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I-TASSER results for job id Rv2348c

[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
10.11 5 3e7lC ZN Rep, Mult 72,75
20.07 3 3as0A SAU Rep, Mult 43,45,90
30.07 3 2a68P MG Rep, Mult 75,78
40.04 2 1wdc2 III Rep, Mult 72,73,74,75,76,77,78,79,80,81,82,83,84,85,88,89
50.04 2 1c6v1 III Rep, Mult 15,17,18,25
60.04 2 2wsc4 CLA Rep, Mult 24,29,39,45,46
70.02 1 2wsc3 CLA Rep, Mult 24,28,29,31
80.02 1 4jbeA CA Rep, Mult 69,72
90.02 1 3fy4C PO4 Rep, Mult 91,92,95
100.02 1 1utzA PF3 Rep, Mult 103,104
110.02 1 3gyyA ZN Rep, Mult 81,85
120.02 1 4a8fA MG Rep, Mult 71,108

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
10.0603hbxA0.4154.730.0670.7784.1.1.1548
20.0601a6rA0.4244.330.0400.7323.4.22.40,3.4.22.-NA
30.0601ywgO0.4144.340.0710.7321.2.1.12NA
40.0602hfuA0.4164.370.0490.7132.7.1.36NA
50.0601k3uA0.4234.490.0530.7684.2.1.20NA
60.0601rv8B0.3274.840.0960.6204.1.2.13NA
70.0602gwdA0.4514.690.0930.8806.3.2.2NA
80.0602bkwA0.4224.310.0390.7592.6.1.44NA
90.0601p57A0.2804.870.0130.5373.4.21.10626,36,50
100.0602jc9A0.4154.120.0500.6943.1.3.5NA
110.0602hzpA0.4344.350.0580.7783.7.1.39,13
120.0601k6yA0.4194.100.0100.7132.7.7.4959
130.0601bjoA0.4264.380.0580.7782.6.1.52NA
140.0602a2dA0.4194.160.0220.6762.7.1.157,2.7.1.-NA
150.0603f9kI0.4454.580.0430.8062.7.7.4978,80,93
160.0601c7jA0.3644.430.0820.6853.1.1.-NA
170.0601cb7B0.4164.080.0700.7225.4.99.1NA
180.0601xizB0.4284.820.0610.8152.7.1.6927
190.0602hfsA0.4184.460.0490.7222.7.1.3665

(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
00.130.2855.380.050.601yl5A GO:0005618 GO:0005737 GO:0005829 GO:0005886 GO:0008652 GO:0008839 GO:0009085 GO:0009089 GO:0016491 GO:0016726 GO:0019877 GO:0050661 GO:0051287 GO:0055114 GO:0070402 GO:0070404
10.070.4524.300.050.791e1dA GO:0003824 GO:0005737 GO:0016491 GO:0016661 GO:0046872 GO:0050418 GO:0051536 GO:0051539 GO:0055114
20.060.3784.600.070.732ivnA GO:0000049 GO:0000408 GO:0002949 GO:0003727 GO:0005737 GO:0008033 GO:0016740 GO:0016746 GO:0046872 GO:0061711
30.060.3664.760.040.663pasB GO:0003677 GO:0006351 GO:0006355
40.060.3684.210.050.674gq0A GO:0001523 GO:0001758 GO:0004033 GO:0005576 GO:0005764 GO:0005829 GO:0006081 GO:0007586 GO:0008202 GO:0016488 GO:0016491 GO:0044597 GO:0044598 GO:0045550 GO:0047718 GO:0055114 GO:0070062
50.060.3504.580.050.694bgaC GO:0000166 GO:0005524 GO:0006040 GO:0006508 GO:0008233 GO:0008237 GO:0009254 GO:0016773 GO:0046872
60.060.3434.810.050.663b8bA GO:0000103 GO:0000287 GO:0005737 GO:0008441 GO:0016020 GO:0016311 GO:0046854
70.060.3365.010.010.663bubA GO:0000139 GO:0003824 GO:0004553 GO:0004559 GO:0004572 GO:0005783 GO:0005794 GO:0005795 GO:0005975 GO:0006013 GO:0006486 GO:0006487 GO:0006491 GO:0006517 GO:0008152 GO:0008270 GO:0015923 GO:0016020 GO:0016021 GO:0016063 GO:0016787 GO:0016798 GO:0030246 GO:0035010 GO:0046872
80.060.4494.390.070.801gnlA GO:0003824 GO:0005737 GO:0016491 GO:0016661 GO:0046872 GO:0050418 GO:0051536 GO:0051539 GO:0055114
90.060.2845.160.090.622aizP GO:0009279 GO:0016020 GO:0016021
100.060.3184.970.050.621qzmA GO:0000166 GO:0003677 GO:0004176 GO:0004252 GO:0005524 GO:0005737 GO:0005829 GO:0006508 GO:0006515 GO:0008233 GO:0008236 GO:0009408 GO:0016787 GO:0016887 GO:0030163 GO:0033554 GO:0043565
110.060.3515.000.060.734mo5A GO:0000166 GO:0005524 GO:0005975 GO:0006040 GO:0009254 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0097175
120.060.3144.610.060.572krkA GO:0000165 GO:0000166 GO:0000209 GO:0000502 GO:0002223 GO:0002479 GO:0003712 GO:0005102 GO:0005524 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0005838 GO:0006366 GO:0006521 GO:0008134 GO:0008540 GO:0016020 GO:0016234 GO:0016787 GO:0016887 GO:0017025 GO:0022624 GO:0030163 GO:0030433 GO:0031145 GO:0031410 GO:0031531 GO:0031595 GO:0031597 GO:0033209 GO:0036402 GO:0038061 GO:0038095 GO:0043069 GO:0043161 GO:0043488 GO:0045892 GO:0045893 GO:0045899 GO:0050852 GO:0051436 GO:0051437 GO:0060071 GO:0070062 GO:0072562 GO:0090090 GO:0090261 GO:0090263 GO:1901800
130.060.4504.860.050.874zfvA GO:0005524 GO:0006040 GO:0009254 GO:0016301 GO:0016310 GO:0016740 GO:0016773
140.060.3274.890.060.654tlxA GO:0000166 GO:0004497 GO:0016491 GO:0055114
150.060.4025.040.030.803qbxB GO:0000166 GO:0005524 GO:0005975 GO:0006040 GO:0009254 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0097175
160.060.3804.690.060.732pizA GO:0004180 GO:0004181 GO:0005576 GO:0005615 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0046872
170.060.3115.440.050.693cqyA GO:0000166 GO:0005524 GO:0005975 GO:0006040 GO:0009254 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0097175
180.060.3044.770.030.593ktbA GO:0003677 GO:0045892 GO:0046685


Consensus prediction of GO terms
 
Molecular Function GO:0003824
GO-Score 0.33
Biological Processes GO:0044710
GO-Score 0.47
Cellular Component GO:0044444
GO-Score 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.