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I-TASSER results for job id Rv3706c

[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
10.16 8 3e5uC 3C4 Rep, Mult 35,38,39
20.13 6 1l6lB BOG Rep, Mult 40,43,44,46
30.04 2 2x2vH DPV Rep, Mult 32,40
40.04 2 4hytB CLR Rep, Mult 44,47,48
50.04 2 2dqsA PTY Rep, Mult 28,32,39,97
60.04 2 4ku8A GLY Rep, Mult 28,32
70.02 1 3mz8A ZN Rep, Mult 3,63
80.02 1 1ocyA ZN Rep, Mult 58,60
90.02 1 3qksA III Rep, Mult 20,28

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
10.0603djlA0.4984.100.0760.7921.3.99.-NA
20.0601mhsA0.5063.770.0390.7453.6.3.6NA
30.0601b8fA0.5414.110.0990.9244.3.1.3NA
40.0601ivhA0.4773.940.0380.8021.3.99.10NA
50.0602pg0A0.4803.780.0500.7741.3.99.3NA
60.0601k62B0.4763.990.0320.7554.3.2.1NA
70.0603cf4A0.5023.950.0600.7831.2.99.2NA
80.0603czoB0.4884.140.0500.8304.3.1.3NA
90.0603e04D0.4743.890.0480.7744.2.1.224
100.0603k9fA0.4973.350.0320.7265.99.1.-NA
110.0601bucA0.4894.130.0490.7921.3.99.233
120.0602z8yD0.5083.910.0590.7831.2.7.4,1.2.99.230
130.0603dpgA0.4794.360.0510.7553.1.21.4NA
140.0602p0mB0.4824.550.0190.7921.13.11.33NA
150.0602p4qA0.4804.350.0190.8021.1.1.44NA
160.0603fofA0.4673.740.0110.7365.99.1.-NA
170.0601dc1B0.4763.780.0470.7263.1.21.431
180.0601rx0A0.4873.800.0500.7741.3.99.-NA
190.0602wl2B0.4963.260.0740.7265.99.1.3NA

(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
00.160.4574.160.040.723b8eA GO:0000166 GO:0002028 GO:0005391 GO:0005524 GO:0005886 GO:0005890 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0006883 GO:0010107 GO:0010248 GO:0015991 GO:0016020 GO:0016021 GO:0016787 GO:0030007 GO:0030955 GO:0031402 GO:0036376 GO:0042383 GO:0043231 GO:0046872 GO:0051117 GO:0086009 GO:0090662 GO:1990573
10.070.5063.850.090.821gk2A GO:0003824 GO:0004397 GO:0005737 GO:0006547 GO:0006548 GO:0016829 GO:0016841 GO:0019556 GO:0019557
20.070.5063.770.040.751mhsA GO:0000166 GO:0005524 GO:0005886 GO:0005887 GO:0006754 GO:0006810 GO:0006811 GO:0008553 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0043231 GO:0046872 GO:0051453 GO:1902600
30.070.4854.020.050.753b8cA GO:0000166 GO:0000287 GO:0005524 GO:0005886 GO:0005887 GO:0006754 GO:0006810 GO:0006811 GO:0008553 GO:0015991 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0046872 GO:0051453
40.070.4684.480.020.753ixzA GO:0000166 GO:0000287 GO:0005391 GO:0005524 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0006883 GO:0008900 GO:0010107 GO:0010248 GO:0015991 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030007 GO:0036376 GO:0043231 GO:0046872
50.070.5123.420.030.743w5bA GO:0000166 GO:0005388 GO:0005509 GO:0005524 GO:0005783 GO:0005789 GO:0005793 GO:0006810 GO:0006811 GO:0006816 GO:0006942 GO:0016020 GO:0016021 GO:0016529 GO:0016787 GO:0031448 GO:0031673 GO:0031674 GO:0033017 GO:0045988 GO:0046872 GO:0048471 GO:0070588
60.070.5304.110.020.861y2mB GO:0003824 GO:0005737 GO:0006559 GO:0009698 GO:0009800 GO:0016829 GO:0016841 GO:0045548 GO:0052883
70.070.4524.340.050.792o6yA GO:0003824 GO:0006572 GO:0009698 GO:0009699 GO:0016829 GO:0016841 GO:0042802 GO:0051289 GO:0052883
80.070.4624.100.020.723a3yA GO:0000166 GO:0005391 GO:0005524 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0010248 GO:0016020 GO:0016021 GO:0016787 GO:0046872 GO:0090662
90.070.4904.280.090.852nyfA GO:0003824 GO:0005737 GO:0009072 GO:0009698 GO:0009699 GO:0009800 GO:0016829 GO:0016841 GO:0045548 GO:0051289
100.070.4174.270.040.693unvA GO:0003824
110.070.4384.310.040.694umvA GO:0000166 GO:0005886 GO:0006812 GO:0016020 GO:0016021 GO:0016787 GO:0019829 GO:0030001 GO:0046872 GO:0098655
120.060.4653.910.050.744c6gB GO:0003824 GO:0005737 GO:0006558 GO:0006559 GO:0009698 GO:0009800 GO:0009820 GO:0009821 GO:0016829 GO:0016841 GO:0016853 GO:0016869 GO:0042617 GO:0045548 GO:0051289
130.060.4683.880.090.703czoB GO:0003824 GO:0004397 GO:0005737 GO:0009072 GO:0009698 GO:0009699 GO:0009800 GO:0016829 GO:0016841 GO:0045548 GO:0051289
140.060.4533.530.020.671w27A GO:0003824 GO:0005737 GO:0006559 GO:0009698 GO:0009800 GO:0016829 GO:0016841 GO:0045548
150.060.4713.740.020.693nz4B GO:0003824 GO:0005737 GO:0006558 GO:0006559 GO:0009698 GO:0009800 GO:0009820 GO:0009821 GO:0016829 GO:0016841 GO:0016853 GO:0016869 GO:0042617 GO:0045548 GO:0051289
160.060.4294.320.060.673kdyA GO:0003824 GO:0009403 GO:0016829 GO:0016841 GO:0016853 GO:0017000 GO:0050368 GO:0052883
170.060.5234.170.040.874v2rB GO:0003824 GO:0005737 GO:0006558 GO:0006559 GO:0009698 GO:0009800 GO:0009820 GO:0009821 GO:0016829 GO:0016841 GO:0016853 GO:0016869 GO:0042617 GO:0045548 GO:0051289
180.060.3554.410.050.582caiB GO:0004364 GO:0016740


Consensus prediction of GO terms
 
Molecular Function GO:0008556 GO:0015081 GO:0031420 GO:0019899 GO:0005524
GO-Score 0.43 0.43 0.32 0.32 0.32
Biological Processes GO:0015988 GO:0090662 GO:0030004 GO:0071436 GO:0055075 GO:0055078 GO:0071805 GO:0006875 GO:0098739 GO:0010959 GO:0042391
GO-Score 0.53 0.53 0.43 0.43 0.43 0.43 0.43 0.43 0.32 0.32 0.32
Cellular Component GO:0043229 GO:0043227 GO:0031226 GO:0098797 GO:0090533
GO-Score 0.53 0.53 0.37 0.32 0.32

(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.