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I-TASSER results for job id Rv0295c

[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
10.50 12 1texB TRE Rep, Mult 14,36,39,48,53,105,163,164
20.21 9 3mgcA PME Rep, Mult 15,17,19,20,143,152,211
30.02 1 3mg9A UUU Rep, Mult 21,22,24,25,28,29
40.02 1 2zvqX 1NP Rep, Mult 142,143,144,188,210,212
50.02 1 1texA TRE Rep, Mult 33,93

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
10.0941lvgA0.4803.590.1050.5962.7.4.8NA
20.0661kofA0.4613.940.1020.5992.7.1.1217,37
30.0661tevA0.4933.850.0530.6372.7.4.14100
40.0661khtB0.4784.120.0760.6222.7.4.317,19
50.0663hjnA0.4714.070.0600.6072.7.4.941
60.0662cdnA0.4704.090.0580.6182.7.4.3155
70.0661rkbA0.4584.210.1130.6072.7.4.317,19
80.0662p0eA0.4733.760.0760.5992.7.1.2217,19
90.0661qf9A0.4884.320.0650.6672.7.4.14232
100.0663cm0A0.4674.010.0660.6142.7.4.3189,196
110.0661z83A0.4864.110.0720.6402.7.4.3NA
120.0661z6gA0.4893.430.0800.6032.7.4.817,209
130.0661ukyA0.4884.120.0670.6402.7.4.-NA
140.0601q44A0.5233.910.0860.6822.8.2.-NA
150.0603tmkA0.4944.620.0730.6672.7.4.9NA
160.0602ccgA0.4974.020.0500.6442.7.4.9NA
170.0601s3gA0.4924.700.0470.6932.7.4.3NA
180.0601t8uB0.5724.050.1270.7492.8.2.3017,145
190.0603cklB0.5713.960.0850.7302.8.2.-NA
200.0601aqyA0.5603.970.1060.7272.8.2.4NA
210.0601g3mA0.5643.940.1060.7272.8.2.4NA
220.0603bd9A0.5684.180.0860.7532.8.2.23143
230.0602a2zB0.5044.380.0640.6702.7.1.7436
240.0601zinA0.5034.550.0820.7042.7.4.3155
250.0601p60A0.5134.340.0570.6822.7.1.7436
260.0602gwhB0.5663.910.1010.7272.8.2.-NA
270.0602h8kA0.5003.510.1230.6252.8.2.2NA
280.0601jagA0.5064.290.0850.6672.7.1.113NA
290.0603dkvA0.4974.420.0730.6852.7.4.3196
300.0602bwjA0.4943.770.0800.6292.7.4.317,23,36
310.0602qajB0.4964.530.0780.6892.7.4.317,23
320.0601j99A0.5443.930.0930.7002.8.2.14,2.8.2.2NA

(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
00.600.9050.970.700.931texD GO:0016740
10.220.5893.570.140.744goxA GO:0003824 GO:0008152 GO:0016740 GO:0031177
20.210.5924.030.100.764gbmA GO:0003824 GO:0008152 GO:0016740 GO:0031177 GO:0046872
30.170.5764.090.160.762zq5A
40.160.5413.850.100.693nibA GO:0008146
50.150.5613.520.110.701q20A GO:0000103 GO:0004027 GO:0005634 GO:0005737 GO:0005783 GO:0005829 GO:0006629 GO:0008146 GO:0008202 GO:0016740 GO:0043231 GO:0050294 GO:0050427 GO:0070062
60.120.5513.880.080.701efhB GO:0004062 GO:0004304 GO:0005737 GO:0005829 GO:0006629 GO:0007586 GO:0008146 GO:0008202 GO:0016042 GO:0016740 GO:0030573 GO:0047704 GO:0050294 GO:0050427 GO:0051923
70.120.5413.900.090.704eecA GO:0008146 GO:0016740 GO:0017000
80.090.5443.930.090.701j99A GO:0004062 GO:0004304 GO:0005737 GO:0005829 GO:0006629 GO:0007586 GO:0008146 GO:0008202 GO:0016042 GO:0016740 GO:0030573 GO:0047704 GO:0050294 GO:0050427 GO:0051923
90.070.5934.190.090.773rnlA GO:0016740 GO:0046872
100.070.6084.360.110.802z6vA
110.070.5793.800.140.743ap2A GO:0000139 GO:0005783 GO:0005794 GO:0006478 GO:0008476 GO:0016020 GO:0016021 GO:0016740 GO:0070062
120.070.5723.790.110.722zytX GO:0000103 GO:0004062 GO:0005737 GO:0006584 GO:0006629 GO:0008146 GO:0016740 GO:0051923
130.070.5734.460.120.771x8kA GO:0008146 GO:0046872
140.070.5673.550.120.713bfxA GO:0004062 GO:0005737 GO:0005829 GO:0008146 GO:0009308 GO:0016740 GO:0050427 GO:0051923 GO:0070062
150.070.5663.910.100.732gwhB GO:0004062 GO:0005737 GO:0005829 GO:0008146 GO:0016740 GO:0050427 GO:0051923
160.070.5393.800.100.692ad1A GO:0004062 GO:0005737 GO:0005829 GO:0008146 GO:0016740 GO:0050427 GO:0051923
170.070.5273.890.110.681zd1A GO:0004062 GO:0005737 GO:0005829 GO:0006629 GO:0006790 GO:0008146 GO:0008202 GO:0016740 GO:0050427
180.070.5003.510.120.632h8kA GO:0004027 GO:0004062 GO:0005737 GO:0006790 GO:0008146 GO:0016740


Consensus prediction of GO terms
 
Molecular Function GO:0043169 GO:0031177 GO:0016782
GO-Score 0.42 0.38 0.32
Biological Processes GO:0008152
GO-Score 0.38
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.