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I-TASSER results for job id Rv3194c

[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
10.09 4 2ckjC FES Rep, Mult 240,242,265,266,267,277
20.09 4 3fofC NUC Rep, Mult 236,238
30.07 3 2ckjC FES Rep, Mult 262,263,264,288,291,293,312,314
40.05 2 1fiqA FES Rep, Mult 284,288,289,290,291,293,313
50.03 1 4ypmA MG Rep, Mult 163,238,265,283
60.02 1 2ckjD FES Rep, Mult 265,266,267,268,274,275,276,299,320
70.02 1 1rrgA GDP Rep, Mult 268,272
80.02 1 3f1fP MG Rep, Mult 283,286
90.02 1 3d5bY MG Rep, Mult 279,283
100.02 1 1z0bA CA Rep, Mult 314,315
110.02 1 1vdvA CA Rep, Mult 249,253,254
120.02 1 2ckjD FES Rep, Mult 235,237,277,278,279

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
10.0603fvyA0.4155.800.0360.6323.4.14.4178,236
20.0601qf6A0.3606.660.0360.6216.1.1.3NA
30.0601k32A0.2767.080.0470.4853.4.21.-NA
40.0601yguB0.3656.630.0890.6183.1.3.48NA
50.0601fo4A0.4496.690.0350.7761.17.1.4NA
60.0602pdaA0.3537.060.0420.6441.2.7.1213,243
70.0601vlbA0.3676.980.0490.6531.2.99.7NA
80.0601z1wA0.3157.050.0390.5473.4.11.-NA
90.0602dqmA0.3786.900.0430.6683.4.11.2NA
100.0602vumA0.3606.090.0450.5712.7.7.6205
110.0601pj6A0.3606.760.0360.6241.5.3.10NA
120.0601llwA0.4296.550.0530.7121.4.7.1NA
130.0602vdcA0.4236.800.0580.7321.4.1.13NA
140.0601kogH0.2606.840.0310.4626.1.1.3245
150.0602e1qA0.4586.680.0560.7791.17.3.2,1.17.1.4NA
160.0602je8B0.4056.850.0470.6943.2.1.25NA
170.0602ckjA0.4506.750.0560.7731.17.1.4,1.17.3.2NA
180.0603b9jJ0.2197.150.0210.3941.17.1.4,1.17.3.2239
190.0602zxqA0.3637.420.0320.6713.2.1.97325

