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I-TASSER results for job id Rv0998

[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
10.38 6 4avaA ACO Rep, Mult 173,236,237,238,239,240,245,246,247,248,249,250,251,272,273,277,279,280,282,283,286
20.17 3 4avbA CMP Rep, Mult 48,67,79,80,87,88,89,90,91,98,99,100,102,138,142
30.04 1 3tdcA 0EU Rep, Mult 176,180,181,183,184,185
40.04 1 3ff6B RCP Rep, Mult 256,257,260
50.04 1 3kllA MAL Rep, Mult 214,219,220,249
60.04 1 3ff6C RCP Rep, Mult 91,92,94,95

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
10.0601ofdA0.3916.970.0520.6941.4.7.1NA
20.0603ff6A0.4026.270.0510.6436.4.1.2,6.3.4.14255
30.0602vn4A0.3926.380.0570.6523.2.1.3NA
40.0601fo4A0.3846.310.0850.6191.17.1.4NA
50.0601z1wA0.3976.060.0410.6283.4.11.-NA
60.0602e1qA0.3876.160.0730.6161.17.3.2,1.17.1.4NA
70.0603b9jC0.3526.600.0440.6011.17.3.2,1.17.1.4NA
80.0602a7sA0.4006.250.0580.6586.4.1.3116,117
90.0603gpbA0.3196.730.0590.5492.4.1.1NA
100.0603hz3A0.4056.370.0630.6702.4.1.5170
110.0601fa9A0.3486.790.0610.5952.4.1.1NA
120.0601ojnA0.3547.040.0460.6344.2.2.1NA
130.0602j5wA0.4016.280.0340.6491.16.3.1NA
140.0601c7sA0.3946.530.0480.6703.2.1.52241
150.0601od2A0.3996.100.0500.6316.3.4.14,6.4.1.2NA
160.0602ckjA0.3516.700.0470.6041.17.1.4,1.17.3.2NA
170.0601ethA0.3856.510.0690.6553.1.1.3NA
180.0601llwA0.3857.040.0530.6851.4.7.1NA
190.0601ea0A0.3756.650.0350.6401.4.1.13NA

(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
00.710.9740.631.000.984avaA GO:0008080 GO:0016407 GO:0016740 GO:0016746 GO:0030552 GO:0046872
10.500.8332.870.540.954orfA GO:0008080 GO:0016740 GO:0016746 GO:0046872
20.200.3723.250.230.443gydB GO:0000166
30.140.3714.680.130.481cx4A GO:0000166 GO:0001932 GO:0004862 GO:0005737 GO:0005743 GO:0005813 GO:0005886 GO:0005952 GO:0006631 GO:0007612 GO:0008603 GO:0016020 GO:0019901 GO:0019904 GO:0030425 GO:0030552 GO:0031625 GO:0034236 GO:0043025 GO:0043197 GO:0043198 GO:0045121 GO:0045859 GO:0048471 GO:0070062 GO:0097332 GO:0097338 GO:0097546 GO:2000480
40.120.3934.530.130.503of1A GO:0000166 GO:0000790 GO:0001932 GO:0004862 GO:0005634 GO:0005737 GO:0005886 GO:0005952 GO:0008603 GO:0030552 GO:0042802 GO:0045762 GO:0045859 GO:0046580 GO:0071901 GO:0097271
50.110.3464.220.160.444ev0D GO:0000166 GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0010628 GO:0030552 GO:0042803 GO:0043565 GO:0044212 GO:0045893
60.100.3472.730.180.392vi7C GO:0004596 GO:0008080 GO:0017189 GO:0031248
70.090.3483.290.130.413i54D GO:0000166 GO:0003677 GO:0003700 GO:0005618 GO:0005886 GO:0006351 GO:0006355 GO:0009405 GO:0030552 GO:0040007 GO:0045892 GO:0045893
80.090.3823.280.290.444nxyA GO:0008080 GO:0048037
90.080.3394.180.120.423dkwA GO:0003677 GO:0006351 GO:0006355 GO:0051173 GO:0051353 GO:0071731
100.080.3613.220.210.425bv6A GO:0000166 GO:0004672 GO:0004674 GO:0004692 GO:0005524 GO:0005829 GO:0005886 GO:0006468 GO:0007165 GO:0016020 GO:0016301 GO:0016310 GO:0016324 GO:0016740 GO:0030553 GO:0031965 GO:0036289 GO:0042803 GO:0050999 GO:0072661
110.070.3434.080.120.424byyA GO:0000166 GO:0003677 GO:0006351 GO:0006355 GO:0016301 GO:0016310 GO:0016740 GO:0030552 GO:2000874
120.070.3542.900.160.402j8mA
130.060.3512.850.190.401vhsA GO:0004596 GO:0006474 GO:0008080 GO:0009635 GO:0016740 GO:0016746 GO:0031248 GO:0046677
140.060.3413.120.210.394bmhA GO:0008080 GO:0016740
150.060.3553.690.120.423u10A GO:0000166 GO:0005216 GO:0005222 GO:0005244 GO:0005248 GO:0005249 GO:0005267 GO:0005272 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0007267 GO:0008076 GO:0016020 GO:0016021 GO:0030552 GO:0034765 GO:0035725 GO:0042391 GO:0042802 GO:0055085 GO:0060078 GO:0071320 GO:0071321 GO:0071805
160.060.3573.060.210.415j3uA GO:0016301 GO:0016310
170.060.3533.650.130.422q0aA GO:0000166 GO:0005216 GO:0005222 GO:0005244 GO:0005248 GO:0005249 GO:0005267 GO:0005272 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0016020 GO:0016021 GO:0030552 GO:0034765 GO:0035725 GO:0042391 GO:0042802 GO:0055085 GO:0060078 GO:0071320 GO:0071321 GO:0071805
180.060.3543.460.190.424d7sA GO:0000166 GO:0016020 GO:0016021


Consensus prediction of GO terms
 
Molecular Function GO:0008080 GO:0046872 GO:0030552 GO:0030291
GO-Score 0.85 0.85 0.78 0.48
Biological Processes GO:0043549 GO:0031399 GO:0006468
GO-Score 0.48 0.48 0.48
Cellular Component GO:0044424 GO:1902554 GO:0071944 GO:0016020
GO-Score 0.48 0.48 0.48 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.