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I-TASSER results for job id Rv2209

[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 4 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
10.07 4 5eqgA 5RE Rep, Mult 68,129,153,156,240,344,360,364,367,368
20.06 3 4zwbA MAL Rep, Mult 31,153,156,157,160,240,241,245,336,337,344,371
30.04 2 3pxwA NO Rep, Mult 491,495,501
40.04 2 5c65A Y01 Rep, Mult 69,234,238,242,366,369,374
50.04 2 3tj6A III Rep, Mult 84,115,121,125,129,132,133
60.04 2 1le5E NUC Rep, Mult 470,478,486
70.04 2 2gdcA III Rep, Mult 44,84,114,121,125,128,129,132
80.02 1 2ibfA III Rep, Mult 111,112,114,115,118,119,122,125,126
90.02 1 3dasA CA Rep, Mult 500,508,509
100.02 1 1pl6A ZN Rep, Mult 473,494
110.02 1 1gkiA ADP Rep, Mult 235,500
120.02 1 3aodA MIY Rep, Mult 136,140,146
130.02 1 3nudB PO4 Rep, Mult 467,468,475
140.02 1 3rf3A III Rep, Mult 285,286,290,293
150.02 1 2wse4 CLA Rep, Mult 451,466
160.02 1 4zp0A DXC Rep, Mult 31,32,61,160,245,367,368
170.02 1 3lw52 CLA Rep, Mult 399,403

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
10.0601h0hA0.3387.580.0360.5571.2.1.2NA
20.0601y8bA0.3467.140.0350.5412.3.3.9NA
30.0603b9jC0.2807.510.0540.4571.17.3.2,1.17.1.4NA
40.0602ckjA0.3017.610.0360.5001.17.1.4,1.17.3.2NA
50.0601ea0A0.3227.710.0350.5431.4.1.13NA
60.0605acnA0.3087.800.0380.5164.2.1.3NA
70.0601ofdA0.3107.760.0470.5271.4.7.1NA
80.0603es9B0.2707.600.0350.4431.6.2.4NA
90.0603l4uA0.3198.170.0560.5683.2.1.20,3.2.1.3120
100.0602eabA0.3398.030.0490.5883.2.1.6323
110.0602e1qA0.3307.760.0440.5621.17.3.2,1.17.1.4NA
120.0602vdcA0.3217.660.0350.5411.4.1.13NA
130.0602vdcF0.3217.650.0420.5371.4.1.13NA
140.0601fdiA0.3207.320.0390.5181.2.1.2NA
150.0602cseW0.3307.420.0420.5333.6.4.13NA
160.0601d8cA0.3297.560.0610.5392.3.3.9NA
170.0603eqlM0.3337.710.0510.5592.7.7.6131
180.0601szqA0.3287.120.0480.5164.2.1.79NA
190.0603g61A0.3246.380.0500.4673.6.3.44136,147

