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I-TASSER results for job id Rv2974c

[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
10.12 7 1i43A PLP Rep, Mult 118,119,120,147,195,228,230,274,276,277
20.05 3 3adrA ZN Rep, Mult 205,207,346,389
30.03 2 3w1jB THJ Rep, Mult 424
40.03 2 1rvyB PLG Rep, Mult 117,119,125
50.03 2 2vmqA MPD Rep, Mult 124,128,159,166
60.02 1 4katC DU Rep, Mult 14,17
70.02 1 3fz7A PO4 Rep, Mult 128,129,130,298,300,301
80.02 1 1htwA MG Rep, Mult 114,117
90.02 1 1ocyA ZN Rep, Mult 205,207
100.02 1 1c3xB CA Rep, Mult 189,190
110.02 1 3w1jB THJ Rep, Mult 88,300,305
120.02 1 3ee6A ZN Rep, Mult 207,463
130.02 1 2viaA MPD Rep, Mult 181,186,217,221,222
140.02 1 4l6v6 CLA Rep, Mult 8,12
150.02 1 1rvyA PO4 Rep, Mult 168,170,185
160.02 1 2g7zA ZN Rep, Mult 396,397
170.02 1 3rl3A MN Rep, Mult 420,422
180.02 1 3w1jA THJ Rep, Mult 382,383
190.02 1 1bjyA CTC Rep, Mult 181,185

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
10.0601ordA0.4945.880.0670.6984.1.1.17NA
20.0602dgmC0.4795.910.0610.6834.1.1.15306
30.0603gbxA0.4595.160.0890.6062.1.2.1NA
40.0601j04A0.4605.690.0840.6342.6.1.44NA
50.0601wyuB0.4826.000.1020.6851.4.4.2NA
60.0601ejiA0.4875.740.0700.6702.1.2.1NA
70.0601d7rA0.4506.080.0770.6514.1.1.64NA
80.0602hufA0.4595.740.0960.6362.6.1.44123
90.0603dxvB0.4626.000.1030.6555.1.1.15NA
100.0602jg2A0.4515.350.0770.6022.3.1.50NA
110.0601oatA0.4516.320.0810.6682.6.1.13NA
120.0601dfoB0.4875.260.0900.6492.1.2.1NA
130.0602hdyA0.4506.270.0810.6684.4.1.16NA
140.0601sf2A0.4456.080.0730.6402.6.1.19,2.6.1.22NA
150.0601vjoA0.4515.870.0760.6322.6.1.44NA
160.0602dkjA0.4825.050.1120.6322.1.2.1NA
170.0603f9tA0.4765.220.0610.6284.1.1.25NA
180.0601szkC0.4456.230.0820.6492.6.1.19,2.6.1.22119,177
190.0602zsmA0.4515.790.0650.6255.4.3.8NA

(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
00.120.4745.060.110.621kkjA GO:0003824 GO:0004372 GO:0005737 GO:0006544 GO:0006545 GO:0006563 GO:0006730 GO:0008652 GO:0016740 GO:0019264 GO:0030170 GO:0035999
10.070.4945.880.070.701ordA GO:0003824 GO:0004586 GO:0005737 GO:0006520 GO:0016829 GO:0016831
20.070.5095.260.090.682aeuA GO:0003824 GO:0004125 GO:0097056
30.070.4865.560.090.664uqvG GO:0003824 GO:0004372 GO:0005737 GO:0006544 GO:0006545 GO:0006563 GO:0006730 GO:0008652 GO:0016740 GO:0016829 GO:0019264 GO:0030170
40.070.4816.020.060.693n75A GO:0003824 GO:0005737 GO:0006520 GO:0006554 GO:0008923 GO:0016829 GO:0016831 GO:0042802
50.070.4815.950.060.692vycA GO:0003824 GO:0005737 GO:0005829 GO:0006520 GO:0006527 GO:0008792 GO:0016829 GO:0016831 GO:0030170 GO:0051454
60.070.4885.370.060.664oytA GO:0003824 GO:0008168 GO:0016740 GO:0032259
70.070.4855.310.080.654n0wA GO:0003824 GO:0004372 GO:0005737 GO:0006544 GO:0006545 GO:0006563 GO:0006730 GO:0008168 GO:0008652 GO:0016740 GO:0019264 GO:0030170 GO:0032259 GO:0035999
80.070.4815.340.070.644o6zA GO:0003824 GO:0004372 GO:0005737 GO:0005739 GO:0006730 GO:0008168 GO:0016740 GO:0020011 GO:0032259 GO:0070178
90.070.4825.050.110.632dkjA GO:0003824 GO:0004372 GO:0005737 GO:0006544 GO:0006545 GO:0006563 GO:0006730 GO:0008652 GO:0016740 GO:0019264 GO:0030170 GO:0035999
100.070.4755.360.080.634msoA GO:0003824 GO:0004372 GO:0005737 GO:0006544 GO:0006545 GO:0006563 GO:0006730 GO:0008168 GO:0008652 GO:0016740 GO:0019264 GO:0030170 GO:0032259 GO:0035999
110.070.4705.230.080.623pgyB GO:0003824 GO:0004372 GO:0005737 GO:0006544 GO:0006545 GO:0006563 GO:0006730 GO:0008652 GO:0016740 GO:0019264 GO:0030170 GO:0035999
120.070.4615.260.080.613n0lB GO:0003824 GO:0004372 GO:0005737 GO:0006544 GO:0006545 GO:0006563 GO:0006730 GO:0008652 GO:0016740 GO:0019264 GO:0030170 GO:0035999
130.070.4575.350.100.614p3mB GO:0003824 GO:0004372 GO:0005737 GO:0006544 GO:0006545 GO:0006563 GO:0006730 GO:0008652 GO:0016740 GO:0019264 GO:0030170 GO:0035999
140.070.4645.810.060.652x3lB GO:0003824
150.070.4595.590.090.643wksB GO:0003824 GO:0006412 GO:0016740 GO:0043766 GO:0071952
160.070.4425.560.100.604bhdB GO:0003824 GO:0004372 GO:0005737 GO:0006544 GO:0006545 GO:0006563 GO:0006730 GO:0008652 GO:0016740 GO:0016829 GO:0019264 GO:0030170
170.070.4375.150.070.573jzlA GO:0003824 GO:0030170
180.060.4254.970.100.541pg8A GO:0003824 GO:0016829 GO:0018826 GO:0030170 GO:0047982


Consensus prediction of GO terms
 
Molecular Function GO:0048037 GO:0016742 GO:0043168
GO-Score 0.36 0.36 0.36
Biological Processes GO:0008652 GO:0009070 GO:0006544
GO-Score 0.36 0.36 0.36
Cellular Component GO:0044424
GO-Score 0.57

(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.