 GO:0043123 GO:0043627 GO:0044822 GO:0045087 GO:0046596 GO:0046597 GO:0046872 GO:0051091 GO:0051092 GO:0051607 GO:1902186 GO:1902187 GO:1904264
150.060.3534.840.040.572wgbB GO:0003677 GO:0006351 GO:0006355
160.060.4315.200.050.765a0yB GO:0015948 GO:0016740 GO:0050524
170.060.3445.100.060.683r6uA GO:0005215 GO:0005886 GO:0006810 GO:0006865 GO:0016020 GO:0071705
180.060.3544.290.050.623japl GO:0001731 GO:0003729 GO:0003743 GO:0005850 GO:0006412 GO:0006413 GO:0016282 GO:0031369 GO:0043614 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0008289 GO:0003779
GO-Score 0.57 0.39
Biological Processes GO:0012501 GO:0006897 GO:0050794 GO:0051715
GO-Score 0.57 0.57 0.49 0.35
Cellular Component GO:0098589 GO:0030662 GO:0030136 GO:0031981 GO:0005856
GO-Score 0.57 0.57 0.57 0.49 0.39

(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.