(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
00.220.5574.950.140.754fwhA GO:0004176 GO:0004252 GO:0005524 GO:0006508 GO:0030163
10.210.5545.070.120.744fw9A GO:0004176 GO:0004252 GO:0005524 GO:0006508 GO:0030163
20.210.4782.230.170.521xhkB GO:0000166 GO:0004176 GO:0004252 GO:0005524 GO:0005886 GO:0006508 GO:0008233 GO:0008236 GO:0016020 GO:0016021 GO:0016787 GO:0030163
30.190.8622.710.150.974yplC GO:0000166 GO:0004176 GO:0004252 GO:0005524 GO:0005737 GO:0006508 GO:0006515 GO:0008233 GO:0008236 GO:0016787 GO:0016887 GO:0030163 GO:0033554 GO:0043565
40.140.4922.200.190.542x36C GO:0000002 GO:0000166 GO:0001666 GO:0003677 GO:0003697 GO:0003727 GO:0004176 GO:0004252 GO:0005524 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005759 GO:0006508 GO:0006515 GO:0007005 GO:0007568 GO:0008233 GO:0008236 GO:0009725 GO:0010044 GO:0016020 GO:0016787 GO:0016887 GO:0030163 GO:0032042 GO:0034599 GO:0042645 GO:0043531 GO:0043565 GO:0043623 GO:0051131 GO:0051260 GO:0051603 GO:0051880 GO:0070182 GO:0070361 GO:0070362 GO:0070363 GO:0070364 GO:0070407 GO:0090296
50.130.7463.610.140.893m6aA GO:0000166 GO:0004176 GO:0004252 GO:0005524 GO:0005737 GO:0006508 GO:0006515 GO:0008233 GO:0008236 GO:0016787 GO:0016887 GO:0030163 GO:0033554 GO:0043565
60.120.4782.100.190.523wu6E GO:0000166 GO:0003677 GO:0004176 GO:0004252 GO:0005524 GO:0005737 GO:0006508 GO:0006515 GO:0008233 GO:0008236 GO:0016787 GO:0016887 GO:0030163 GO:0033554 GO:0043565
70.120.4832.380.170.531z0bA GO:0000166 GO:0004176 GO:0004252 GO:0005524 GO:0005886 GO:0006355 GO:0006508 GO:0008134 GO:0008233 GO:0008236 GO:0016020 GO:0016021 GO:0016787 GO:0030163
80.070.5844.920.130.763k1jA GO:0000166 GO:0004176 GO:0004252 GO:0005524 GO:0006355 GO:0006508 GO:0008134 GO:0008233 GO:0016020 GO:0016021 GO:0030163
90.060.3965.330.040.572ce7D GO:0000166 GO:0004176 GO:0004222 GO:0005524 GO:0005886 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0030163 GO:0046872
100.060.3985.800.060.605c18E GO:0000166 GO:0000502 GO:0005102 GO:0005524 GO:0005634 GO:0005654 GO:0005737 GO:0005783 GO:0005789 GO:0005811 GO:0005829 GO:0006281 GO:0006302 GO:0006511 GO:0006734 GO:0006810 GO:0006888 GO:0006919 GO:0006974 GO:0008289 GO:0010918 GO:0016567 GO:0016787 GO:0016887 GO:0018279 GO:0019079 GO:0019903 GO:0019904 GO:0019985 GO:0030433 GO:0030968 GO:0030970 GO:0031334 GO:0031593 GO:0031625 GO:0032403 GO:0032436 GO:0034098 GO:0034214 GO:0035800 GO:0035861 GO:0036435 GO:0036503 GO:0036513 GO:0042288 GO:0042802 GO:0042981 GO:0043161 GO:0043209 GO:0043231 GO:0043234 GO:0043531 GO:0044389 GO:0044822 GO:0045184 GO:0045732 GO:0046034 GO:0048471 GO:0051260 GO:0070062 GO:0070842 GO:0070987 GO:0071712 GO:0072389 GO:1903006 GO:1903007 GO:1903715 GO:1903862 GO:1904288 GO:1990381 GO:1990730 GO:2001171
110.060.3365.170.040.473kdsE GO:0000166 GO:0004176 GO:0004222 GO:0005524 GO:0005886 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0030163 GO:0046872
120.060.3256.540.050.544ww0B GO:0000166 GO:0004176 GO:0004222 GO:0005524 GO:0005886 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0030163 GO:0046872
130.060.3766.630.060.641ksfX GO:0000166 GO:0004176 GO:0005524 GO:0005829 GO:0006508 GO:0006979 GO:0016887 GO:0019538 GO:0043335
140.060.3046.040.040.481sxjC GO:0000166 GO:0003677 GO:0003689 GO:0005524 GO:0005634 GO:0005663 GO:0005829 GO:0006260 GO:0006272 GO:0006298 GO:0007049 GO:0007062 GO:0016887 GO:0031389 GO:0031390 GO:0031391
150.060.3886.680.080.664d2qA GO:0000166 GO:0005524 GO:0005737 GO:0005829 GO:0006986 GO:0009408 GO:0016020 GO:0016485 GO:0019538 GO:0042623 GO:0042802
160.060.4065.720.060.615c1aK GO:0000166 GO:0000502 GO:0005102 GO:0005524 GO:0005634 GO:0005654 GO:0005737 GO:0005783 GO:0005789 GO:0005811 GO:0005829 GO:0006281 GO:0006302 GO:0006511 GO:0006734 GO:0006810 GO:0006888 GO:0006919 GO:0006974 GO:0008289 GO:0010918 GO:0016567 GO:0016787 GO:0016887 GO:0018279 GO:0019079 GO:0019903 GO:0019904 GO:0019985 GO:0030433 GO:0030968 GO:0030970 GO:0031334 GO:0031593 GO:0031625 GO:0032403 GO:0032436 GO:0034098 GO:0034214 GO:0035800 GO:0035861 GO:0036435 GO:0036503 GO:0036513 GO:0042288 GO:0042802 GO:0042981 GO:0043161 GO:0043209 GO:0043231 GO:0043234 GO:0043531 GO:0044389 GO:0044822 GO:0045184 GO:0045732 GO:0046034 GO:0048471 GO:0051260 GO:0070062 GO:0070842 GO:0070987 GO:0071712 GO:0072389 GO:1903006 GO:1903007 GO:1903715 GO:1903862 GO:1904288 GO:1990381 GO:1990730 GO:2001171
170.060.2626.730.040.444r7yA GO:0000166 GO:0003677 GO:0004386 GO:0004519 GO:0005524 GO:0006260 GO:0016539 GO:0016787 GO:0046872 GO:0051301 GO:0090305
180.060.3046.020.050.482chqA GO:0000166 GO:0003677 GO:0003689 GO:0005524 GO:0005663 GO:0006260


Consensus prediction of GO terms
 
Molecular Function GO:0004176 GO:0004252 GO:0005524 GO:0003677
GO-Score 0.66 0.66 0.66 0.60
Biological Processes GO:0051603 GO:0051716 GO:0006950
GO-Score 0.60 0.37 0.37
Cellular Component GO:0044424 GO:0071944 GO:0031224
GO-Score 0.60 0.41 0.33

(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.