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I-TASSER results for job id Rv2915c

[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 1 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
10.71 162 3cakB EFS Rep, Mult 63,65,158,197,217,289
20.10 23 5ch9B CO Rep, Mult 63,158,197,217
30.09 24 3n2cB LWY Rep, Mult 63,65,128,158,164,197,199,217,242,243,289
40.03 9 3mtwA M3R Rep, Mult 63,128,158,163,164,197,199,217,239,242,263,266,270,289
50.01 3 3mkvG CO3 Rep, Mult 128,163,164,197,199
60.01 2 3be7F MG Rep, Mult 114,364
70.00 1 3dugA ZN Rep, Mult 278,315

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
10.4103d6nA0.7483.510.1180.8813.5.2.3288,289
20.4082gokA0.7653.360.1700.8923.5.2.7289
30.3361zzmA0.5253.370.1300.6223.1.21.-288
40.2462qt3A0.7323.110.1490.8513.5.99.457,326,328
50.2422qt3B0.7313.130.1430.8513.5.99.457,326,328
60.1552vhlB0.7093.470.1150.8433.5.1.25NA
70.1422vunD0.7282.980.1750.8323.5.2.18NA
80.1311ybqA0.7093.530.1410.8383.4.19.184,100,292
90.1153iv8D0.7043.440.1070.8353.5.1.25NA
100.1152p50A0.7023.470.1460.8323.5.1.25NA
110.1131ra0A0.7453.540.1220.8863.5.4.1NA
120.0942uz9A0.7463.310.1020.8783.5.4.3323
130.0923e0lA0.7433.220.1110.8733.5.4.3NA
140.0851v77A0.4562.810.1150.5163.1.26.5216
150.0771xrtA0.7143.310.1180.8323.5.2.3288,289
160.0662wjfA0.4663.940.0870.5813.1.3.48325
170.0603gipA0.7593.910.1420.9243.5.1.82NA
180.0602ftwA0.7304.030.1280.9003.5.2.2289
190.0602oofA0.7433.360.1410.8783.5.2.7NA
200.0603egjA0.7043.400.1140.8323.5.1.25196,201
210.0601kraC0.7283.690.1530.8653.5.1.5302
220.0601p1mA0.7472.930.1490.8513.5.4.28NA
230.0602puzA0.7653.370.1700.8923.5.2.7NA
240.0601onxA0.7113.550.1450.8383.4.19.-289
250.0601nfgA0.7274.050.1460.8923.5.2.2289
260.0601ie7C0.7223.760.1310.8623.5.1.5NA
270.0601k6wA0.7473.400.1230.8783.5.4.1302
280.0601e9yB0.7213.650.1260.8543.5.1.5NA
290.0602vr2A0.7214.080.1200.8923.5.2.2288,289
300.0602i9uA0.7363.350.1090.8703.5.4.3NA
310.0603hm7B0.7313.740.1360.8783.5.2.5148
320.0603griB0.7173.700.1180.8573.5.2.3185
330.0602g3fA0.7823.060.1780.8953.5.2.7NA
340.0601k1dA0.7313.990.1340.8953.5.2.-289

