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I-TASSER results for job id Rv0739

[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
10.08 4 1k6lL BPH Rep, Mult 72,76,80
20.08 4 1brrC ARC Rep, Mult 78,101,105
30.04 2 2vk6A MG Rep, Mult 145,146
40.04 2 5cwfC CA Rep, Mult 81,84,139
50.02 1 2vn4A MAN Rep, Mult 246,262
60.02 1 3umkA CU Rep, Mult 15,49
70.02 1 4zdrB TME Rep, Mult 20,23
80.02 1 3ak3D EDO Rep, Mult 83,86
90.02 1 1xrmA III Rep, Mult 101,104
100.02 1 3s8gA OLC Rep, Mult 72,76,109,110,112
110.02 1 2qcsB ANP Rep, Mult 43,45,46
120.02 1 3u3fC III Rep, Mult 177,180,181,184,187,214,217,218
130.02 1 3i0oA MG Rep, Mult 229,242
140.02 1 1re4C CA Rep, Mult 93,118
150.02 1 1f61A MG Rep, Mult 64,119
160.02 1 3sjqC PHU Rep, Mult 98,101
170.02 1 4xgcC III Rep, Mult 95,96

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
10.0603b8eA0.4386.030.0460.7313.6.3.9NA
20.0601occA0.4835.490.0460.7571.9.3.1NA
30.0601mhsA0.4056.440.0410.7393.6.3.6NA
40.0601fbvA0.4434.820.0410.6126.3.2.19NA
50.0601jqkF0.4275.740.0490.6751.2.99.2239
60.0601t3tA0.4166.050.0810.7026.3.5.3179
70.0603b8cB0.4126.110.0410.6723.6.3.678
80.0601qleA0.4775.300.0470.7461.9.3.121
90.0603cf4A0.4625.520.0440.7241.2.99.2NA
100.0602z8yP0.3675.450.0470.5412.3.1.16954
110.0602iukB0.3796.080.0560.6421.13.11.12NA
120.0601w07B0.4115.380.0840.6421.3.3.6NA
130.0603cskA0.4126.220.0510.6873.4.14.421,85
140.0601m21A0.4066.260.0870.6723.5.1.-NA
150.0603b8eC0.4415.770.0260.7093.6.3.920,49,51
160.0601eulA0.4025.810.0530.6343.6.3.8NA
170.0603ecnB0.4085.810.0650.6683.1.4.1771
180.0601n1hA0.4115.980.0630.6902.7.7.4865,123
190.0602r7oA0.4065.530.0550.6272.7.7.48155

(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
00.160.4515.710.060.733o0rB 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
10.130.4865.120.060.751m56A 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
20.110.4835.490.050.761occA 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
30.070.4655.690.040.755djqA 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
40.070.4775.300.050.751qleA 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
50.070.4514.390.080.633eh3A 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
60.070.4735.420.050.751fftA 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
70.070.4575.380.060.702yevA 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
80.060.3875.760.040.633mm5B GO:0006790 GO:0009055 GO:0016020 GO:0016491 GO:0018551 GO:0020037 GO:0046872 GO:0051536 GO:0051539 GO:0055114
90.060.3126.020.020.523ga7A GO:0005737 GO:0008152 GO:0016787 GO:0052689
100.060.2985.130.060.435ekqD GO:0009279 GO:0016020 GO:0043165 GO:0051205 GO:1990063
110.060.2956.720.040.543gdeA 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
120.060.2996.820.040.562p5oB 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
130.060.2473.980.060.324iwbA GO:0044780
140.060.2185.210.060.342wgbB GO:0003677 GO:0006351 GO:0006355
150.060.2305.190.040.352xz4A GO:0002376 GO:0005887 GO:0006952 GO:0008270 GO:0008340 GO:0008745 GO:0009253 GO:0009617 GO:0016020 GO:0016021 GO:0019731 GO:0031240 GO:0042834 GO:0045087 GO:0046329 GO:0061057 GO:0098542
160.060.1692.430.040.192w2uA GO:0005524
170.060.1834.140.040.242o5aA GO:0005737 GO:0006417 GO:0017148 GO:0042256 GO:0090071
180.060.1573.820.020.211oscF GO:0005507 GO:0008104 GO:0010038 GO:0016020 GO:0019899 GO:0051260


Consensus prediction of GO terms
 
Molecular Function GO:0020037 GO:0004129 GO:0005506 GO:0016662
GO-Score 0.43 0.43 0.43 0.32
Biological Processes GO:1902600 GO:0009060 GO:0006119 GO:0071941
GO-Score 0.43 0.43 0.33 0.32
Cellular Component GO:0070469 GO:0016021 GO:0005886
GO-Score 0.43 0.43 0.36

(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.