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I-TASSER results for job id Rv0923c

[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
10.25 8 4wcmA ZN Rep, Mult 187,192,250
20.12 4 2bo9A VAL Rep, Mult 188,225,226,263,314,316
30.03 1 3rbhA C8E Rep, Mult 10,63
40.03 1 2c6pA UUU Rep, Mult 120,123,124,127
50.03 1 2c41G CL Rep, Mult 113,117
60.03 1 3jucA PCA Rep, Mult 10,11,12,13,14,48,77,83
70.03 1 3dgvB UUU Rep, Mult 4,26,66,67,68

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
10.0602hb6B0.4084.300.0510.5203.4.11.1NA
20.0601cpbA0.1173.990.0950.1473.4.17.263,102
30.0601z8lA0.4785.680.0520.6953.4.17.21NA
40.0601gytJ0.4064.270.0410.5203.4.11.176
50.0602boaA0.4754.850.0770.6383.4.17.-NA
60.0603fedA0.4745.570.0440.6843.4.17.21NA
70.0603kzwA0.4104.310.0390.5233.4.11.179
80.0601pcaA0.4724.900.0820.6383.4.17.1NA
90.0601pytA0.1184.350.0430.1523.4.17.187
100.0602ecfA0.4126.640.0620.6783.4.14.5NA
110.0601ayeA0.4784.800.0720.6383.4.17.15NA
120.0601pytB0.3834.590.0680.5143.4.17.1NA
130.0603h8eA0.4024.330.0530.5113.4.11.159
140.0601cpbB0.2864.470.1270.3763.4.17.2NA
150.0601jqgA0.4774.770.0530.6333.4.17.1NA
160.0603dgvA0.4585.140.0760.6383.4.17.20NA
170.0601gytA0.4054.210.0440.5173.4.11.1NA
180.0603gpbA0.3976.240.0420.6302.4.1.1NA
190.0601ob2A0.2916.980.0310.5083.6.1.48NA

(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
00.120.3624.660.040.481ampA GO:0004177 GO:0005576 GO:0006508 GO:0008233 GO:0016787 GO:0046872
10.070.5141.790.250.553a9lA GO:0016787 GO:0046872
20.070.4885.530.060.701cx8A GO:0001558 GO:0001618 GO:0001666 GO:0001948 GO:0003725 GO:0004998 GO:0005576 GO:0005615 GO:0005739 GO:0005768 GO:0005886 GO:0005887 GO:0005905 GO:0006879 GO:0006897 GO:0006898 GO:0006953 GO:0007568 GO:0007584 GO:0009897 GO:0009986 GO:0010033 GO:0010035 GO:0010039 GO:0010042 GO:0016020 GO:0016021 GO:0016023 GO:0016032 GO:0016323 GO:0030316 GO:0030544 GO:0032526 GO:0033570 GO:0033572 GO:0035690 GO:0042127 GO:0042470 GO:0042802 GO:0042803 GO:0043231 GO:0044822 GO:0045780 GO:0046688 GO:0046718 GO:0048471 GO:0051087 GO:0055037 GO:0055038 GO:0070062 GO:0072562 GO:0097286 GO:1903561 GO:1990712
30.070.4795.720.050.705f09A GO:0003824 GO:0004180 GO:0004181 GO:0005737 GO:0005886 GO:0005887 GO:0006508 GO:0006760 GO:0008152 GO:0008233 GO:0008237 GO:0008652 GO:0009986 GO:0016020 GO:0016021 GO:0016787 GO:0016805 GO:0035609 GO:0046872 GO:0070062 GO:1904492 GO:1904493
40.070.4805.780.060.704tweA GO:0003824 GO:0004180 GO:0005886 GO:0006508 GO:0008152 GO:0008233 GO:0008237 GO:0016020 GO:0016021 GO:0016324 GO:0016787 GO:0016805 GO:0046872
50.070.4745.570.040.683fedA GO:0003824 GO:0004180 GO:0005886 GO:0006508 GO:0008152 GO:0008233 GO:0008236 GO:0008237 GO:0008239 GO:0008652 GO:0016020 GO:0016021 GO:0016787 GO:0016805 GO:0042135 GO:0046872 GO:0050129
60.070.4355.670.040.632ek8A GO:0004177 GO:0006508 GO:0046872
70.060.4365.860.030.664r12A GO:0016020 GO:0016021 GO:0016485 GO:0046872
80.060.4325.710.040.643iibA GO:0046872
90.060.3226.850.070.561mabB GO:0000166 GO:0000275 GO:0005509 GO:0005524 GO:0005739 GO:0005743 GO:0005753 GO:0006754 GO:0006810 GO:0006811 GO:0006898 GO:0015986 GO:0015991 GO:0015992 GO:0016020 GO:0016787 GO:0016820 GO:0016887 GO:0030228 GO:0033178 GO:0045261 GO:0046034 GO:0046933
100.060.2747.110.020.493eifA GO:0004252 GO:0005618 GO:0006508 GO:0008233 GO:0008236 GO:0016020 GO:0016787
110.060.2787.050.020.492g50D GO:0000166 GO:0000287 GO:0003824 GO:0004743 GO:0005524 GO:0005634 GO:0005737 GO:0006096 GO:0008152 GO:0016301 GO:0016310 GO:0016740 GO:0030955 GO:0046872
120.060.2716.850.030.463itgB GO:0000986 GO:0001141 GO:0003677 GO:0003700 GO:0003824 GO:0003842 GO:0004029 GO:0004657 GO:0006351 GO:0006355 GO:0006560 GO:0006561 GO:0008152 GO:0009898 GO:0010133 GO:0016491 GO:0016620 GO:0043565 GO:0045892 GO:0050660 GO:0055114
130.060.2536.460.040.423qedB GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0046872
140.060.3694.560.050.481f2oA GO:0004177 GO:0004252 GO:0005576 GO:0006508 GO:0008233 GO:0016787 GO:0046872
150.060.2895.660.070.433nrgA GO:0003677 GO:0003700 GO:0006351 GO:0006355
160.060.2486.880.040.422rduA GO:0001561 GO:0003824 GO:0003973 GO:0005102 GO:0005777 GO:0005782 GO:0006979 GO:0008891 GO:0010181 GO:0016491 GO:0046296 GO:0046487 GO:0047969 GO:0052852 GO:0052853 GO:0052854 GO:0055114
170.060.2616.260.040.424j4wA GO:0003723 GO:0019013
180.060.2626.120.080.423ov9A GO:0003723 GO:0019012 GO:0019013 GO:0019028 GO:0019029


Consensus prediction of GO terms
 
Molecular Function GO:0043169 GO:0003824
GO-Score 0.56 0.39
Biological Processes GO:0019538
GO-Score 0.46
Cellular Component GO:0071944
GO-Score 0.37

(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.