(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
00.560.9211.940.230.982qs8A GO:0016787 GO:0016810 GO:0046872
10.500.9601.110.220.983mtwA GO:0016787 GO:0016810 GO:0046872
20.500.9271.700.210.983n2cA
30.470.9281.750.230.983mkvA GO:0016787 GO:0016810 GO:0046872
40.470.9461.370.200.983be7A
50.400.7653.360.170.892gokA GO:0005506 GO:0005737 GO:0006547 GO:0006548 GO:0008270 GO:0016787 GO:0016810 GO:0016812 GO:0019556 GO:0019557 GO:0046872 GO:0050480
60.390.7323.920.140.891gkpA GO:0005737 GO:0016787 GO:0016810 GO:0046872
70.370.8652.850.190.964whbA GO:0016787 GO:0016810
80.350.7143.310.120.831xrtA GO:0004151 GO:0006221 GO:0008270 GO:0016787 GO:0016810 GO:0016812 GO:0044205 GO:0046872
90.350.8652.950.190.974ub9A GO:0016787 GO:0016810
100.340.8702.630.250.962p9bA GO:0016787 GO:0016810
110.330.7313.740.140.883hm7B GO:0000256 GO:0004038 GO:0006144 GO:0008270 GO:0016787 GO:0016810 GO:0016812 GO:0046872 GO:0050897
120.320.7613.240.160.892oofA GO:0005506 GO:0005737 GO:0006547 GO:0006548 GO:0008270 GO:0016787 GO:0016810 GO:0016812 GO:0019556 GO:0019557 GO:0046872 GO:0050480
130.320.7363.350.110.872i9uA GO:0006147 GO:0008270 GO:0008892 GO:0016787 GO:0016810 GO:0046872
140.230.7313.990.110.893sfwA GO:0005737 GO:0016787 GO:0016810 GO:0046872
150.220.7093.530.140.841ybqA GO:0005737 GO:0005829 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008798 GO:0016787 GO:0016810 GO:0046872
160.210.8772.590.220.974c60A GO:0006508 GO:0016787 GO:0016805 GO:0016810 GO:0046872 GO:0102009 GO:1900817
170.190.7273.710.140.871gkrA GO:0000256 GO:0004038 GO:0008270 GO:0016787 GO:0016810 GO:0046872 GO:0050897
180.180.6813.700.140.813ooqF GO:0016787 GO:0016810 GO:0019239
190.150.7133.520.180.853nqbA GO:0000034 GO:0006146 GO:0016787 GO:0016810
200.150.7722.890.150.884v1xE GO:0005737 GO:0016787 GO:0016810 GO:0018788 GO:0019381 GO:0046872
210.150.7304.050.150.891nfgA GO:0005737 GO:0016787 GO:0016810 GO:0046872
220.140.7593.910.140.923gipA GO:0016787 GO:0016810 GO:0016811 GO:0047421
230.140.7573.060.130.882oodA GO:0006147 GO:0008270 GO:0008892 GO:0016787 GO:0016810 GO:0046098 GO:0046872
240.140.7463.520.130.893g77A GO:0004131 GO:0005829 GO:0006209 GO:0008198 GO:0008270 GO:0016787 GO:0016810 GO:0019858 GO:0035888 GO:0042802 GO:0046872
250.140.7702.870.170.884dykA GO:0004000 GO:0016787 GO:0016810 GO:0019700 GO:0046872 GO:0050270
260.140.7483.500.110.884bjhA GO:0004151 GO:0006221 GO:0008270 GO:0016787 GO:0016810 GO:0016812 GO:0044205 GO:0046872
270.140.7294.020.120.894kirA GO:0004157 GO:0005737 GO:0016787 GO:0016810 GO:0046872
280.130.7383.650.140.883mpgA GO:0004151 GO:0006221 GO:0008270 GO:0009220 GO:0016787 GO:0016810 GO:0016812 GO:0044205 GO:0046872
290.120.7043.440.110.843iv8D GO:0005975 GO:0006044 GO:0006046 GO:0008448 GO:0016787 GO:0016810 GO:0019262 GO:0046872 GO:0051289
300.110.7522.780.170.853hpaA
310.100.7293.720.160.882z00A GO:0004151 GO:0006221 GO:0008270 GO:0016787 GO:0016810 GO:0016812 GO:0044205 GO:0046872
320.100.7093.470.120.842vhlB GO:0005506 GO:0005975 GO:0006044 GO:0006046 GO:0008448 GO:0016787 GO:0016810 GO:0019262 GO:0042803 GO:0046872
330.100.7043.400.110.833egjA GO:0005975 GO:0006044 GO:0006046 GO:0008448 GO:0016787 GO:0016810 GO:0019262 GO:0046872 GO:0051289
340.100.7313.990.130.891k1dA GO:0005737 GO:0016787 GO:0016810 GO:0046872
350.080.7303.440.130.853ighX GO:0006259 GO:0016810 GO:0016888
360.080.7274.030.130.894tqtD GO:0004157 GO:0005737 GO:0016787 GO:0016810
370.080.7304.040.140.904gz7A GO:0005737 GO:0016787 GO:0016810 GO:0046872
380.080.7293.860.120.894b3zD GO:0000226 GO:0005737 GO:0005815 GO:0005819 GO:0005829 GO:0005856 GO:0006139 GO:0007399 GO:0007411 GO:0010977 GO:0016787 GO:0016810 GO:0031005 GO:0048666 GO:1904530
390.080.7354.030.130.912ftyA GO:0004157 GO:0016787 GO:0016810 GO:0046872
400.070.7294.070.110.904cnuA GO:0005615 GO:0005737 GO:0005829 GO:0010975 GO:0010976 GO:0010977 GO:0016787 GO:0016810 GO:0017124 GO:0030027 GO:0030334 GO:0030336 GO:0030426 GO:0031005 GO:0031941 GO:0035374 GO:0042995 GO:0044297 GO:0048666 GO:0048678 GO:0051017 GO:0051260 GO:0051491 GO:0051764 GO:0070382 GO:0071345
410.070.7133.450.140.833icjA GO:0006259 GO:0016810 GO:0016888 GO:0046872
420.070.7244.030.140.893dc8A GO:0005737 GO:0016787 GO:0016810 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0046872 GO:0016810
GO-Score 0.88 0.88
Biological Processes
GO-Score
Cellular Component
GO-Score

(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.