(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
00.240.6543.270.070.753o7qA 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
10.170.6074.430.110.754j05A GO:0005215 GO:0016020 GO:0016021 GO:0022857 GO:0055085
20.170.5795.410.100.784uvmA GO:0005215 GO:0006810 GO:0006857 GO:0015197 GO:0015833 GO:0016020 GO:0016021
30.160.5655.630.090.774oh3B 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
40.160.5465.010.100.712xutA GO:0005215 GO:0006810 GO:0006857 GO:0015197 GO:0015833 GO:0016020 GO:0016021
50.150.5645.590.100.774ikvA GO:0005215 GO:0006810 GO:0006857 GO:0015197 GO:0015833 GO:0016020 GO:0016021
60.140.5725.170.090.764oh3A 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
70.130.6144.140.110.754yb9D 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
80.110.5545.050.070.724tpgA GO:0005215 GO:0005427 GO:0006810 GO:0006857 GO:0015197 GO:0015833 GO:0016020 GO:0016021 GO:0035672 GO:0042802
90.110.6963.510.100.804zw9A 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
100.110.6823.600.100.794ybqB 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
110.100.6843.640.120.794gbyA 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
120.070.6204.300.110.775eqgA 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
130.070.6154.180.090.754zp0A 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
140.070.5914.560.130.744ldsA GO:0005215 GO:0006810 GO:0016020 GO:0016021 GO:0022857 GO:0022891 GO:0055085
150.070.5814.830.130.754ja4A 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
160.070.5755.190.100.774xnjA GO:0005215 GO:0006810 GO:0006857 GO:0015197 GO:0015833 GO:0016020 GO:0016021 GO:0042802
170.070.5615.510.090.765a2nA 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
180.070.5205.840.110.735ayoA GO:0005381 GO:0016020 GO:0016021 GO:0034755
190.070.5535.120.090.734q65A 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
200.070.5355.680.110.742cfpA 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
210.070.5165.340.090.692gfpA GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0015893 GO:0016020 GO:0016021 GO:0055085
220.060.2756.970.060.435i1mV GO:0000220 GO:0000324 GO:0000329 GO:0005773 GO:0005774 GO:0006461 GO:0006797 GO:0006810 GO:0006811 GO:0007035 GO:0015078 GO:0015986 GO:0015991 GO:0015992 GO:0016020 GO:0016021 GO:0016049 GO:0033179 GO:0046961 GO:0051117 GO:0070072
230.060.2487.110.030.394jevB GO:0003824 GO:0003992 GO:0005737 GO:0005829 GO:0006520 GO:0006525 GO:0006526 GO:0008483 GO:0008652 GO:0009016 GO:0009085 GO:0009089 GO:0016740 GO:0030170 GO:0042802
240.060.2126.350.040.313kexA GO:0000165 GO:0000166 GO:0003197 GO:0004672 GO:0004713 GO:0004888 GO:0005088 GO:0005524 GO:0005576 GO:0005615 GO:0005622 GO:0005886 GO:0005887 GO:0006468 GO:0007162 GO:0007165 GO:0007169 GO:0007422 GO:0007507 GO:0009968 GO:0014037 GO:0014065 GO:0014066 GO:0014068 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016323 GO:0016324 GO:0016328 GO:0016740 GO:0018108 GO:0019838 GO:0021545 GO:0030296 GO:0038128 GO:0038132 GO:0042060 GO:0042127 GO:0042802 GO:0042803 GO:0043235 GO:0043524 GO:0043547 GO:0046854 GO:0046934 GO:0046982 GO:0048015 GO:0051048 GO:0051402 GO:0061098 GO:0070886 GO:0097192 GO:2000145
250.060.2597.790.060.442d0oA GO:0000166 GO:0005524 GO:0046872
260.060.2048.180.040.361dceA GO:0004659 GO:0004663 GO:0005968 GO:0008270 GO:0008318 GO:0016740 GO:0017137 GO:0018342 GO:0018344
270.060.2067.000.050.321pquA GO:0003942 GO:0004073 GO:0005737 GO:0006520 GO:0008652 GO:0009085 GO:0009086 GO:0009088 GO:0009089 GO:0009097 GO:0016491 GO:0016620 GO:0019877 GO:0046983 GO:0050661 GO:0051287 GO:0055114 GO:0071266
280.060.2074.900.040.261q90B GO:0005506 GO:0009055 GO:0009507 GO:0009535 GO:0009536 GO:0009579 GO:0015979 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0022900 GO:0022904 GO:0045158 GO:0046872 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0009679 GO:0005354 GO:0042900 GO:0015150 GO:0015103
GO-Score 0.48 0.48 0.48 0.48 0.32
Biological Processes GO:0015750 GO:0008645 GO:0019318 GO:0055085 GO:0006857 GO:0006950 GO:1901698 GO:0071365 GO:0015698 GO:0009636 GO:0009755 GO:0009415 GO:0071941 GO:0042126
GO-Score 0.48 0.48 0.48 0.47 0.41 0.32 0.32 0.32 0.32 0.32 0.32 0.32 0.32 0.32
Cellular Component GO:0016021 GO:0031226
GO-Score 0.63 0.48

(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.