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I-TASSER results for job id Rv3603c

[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
10.36 29 3plrA NAI Rep, Mult 18,20,21,22,42,43,44,47,76,77,78,105,106,128,130,132,183
20.06 5 2amfA PRO Rep, Mult 22,104,127,128,130
30.03 2 3d1lB MPR Rep, Mult 130,183,186,190,191
40.03 2 3d1lB MPR Rep, Mult 234,251,252
50.02 2 3fwnB ATR Rep, Mult 42,43,44,47,77,78,81,84
60.01 1 2gr9B UUU Rep, Mult 143,144,165,166,167,168
70.01 1 2i76A NDP Rep, Mult 251,256
80.01 1 1muuC SUC Rep, Mult 13,68,69,70,71,98,99
90.01 1 3d1lA MPR Rep, Mult 190,191

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
10.2123gt0A0.5133.380.1260.6211.5.1.225,107,128,131
20.0663dojA0.5554.140.0730.7131.1.1.79NA
30.0661np3A0.6004.760.1100.8121.1.1.86NA
40.0602o3jA0.5684.510.1130.7361.1.1.22NA
50.0603itkC0.5674.250.0950.7291.1.1.22105
60.0601mfzA0.6484.530.0890.8841.1.1.132NA
70.0603gg2A0.5903.530.1090.7261.1.1.22115
80.0601dliA0.5414.380.0860.6961.1.1.22NA
90.0602h78A0.5414.170.1200.6771.1.1.31NA
100.0601x0xA0.5554.330.0990.7361.1.1.8NA
110.0603ckyC0.5304.220.0980.6601.1.1.29123,145,180,186
120.0602jkvA0.6304.260.0820.8481.1.1.44NA
130.0601txgA0.5504.570.1180.7391.1.1.94NA
140.0601yj8A0.5464.630.0880.7391.1.1.8NA
150.0601pgjA0.6264.570.0790.8611.1.1.44NA
160.0602amfE0.6173.690.1410.7691.5.1.225,107,130,172,193
170.0602i9pB0.5264.150.1090.6571.1.1.31145,173
180.0602f1kA0.5514.100.1400.6771.3.1.43NA
190.0601txgB0.5484.610.1240.7361.1.1.94109
200.0603h2zA0.5724.670.1120.7851.1.1.1776,109,188
210.0602izzB0.6213.820.1160.7921.5.1.2NA
220.0603khuB0.5694.300.0990.7331.1.1.22NA

(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
00.510.8111.380.200.843d1lB GO:0055114
10.250.6253.650.130.782i76A GO:0000166 GO:0055114
20.240.6624.060.100.864oqyB GO:0000166 GO:0004616 GO:0016491 GO:0055114
30.200.6384.530.080.883zgyD GO:0000166 GO:0004616 GO:0016020 GO:0016021 GO:0016491 GO:0055114
40.200.6674.310.100.883l6dB GO:0004616 GO:0016491 GO:0055114
50.190.6494.130.120.854oqzA GO:0004616 GO:0016491 GO:0055114
60.180.5974.810.110.845a9rA GO:0004616 GO:0016491 GO:0055114
70.180.5854.480.110.763gggD GO:0000166 GO:0004665 GO:0006571 GO:0008977 GO:0055114 GO:0070403
80.150.6054.790.090.853fwnA GO:0004616 GO:0005829 GO:0006098 GO:0016491 GO:0019521 GO:0042802 GO:0042803 GO:0055114
90.070.5514.200.100.704dllA GO:0004616 GO:0008679 GO:0016491 GO:0051287 GO:0055114
100.070.5984.820.080.832w90B
110.070.5384.100.120.673obbA GO:0000166 GO:0004616 GO:0006565 GO:0008442 GO:0009083 GO:0016491 GO:0016616 GO:0051287 GO:0051289 GO:0055114
120.070.5614.000.100.713w6zA GO:0000166 GO:0004616 GO:0016491 GO:0051287 GO:0055114
130.070.5514.210.110.711vpdA GO:0004616 GO:0008679 GO:0016491 GO:0046392 GO:0046487 GO:0051287 GO:0055114
140.070.5543.990.090.712uyyA GO:0003677 GO:0004616 GO:0005634 GO:0005654 GO:0005737 GO:0005794 GO:0016491 GO:0035064 GO:0051287 GO:0055114
150.070.5554.140.070.713dojA GO:0003858 GO:0004616 GO:0005737 GO:0005829 GO:0006979 GO:0016491 GO:0016616 GO:0030267 GO:0051287 GO:0055114
160.070.5443.900.090.693pduA GO:0000166 GO:0004616 GO:0016491 GO:0051287 GO:0055114
170.070.5514.190.090.694gbjC GO:0004616 GO:0016491 GO:0051287 GO:0055114
180.070.5533.970.110.713k96A GO:0004367 GO:0005737 GO:0005975 GO:0006072 GO:0006629 GO:0006650 GO:0008654 GO:0009331 GO:0016491 GO:0016616 GO:0036439 GO:0046167 GO:0046168 GO:0047952 GO:0051287 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0000166 GO:0004616
GO-Score 0.55 0.52
Biological Processes GO:0055114
GO-Score 0.82
Cellular Component GO:0031224
GO-Score 0.33

(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.