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I-TASSER results for job id Rv1089

[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
10.05 2 1swuA MPD Rep, Mult 11,83,104,113
20.05 2 3lmtA IOD Rep, Mult 21,25
30.05 2 1qpaA CA Rep, Mult 75,93,101,104,108
40.05 2 1o71B GOL Rep, Mult 37,73,76,77,104,105,108
50.05 2 2vveB CA Rep, Mult 104,108,110
60.05 2 4ogqA 8K6 Rep, Mult 20,24,57,87
70.05 2 5klgA 6UC Rep, Mult 24,27
80.02 1 3t41B CA Rep, Mult 65,67,79
90.02 1 4ea2A MG Rep, Mult 25,96
100.02 1 3keuB MG Rep, Mult 31,108
110.02 1 1kv8A PO4 Rep, Mult 81,106,107
120.02 1 1yvmA NA Rep, Mult 64,65,66,88
130.02 1 3s6lC IOD Rep, Mult 76,88,90
140.02 1 4matA NA Rep, Mult 24,30,31,65
150.02 1 3wmoO CRT Rep, Mult 14,24

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
10.0601imaA0.4094.660.0780.7503.1.3.25NA
20.0601ftaA0.4884.190.0710.7833.1.3.11NA
30.0601wn1A0.5643.900.0550.8833.4.-.-110
40.0602wefA0.5134.700.1160.8833.1.3.7NA
50.0601bk4A0.4874.170.0710.7923.1.3.11NA
60.0601wy2A0.5703.810.0750.8833.4.13.9NA
70.0601awbA0.4234.340.0960.7253.1.3.2562
80.0601fsaA0.5154.000.0930.8253.1.3.11NA
90.0603d1rA0.5064.190.0460.8173.1.3.11NA
100.0601qxwA0.5373.780.0950.8503.4.11.1833
110.0602b3lA0.5693.760.0650.8753.4.11.18NA
120.0602iw2A0.5813.700.0470.8753.4.13.9NA
130.0601pv9B0.5283.880.0490.8253.4.13.9NA
140.0603fmrB0.5543.810.0670.8503.4.11.18NA
150.0602gq1A0.4704.460.0490.8003.1.3.11NA
160.0602ea4A0.5473.950.0840.8673.4.11.18100
170.0601qxyA0.5373.770.0950.8503.4.11.18NA
180.0601lbvA0.5074.460.1040.8253.1.3.25,62
190.0602zsgA0.5484.040.1110.8923.4.11.9NA

(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
00.130.5683.780.070.883mx6B GO:0004177 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0046872 GO:0070006 GO:0070084
10.130.5533.930.040.884matA GO:0004177 GO:0005829 GO:0006508 GO:0008198 GO:0008233 GO:0008235 GO:0016787 GO:0046872 GO:0070006 GO:0070084
20.120.5443.600.060.823iu7A GO:0004177 GO:0005506 GO:0006508 GO:0006555 GO:0008233 GO:0008235 GO:0016151 GO:0016787 GO:0030145 GO:0035551 GO:0046872 GO:0050897 GO:0070006 GO:0070084
30.110.5813.700.050.882iw2A GO:0004177 GO:0004181 GO:0006508 GO:0006520 GO:0008233 GO:0008237 GO:0016787 GO:0016805 GO:0030145 GO:0030574 GO:0046872 GO:0070062 GO:0102009
40.080.5373.780.100.851qxwA GO:0004177 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0046872 GO:0070006 GO:0070084
50.080.5563.850.080.871pv9A GO:0005737 GO:0006508 GO:0008233 GO:0008237 GO:0016787 GO:0016805 GO:0046872 GO:0102009
60.070.5484.040.110.892zsgA GO:0004177 GO:0006508 GO:0016787 GO:0046872
70.070.4983.660.070.763j2iA GO:0003677 GO:0003700 GO:0003723 GO:0005634 GO:0005654 GO:0005730 GO:0005737 GO:0006351 GO:0006355 GO:0006364 GO:0006417 GO:0007050 GO:0008283 GO:0016020 GO:0030529 GO:0031625 GO:0043066 GO:0044822 GO:0045597 GO:0045892 GO:0070062
80.070.5413.470.110.824qr8A GO:0005829 GO:0006508 GO:0008233 GO:0008235 GO:0008237 GO:0016787 GO:0016795 GO:0016805 GO:0030145 GO:0043171 GO:0046872 GO:0070573 GO:0102009
90.070.5673.760.060.873s6bA GO:0004177 GO:0005737 GO:0006464 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0022626 GO:0046872 GO:0070006 GO:0070084
100.070.5674.000.040.904km3A GO:0004177 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0046872 GO:0070006 GO:0070084
110.070.5653.820.070.873ig4A GO:0004177 GO:0006508 GO:0016787 GO:0030145 GO:0046872
120.070.5703.810.070.881wy2A GO:0005737 GO:0006508 GO:0008233 GO:0008237 GO:0016787 GO:0016805 GO:0046872 GO:0102009
130.070.5743.770.070.882bh3A GO:0004177 GO:0005737 GO:0005829 GO:0006508 GO:0008233 GO:0008235 GO:0008237 GO:0016787 GO:0030145 GO:0042802 GO:0046872
140.060.3995.490.030.823v1hA GO:0004436 GO:0005576 GO:0006629 GO:0008081 GO:0009405 GO:0016042 GO:0016829
150.060.3535.320.090.734dllA GO:0004616 GO:0008679 GO:0016491 GO:0051287 GO:0055114
160.060.3745.110.050.721nd1A GO:0004222 GO:0005576 GO:0006508 GO:0006935 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0046872
170.060.5333.680.090.823l24B GO:0004063 GO:0006508 GO:0008233 GO:0008235 GO:0008237 GO:0009636 GO:0016311 GO:0016787 GO:0016795 GO:0016805 GO:0046872 GO:0047862 GO:0102009
180.060.5653.850.030.884s2rP GO:0004177 GO:0006508 GO:0016787 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0046914 GO:0070006
GO-Score 0.43 0.38
Biological Processes GO:0006508 GO:0070084
GO-Score 0.45 0.38
Cellular Component GO:0005829 GO:0070062
GO-Score 0.12 0.11

(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.