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I-TASSER results for job id Rv2186c

[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
10.18 10 4n3eD 2AN Rep, Mult 8,10,19,23,63,65,76,106,107,110
20.08 5 3fxjA MN Rep, Mult 70,71
30.06 3 4a81A 2AN Rep, Mult 8,10,22,51,63,76,78,103,106,107,110,111
40.05 3 3gtsB D3M Rep, Mult 38,51,53,61,63,102,105,109
50.05 3 3gb4A FES Rep, Mult 50,61,63,76
60.02 1 3s7bA BU3 Rep, Mult 44,51
70.02 1 3c0vC TBR Rep, Mult 43,46,48,62
80.02 1 2anuA ZN Rep, Mult 66,75
90.02 1 2qx6A ML1 Rep, Mult 29,55
100.02 1 4dz4A UNK Rep, Mult 43,55
110.02 1 1gqcA MG Rep, Mult 5,8,9
120.02 1 4ryvA ZEA Rep, Mult 6,8,78,80,99,100,103

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
10.1661ul7A0.4883.280.0870.6822.7.11.110,62,110
20.0602ewnA0.5593.300.0340.7606.3.4.15NA
30.0601umfC0.5093.950.0460.7834.2.3.5NA
40.0602v8qA0.5263.130.0930.7132.7.11.165,74
50.0601ciaA0.5203.870.0290.7442.3.1.28NA
60.0602pmgB0.4184.190.0600.6595.4.2.246
70.0601wqlA0.6113.360.0340.8531.14.12.-15
80.0602cghB0.5523.560.0940.7756.3.4.15NA
90.0603en1A0.5493.770.0590.8531.14.12.1115
100.0601wnlA0.5333.770.0600.7676.3.4.15NA
110.0602ej9A0.5344.070.0780.8066.3.4.1547
120.0602zfdB0.5382.920.1100.6982.7.11.112,113
130.0602vq5A0.6632.840.1150.8684.2.1.7848,65
140.0601kfqB0.5693.640.0920.8455.4.2.268,70
150.0601cf3A0.5174.130.0610.7671.1.3.4NA
160.0601crkA0.5323.470.0910.7672.7.3.2NA
170.0602ii4A0.5504.320.0540.8062.3.1.168NA
180.0601q23B0.5283.760.0480.7442.3.1.28NA
190.0601uliC0.6173.290.0260.8531.14.12.1825
200.0601galA0.5093.980.0430.7521.1.3.440,113

(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
00.200.7502.670.130.912rerA GO:0003824 GO:0008152 GO:0008168 GO:0008171 GO:0016740 GO:0017000 GO:0032259
10.100.6672.990.080.872kewA GO:0006950
20.070.4264.100.010.661z05A GO:0003700 GO:0006355 GO:0046872
30.070.4384.690.050.753l2nA GO:0004180 GO:0004181 GO:0006508 GO:0008270 GO:0046872
40.060.3704.430.030.573rd7B GO:0006637 GO:0047617
50.060.3594.940.060.611lldA GO:0003824 GO:0004459 GO:0005737 GO:0005975 GO:0006096 GO:0016491 GO:0016616 GO:0019752 GO:0055114
60.060.3715.130.100.714iilA GO:0005886 GO:0016020
70.060.3484.920.080.652qk4B GO:0000166 GO:0003360 GO:0003824 GO:0004637 GO:0004641 GO:0004644 GO:0005524 GO:0005737 GO:0005829 GO:0006164 GO:0006189 GO:0006544 GO:0008152 GO:0009058 GO:0009113 GO:0009156 GO:0009168 GO:0010033 GO:0010035 GO:0016740 GO:0016742 GO:0016874 GO:0021549 GO:0021987 GO:0046654 GO:0046872 GO:0070062
80.060.3964.380.020.645bsmA GO:0000166 GO:0003824 GO:0005524 GO:0008152 GO:0009698 GO:0016207 GO:0016874
90.060.3075.270.020.584v6wAI GO:0000462 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0022008 GO:0022627 GO:0030529 GO:0035167
100.060.2955.500.060.604d4zB GO:0004497 GO:0005829 GO:0008612 GO:0016491 GO:0019135 GO:0046872 GO:0055114
110.060.3022.680.110.374iylA GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0019843 GO:0030529
120.060.2964.520.090.491fneA GO:0002376 GO:0002504 GO:0006955 GO:0016020 GO:0016021 GO:0019882 GO:0042613
130.060.6822.530.150.834xrtA
140.060.7852.820.140.982m47A
150.060.3654.490.110.603bt5A
160.060.2724.120.030.423hg9B
170.060.7622.650.140.943tfzA
180.060.6892.600.100.882le1A


Consensus prediction of GO terms
 
Molecular Function GO:0008168
GO-Score 0.40
Biological Processes GO:0044249 GO:0016999
GO-Score 0.40 0.40
Cellular Component
GO-Score

(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.