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I-TASSER results for job id Rv2670c

[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 30 1l8qA ADP Rep, Mult 56,57,60,66,109,110,111,112,113,114,234,238,268
20.10 8 2qbyB MG Rep, Mult 113,168,200
30.04 3 5he9A BEF Rep, Mult 108,109,112,200
40.01 1 3r8fC QNA Rep, Mult 148,175,179

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
10.0603b9pA0.4734.130.1650.5993.6.4.3111,113,168,200,235,268
20.0602hyiI0.4215.260.1030.5913.6.4.13113
30.0601in5A0.4674.710.0900.6263.6.4.12NA
40.0603d64B0.3656.750.0510.6183.3.1.1NA
50.0601v8bA0.3896.500.0800.6233.3.1.1NA
60.0601ahpA0.3987.370.0770.7132.4.1.1198
70.0602db3A0.4455.250.0730.6133.6.4.13203
80.0602qllA0.3986.970.0380.6862.4.1.1198
90.0601ygpA0.4066.980.0550.7022.4.1.1NA
100.0603i62A0.4285.480.0840.6103.6.4.13113
110.0601njgA0.4313.970.1140.5452.7.7.7111,138,169,203
120.0603g1uC0.3895.880.0710.5943.3.1.1NA
130.0603n58A0.3886.280.0690.6133.3.1.1NA
140.0601xxiA0.3915.850.1040.5962.7.7.7263,276
150.0601a5tA0.4235.080.0890.5832.7.7.7272
160.0603bg3A0.3826.660.0620.6296.4.1.1NA
170.0603gpbA0.3827.530.0380.7072.4.1.1NA
180.0601w6jA0.3886.920.0670.6535.4.99.7NA
190.0601nsfA0.4624.160.1130.5883.6.4.6112

(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
00.360.5334.640.100.702qbyB GO:0000166 GO:0003677 GO:0005524 GO:0006260
10.310.4622.290.190.502w58A GO:0000166 GO:0004386 GO:0005524
20.270.4574.450.120.591ofhA GO:0000166 GO:0005524 GO:0005737 GO:0006508 GO:0009376 GO:0016887 GO:0043335 GO:0070011
30.270.4661.890.200.502qgzA GO:0005524
40.150.4685.000.080.653j96A GO:0000166 GO:0005524 GO:0005737 GO:0006810 GO:0015031 GO:0016787 GO:0030496 GO:0046872
50.070.4474.510.080.584xgcE GO:0000166 GO:0000808 GO:0003677 GO:0005524 GO:0005634 GO:0005664 GO:0006260 GO:0006261 GO:0006270 GO:0006342 GO:0007052 GO:0007076 GO:0046331
60.070.5032.970.160.582z4rA GO:0000166 GO:0003677 GO:0003688 GO:0005524 GO:0005737 GO:0006260 GO:0006270 GO:0006275 GO:0043565
70.070.5484.580.120.712v1uA GO:0000166 GO:0003677 GO:0005524 GO:0006260
80.070.5394.850.100.722qbyA GO:0000166 GO:0003677 GO:0005524 GO:0006260
90.070.4985.160.080.681ksfX GO:0000166 GO:0004176 GO:0005524 GO:0005829 GO:0006508 GO:0006979 GO:0016887 GO:0019538 GO:0043335
100.070.5125.030.100.701w5sB GO:0000166 GO:0003677 GO:0005524 GO:0006260
110.070.4904.080.100.601l8qA GO:0000166 GO:0003677 GO:0003688 GO:0005524 GO:0005737 GO:0006260 GO:0006270 GO:0006275 GO:0043565
120.070.4914.470.110.653uk6G GO:0000166 GO:0000812 GO:0000979 GO:0000980 GO:0001094 GO:0003678 GO:0004003 GO:0004386 GO:0005524 GO:0005622 GO:0005634 GO:0005654 GO:0005719 GO:0005737 GO:0006281 GO:0006310 GO:0006338 GO:0006351 GO:0006355 GO:0006457 GO:0006974 GO:0016020 GO:0016363 GO:0016568 GO:0016787 GO:0016887 GO:0030529 GO:0031011 GO:0031490 GO:0032508 GO:0034644 GO:0035066 GO:0035267 GO:0040008 GO:0042802 GO:0042803 GO:0043141 GO:0043531 GO:0043967 GO:0043968 GO:0045944 GO:0051082 GO:0051117 GO:0070062 GO:0071169 GO:0071339 GO:0071392 GO:0071733 GO:0071899 GO:0097255 GO:1904874
130.070.4825.140.070.682fnaA GO:0000166 GO:0005524
140.070.4614.590.130.611im2A GO:0000166 GO:0005524 GO:0005737 GO:0006508 GO:0009376 GO:0016887 GO:0043335 GO:0070011
150.070.4763.840.110.593h4mA GO:0000166 GO:0000502 GO:0003924 GO:0005524 GO:0005737 GO:0008540 GO:0010498 GO:0016787 GO:0016887 GO:0017025 GO:0022623 GO:0030163 GO:0030433 GO:0031595 GO:0031597 GO:0036402 GO:0043273 GO:0043335 GO:0045899 GO:1901800
160.070.4684.300.160.604l15A GO:0000166 GO:0000287 GO:0005524 GO:0005634 GO:0007049 GO:0007067 GO:0008017 GO:0008568 GO:0010569 GO:0016787 GO:0016887 GO:0031122 GO:0045931 GO:0046034 GO:0046872 GO:0051301
170.070.4764.480.070.621fnnA GO:0000166 GO:0005524 GO:0006260 GO:0051301
180.070.4724.090.100.603whkA GO:0000166 GO:0000502 GO:0005524 GO:0005634 GO:0005737 GO:0006511 GO:0008540 GO:0010498 GO:0016787 GO:0016887 GO:0017025 GO:0022623 GO:0030163 GO:0030433 GO:0031595 GO:0031597 GO:0036402 GO:0043335 GO:0045899 GO:0070682 GO:1901800
190.070.4714.370.080.615a5bJ GO:0000166 GO:0000502 GO:0005524 GO:0005634 GO:0005737 GO:0006289 GO:0006338 GO:0008540 GO:0016787 GO:0016887 GO:0017025 GO:0019904 GO:0030163 GO:0030433 GO:0031595 GO:0032968 GO:0034515 GO:0036402 GO:0043161 GO:0043433 GO:0045899 GO:0051091 GO:0070651 GO:0070682 GO:1901800
200.070.4635.290.100.644xgcD GO:0000808 GO:0003677 GO:0003688 GO:0005634 GO:0005664 GO:0006260 GO:0006270
210.070.4454.310.140.571g3iA GO:0000166 GO:0005524 GO:0005737 GO:0006508 GO:0009376 GO:0016887 GO:0043335 GO:0070011


Consensus prediction of GO terms
 
Molecular Function GO:0005524 GO:0008233 GO:0003677 GO:0004386 GO:0043169
GO-Score 0.80 0.55 0.36 0.31 0.31
Biological Processes GO:0019538 GO:0006260 GO:0045184 GO:0071702
GO-Score 0.55 0.36 0.31 0.31
Cellular Component GO:0031597
GO-Score 0.55

(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.