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I-TASSER results for job id Rv3178

[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 4 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
10.69 24 3r5yA F42 Rep, Mult 13,20,23,27,29,30,31,32,43,45,46,53,54,55,58,100
20.03 2 3gasB UUU Rep, Mult 43,45,52,53,55,102,103
30.03 2 2ou5A FMN Rep, Mult 32,42,44,114,116
40.02 1 3hy8A PO4 Rep, Mult 35,36,40,42,85,89
50.02 1 1nrgA PO4 Rep, Mult 19,20,25,61,62

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
10.0602a2jA0.6492.880.1100.8491.4.3.5NA
20.0602a4oA0.4474.020.0980.7063.4.22.2859
30.0601a5iA0.4783.660.0660.7233.4.21.68NA
40.0601ky9B0.4853.940.0370.7143.4.21.-NA
50.0601qy6A0.4843.850.0470.7143.4.21.1964
60.0601wv4A0.6182.100.0740.7231.4.3.5NA
70.0601bruP0.4693.010.0890.6553.4.21.71NA
80.0601nrgA0.6492.950.1190.8491.4.3.573
90.0602iphA0.4703.580.0700.6983.4.22.6678,81
100.0602zclP0.4573.830.0340.6893.4.21.77NA
110.0601fizA0.4693.600.0750.7063.4.21.10NA
120.0601ty9B0.6463.050.1400.8491.4.-.-NA
130.0602w1jB0.5214.390.0790.8492.3.2.12NA
140.0601pjpA0.4793.930.1010.6893.4.21.39NA
150.0603rp2A0.4693.860.1020.6813.4.21.-NA
160.0602w1kB0.5084.280.0800.8402.3.2.12NA
170.0601spjA0.4623.660.0680.6813.4.21.35NA
180.0603e90D0.3614.260.0800.6053.4.21.91NA
190.0601kq3A0.4604.430.0380.7981.1.1.662

(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
00.470.9120.750.310.944y9iA GO:0016491 GO:0055114
10.430.8782.030.281.003r5zA GO:0016491 GO:0055114
20.400.8892.000.291.003r5yD GO:0010181 GO:0016491 GO:0055114
30.380.7422.390.340.893r5lA GO:0005618 GO:0005886 GO:0010181 GO:0016020 GO:0016491 GO:0055114 GO:0070967
40.360.8222.340.290.993h96C GO:0016491 GO:0055114
50.230.6742.570.110.822hq9B GO:0000166 GO:0010181 GO:0016491 GO:0055114
60.210.7292.190.160.863tgvA GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
70.200.6762.610.100.833db0B GO:0010181 GO:0016491 GO:0055114
80.200.6362.930.140.843f7eA GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
90.190.6492.430.110.805escA GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
100.180.6272.410.120.772htdB GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
110.170.6673.110.130.884qvbB GO:0004733 GO:0010181 GO:0016491 GO:0030170 GO:0042803 GO:0042816 GO:0042823 GO:0055114
120.130.6542.880.050.852hq7B GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
130.120.6692.650.060.842i02A GO:0000166 GO:0010181 GO:0016491 GO:0055114
140.100.7272.010.100.861vl7A GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
150.090.6752.590.120.823ec6A GO:0000166 GO:0003677 GO:0010181 GO:0016491 GO:0055114
160.070.6143.200.070.853dmbA GO:0010181 GO:0016491 GO:0055114
170.070.6862.580.120.852fg9A GO:0000166 GO:0010181 GO:0016491 GO:0055114
180.070.6382.580.100.812qeaA GO:0010181 GO:0016491 GO:0046872 GO:0055114
190.070.7252.550.160.872arzA GO:0010181 GO:0016491 GO:0055114
200.060.4264.220.020.693uw1A GO:0004751 GO:0006098 GO:0009052 GO:0016853
210.060.3584.500.050.593ct8A GO:0046872
220.060.3295.180.070.643toxA GO:0000166
230.060.3354.880.040.631yb5A GO:0003723 GO:0003730 GO:0003960 GO:0005737 GO:0005829 GO:0007601 GO:0008270 GO:0016491 GO:0042178 GO:0051289 GO:0055114 GO:0070062 GO:0070402 GO:0070404
240.060.2934.110.010.455dfsA GO:0005739 GO:0005758 GO:0005829 GO:0006915 GO:0009055 GO:0020037 GO:0045155 GO:0046872 GO:0055114 GO:0070469
250.060.2904.300.080.511tceA GO:0000165 GO:0000187 GO:0001525 GO:0001666 GO:0001784 GO:0005068 GO:0005088 GO:0005154 GO:0005158 GO:0005159 GO:0005168 GO:0005543 GO:0005634 GO:0005737 GO:0005739 GO:0005759 GO:0005829 GO:0005886 GO:0007165 GO:0007173 GO:0007176 GO:0007265 GO:0007507 GO:0007568 GO:0008284 GO:0008286 GO:0009636 GO:0010008 GO:0014070 GO:0016032 GO:0016337 GO:0030036 GO:0030182 GO:0030971 GO:0031100 GO:0031175 GO:0031532 GO:0032403 GO:0032868 GO:0032869 GO:0035094 GO:0035556 GO:0036498 GO:0038095 GO:0038128 GO:0040008 GO:0042127 GO:0042542 GO:0043547 GO:0045740 GO:0045907 GO:0046875 GO:0048661 GO:0050900 GO:0051219 GO:0051384 GO:0051721 GO:0070435 GO:0071363
260.060.3555.150.040.703ag6A GO:0000166 GO:0004592 GO:0005524 GO:0005737 GO:0015940 GO:0016874
270.060.3484.350.080.603j79M GO:0003735 GO:0005840 GO:0006412 GO:0022625 GO:0030529 GO:0070180
280.060.2865.000.030.562btfP GO:0003779 GO:0005737 GO:0005856 GO:0030036 GO:0030833 GO:0032233
290.060.3144.560.060.553o3fA GO:0003676 GO:0003723 GO:0004518 GO:0004519 GO:0004523 GO:0005737 GO:0006298 GO:0006401 GO:0016787 GO:0030145 GO:0032299 GO:0043137 GO:0046872 GO:0090305 GO:0090502
300.060.3373.800.070.501qfwI GO:0003823


Consensus prediction of GO terms
 
Molecular Function GO:0016491 GO:0010181 GO:0070967
GO-Score 0.93 0.62 0.38
Biological Processes GO:0055114
GO-Score 0.93
Cellular Component GO:0005618 GO:0005886
GO-Score 0.38 0.38

(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.