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I-TASSER results for job id Rv1249c

[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
10.05 3 3ehbA CA Rep, Mult 63,66,67,68,69,72
20.04 2 1gwgA IOD Rep, Mult 209,210,213,216
30.04 2 4g28B 0W8 Rep, Mult 146,147
40.04 2 3dtuC TRD Rep, Mult 76,136,139,140,143
50.02 1 3oibA IOD Rep, Mult 134,137,193
60.02 1 2rh1A CLR Rep, Mult 59,83
70.02 1 2bkoA CA Rep, Mult 127,130
80.02 1 3f33A PFL Rep, Mult 196,199,200,203,230
90.02 1 4ntjA CLR Rep, Mult 173,229,232,233,236
100.02 1 1jb0F CLA Rep, Mult 220,224
110.02 1 2qkhA TAR Rep, Mult 235,238
120.02 1 1lghA DET Rep, Mult 88,95
130.02 1 3fyeA DMU Rep, Mult 196,198,224,225,228,229,232
140.02 1 3l26B MG Rep, Mult 245,256
150.02 1 4mhlA ARF Rep, Mult 60,63
160.02 1 3ifxC TBA Rep, Mult 87,115,118
170.02 1 2xgxA AKG Rep, Mult 116,120
180.02 1 3dtuC DXC Rep, Mult 55,58,59,62,75,78
190.02 1 3cvsD NUC Rep, Mult 114,115,214,216,217,218,232
200.02 1 3ephA MG Rep, Mult 194,198

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
10.0601n1zA0.4105.780.0460.6795.5.1.8NA
20.0601pn0C0.4255.770.0670.6761.14.13.7NA
30.0601qleA0.5055.410.0460.7711.9.3.1200
40.0602occN0.4965.880.0500.8091.9.3.1200,202,230
50.0601udyA0.4064.120.0890.5231.3.99.379
60.0602eabA0.4215.760.0430.6833.2.1.63NA
70.0602r7oA0.4145.890.0800.6452.7.7.48190
80.0603ii9C0.4153.790.0510.5191.3.99.7120
90.0601mo7A0.2606.230.0320.4623.6.3.9138,145
100.0603b8cA0.4326.260.0530.7293.6.3.6NA
110.0601fbvA0.4645.110.0390.6606.3.2.19NA
120.0601u8vA0.4525.860.0380.7375.3.3.3NA
130.0603cf4A0.4155.770.0430.6831.2.99.2NA
140.0602pg0A0.4084.470.0620.5301.3.99.3NA
150.0601vdzA0.4115.150.0600.6223.6.3.14NA
160.0601fohC0.4275.600.0630.6721.14.13.7NA
170.0601xmeA0.4406.070.0650.7521.9.3.1139,200
180.0603djlA0.4115.670.0330.6451.3.99.-NA
190.0603mddA0.3965.070.0830.5461.3.99.3221

(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
00.200.5055.410.050.771qleA GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0006119 GO:0006810 GO:0006811 GO:0009055 GO:0009060 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0022900 GO:0046872 GO:0055114 GO:0070469 GO:1902600
10.190.5095.350.050.771m56A GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0006119 GO:0006810 GO:0006811 GO:0009055 GO:0009060 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0022900 GO:0046872 GO:0055114 GO:0070469 GO:1902600
20.100.4895.440.050.761occA GO:0004129 GO:0005506 GO:0005739 GO:0005743 GO:0006119 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0045277 GO:0046872 GO:0055114 GO:0070469 GO:1902600
30.070.4906.000.050.811fftA GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0005887 GO:0006811 GO:0009055 GO:0009060 GO:0009319 GO:0009486 GO:0015078 GO:0015453 GO:0015990 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0016682 GO:0019646 GO:0020037 GO:0046872 GO:0048039 GO:0055114 GO:0070469
40.070.4365.990.040.734xydA GO:0004129 GO:0005506 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0016491 GO:0016966 GO:0020037 GO:0055114 GO:0070469 GO:1902600
50.070.4285.640.040.682yevA GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0006119 GO:0006810 GO:0006811 GO:0009055 GO:0009060 GO:0015002 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0022900 GO:0022904 GO:0046872 GO:0055114 GO:0070469 GO:1902600
60.070.4395.960.070.743eh3A GO:0004129 GO:0005506 GO:0005886 GO:0006119 GO:0006811 GO:0009055 GO:0009060 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0046872 GO:0055114 GO:0070469 GO:1902600
70.070.4915.710.060.803ayfA GO:0004129 GO:0005506 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0020037 GO:0046872 GO:0055114 GO:1902600
80.070.4895.870.070.805djqA GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0005887 GO:0006119 GO:0009055 GO:0009060 GO:0015078 GO:0015990 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0016705 GO:0019411 GO:0019646 GO:0019825 GO:0020037 GO:0045154 GO:0045278 GO:0046872 GO:0055114 GO:0070069 GO:0070469 GO:0070470 GO:1902600
90.060.4775.530.070.743o0rB GO:0004129 GO:0005506 GO:0005886 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0016491 GO:0016966 GO:0019333 GO:0020037 GO:0046872 GO:0055114 GO:0070469 GO:1902600
100.060.2976.370.020.523gdeA GO:0000166 GO:0003677 GO:0003909 GO:0003910 GO:0005524 GO:0006260 GO:0006281 GO:0006310 GO:0006974 GO:0007049 GO:0016874 GO:0046872 GO:0051103 GO:0051301 GO:0071897
110.060.3096.390.060.564ekzA GO:0000302 GO:0003756 GO:0004656 GO:0005178 GO:0005576 GO:0005783 GO:0005788 GO:0005793 GO:0005886 GO:0005925 GO:0006457 GO:0009897 GO:0016020 GO:0016222 GO:0016853 GO:0018401 GO:0019899 GO:0031012 GO:0034663 GO:0034976 GO:0042158 GO:0042470 GO:0044822 GO:0045454 GO:0046598 GO:0046982 GO:0070062 GO:0071456 GO:1902175
120.060.3165.100.070.464q5rA GO:0004364 GO:0016740
130.060.2936.490.060.535cuvA GO:0000287 GO:0004427 GO:0005737 GO:0006796
140.060.2846.100.040.472p5oB 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
150.060.3014.910.020.435ekqD GO:0009279 GO:0016020 GO:0043165 GO:0051205 GO:1990063
160.060.3115.130.070.462vcvA GO:0004364 GO:0005737 GO:0005829 GO:0006749 GO:0008152 GO:0016740 GO:0070062 GO:1901687
170.060.2557.370.050.523e49A GO:0003824 GO:0016740 GO:0019475 GO:0046872
180.060.2565.790.080.421kgsA GO:0000160 GO:0003677 GO:0005622 GO:0006351 GO:0006355 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0005506 GO:0004129 GO:0020037 GO:0005507
GO-Score 0.49 0.49 0.49 0.40
Biological Processes GO:0009060 GO:1902600 GO:0006119 GO:0022900
GO-Score 0.49 0.46 0.42 0.35
Cellular Component GO:0016021 GO:0070469 GO:0005886
GO-Score 0.49 0.49 0.40

(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.