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I-TASSER results for job id Rv2136c

[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
10.04 2 4jreD GYP Rep, Mult 87,234,237,238,256,257,260,261
20.04 2 4jr9A GYP Rep, Mult 87,230,233,234,259,260,263
30.04 2 1o5qA MG Rep, Mult 38,113
40.02 1 3ehbB HEA Rep, Mult 90,199
50.02 1 1s4eB MG Rep, Mult 22,24
60.02 1 4zp2A LDA Rep, Mult 94,97,231
70.02 1 1e3mB QNA Rep, Mult 160,162,166
80.02 1 3wu2h CLA Rep, Mult 118,122
90.02 1 3rkoN LFA Rep, Mult 189,192,193,196
100.02 1 3rkoN LFA Rep, Mult 97,98,101,122,123
110.02 1 1q19B MG Rep, Mult 22,229
120.02 1 2r9rB PGW Rep, Mult 42,43
130.02 1 1vykA ZN Rep, Mult 171,175,255
140.02 1 3bjeA R1P Rep, Mult 26,80
150.02 1 1mz9A VDY Rep, Mult 224,227,238
160.02 1 3tijA DMU Rep, Mult 231,238
170.02 1 2iidA UUU Rep, Mult 80,81,84
180.02 1 4fe1B CLA Rep, Mult 240,244,248
190.02 1 2abmA POQ Rep, Mult 92,244
200.02 1 1wdc2 III Rep, Mult 39,41,42,43,44,45,46,47,48,49,50,51,52,53,54,56,57,59,60,62,63

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
10.0601kc7A0.4085.990.0640.6812.7.9.1NA
20.0602p0mB0.3934.400.0700.5361.13.11.33NA
30.0601qxoC0.4166.230.0460.7214.2.3.5NA
40.0601u8vA0.4016.020.0530.6745.3.3.3NA
50.0602cseW0.3995.910.0680.6633.6.4.13NA
60.0603b9jJ0.3215.610.0860.4961.17.1.4,1.17.3.2156
70.0601ue8A0.4045.420.0500.6161.14.-.-82
80.0601g8kA0.4006.540.0510.7211.20.98.1NA
90.0601kqfA0.4106.320.0530.7171.2.1.2NA
100.0601fo4A0.4356.400.0500.7541.17.1.4NA
110.0601qmgA0.4166.040.0450.6961.1.1.86NA
120.0601yrlA0.4095.940.0790.6701.1.1.86NA
130.0603fr8B0.4096.150.0630.6961.1.1.86NA
140.0602iukB0.4035.740.0150.6161.13.11.12NA
150.0602yyjA0.4026.160.0410.6771.14.13.3NA
160.0601ti2A0.3916.820.0490.7251.97.1.2NA
170.0601fl2A0.2866.900.0620.5331.8.1.-NA
180.0602wm4A0.3975.200.0540.5871.14.-.-82
190.0602e1qA0.4286.280.0350.7541.17.3.2,1.17.1.4NA

(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
00.120.6983.960.080.864zp0A GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015385 GO:0015386 GO:0016020 GO:0016021 GO:0030641 GO:0035725 GO:0046677 GO:0055085 GO:0071805
10.070.6224.590.050.834ldsA GO:0005215 GO:0006810 GO:0016020 GO:0016021 GO:0022857 GO:0022891 GO:0055085
20.070.6094.360.070.814j05A GO:0005215 GO:0016020 GO:0016021 GO:0022857 GO:0055085
30.070.5794.760.050.804q65A GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006857 GO:0015031 GO:0015197 GO:0015333 GO:0015833 GO:0015992 GO:0016020 GO:0016021 GO:0042936 GO:0042938
40.070.5564.630.070.772gfpA GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0015893 GO:0016020 GO:0016021 GO:0055085
50.070.5774.020.070.734ja4A GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0008643 GO:0015293 GO:0015519 GO:0015753 GO:0016020 GO:0016021 GO:0022857 GO:0022891 GO:0055085
60.070.6064.200.050.795eqgA GO:0000139 GO:0001939 GO:0005215 GO:0005355 GO:0005622 GO:0005737 GO:0005829 GO:0005886 GO:0005887 GO:0005901 GO:0005911 GO:0005989 GO:0006461 GO:0006810 GO:0006970 GO:0008643 GO:0015758 GO:0016020 GO:0016021 GO:0016323 GO:0016324 GO:0019852 GO:0019900 GO:0022857 GO:0022891 GO:0030496 GO:0030864 GO:0031982 GO:0033300 GO:0042149 GO:0042470 GO:0042802 GO:0042908 GO:0042910 GO:0043621 GO:0045121 GO:0050796 GO:0055056 GO:0055085 GO:0070062 GO:0070837 GO:0072562 GO:1904659
70.070.6094.470.070.814gbyA GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0008643 GO:0015293 GO:0015519 GO:0015753 GO:0016020 GO:0016021 GO:0022857 GO:0022891 GO:0055085
80.070.5053.720.080.654yb9D GO:0003044 GO:0005215 GO:0005353 GO:0005886 GO:0005887 GO:0006810 GO:0008643 GO:0009750 GO:0015755 GO:0016020 GO:0016021 GO:0016324 GO:0022857 GO:0022891 GO:0042383 GO:0055085 GO:0070061 GO:0071332 GO:1990539
90.070.5984.330.070.794zw9A GO:0005215 GO:0005355 GO:0005536 GO:0005886 GO:0005887 GO:0005975 GO:0006810 GO:0008643 GO:0015758 GO:0016020 GO:0016021 GO:0019852 GO:0022857 GO:0022891 GO:0033300 GO:0055056 GO:0055085 GO:0070062 GO:0070837 GO:1904659
100.070.5984.150.050.794ybqB GO:0003044 GO:0005215 GO:0005353 GO:0005355 GO:0005886 GO:0005887 GO:0006810 GO:0008643 GO:0015755 GO:0015758 GO:0016020 GO:0016021 GO:0016324 GO:0022857 GO:0022891 GO:0042383 GO:0055085 GO:0070061 GO:0071332 GO:1904659 GO:1990539
110.060.3066.810.050.573fhdA GO:0003677 GO:0004518 GO:0004527 GO:0046872 GO:0090305
120.060.2876.260.060.501z6aA GO:0004386 GO:0005524
130.060.3035.100.060.431q90B GO:0005506 GO:0009055 GO:0009507 GO:0009535 GO:0009536 GO:0009579 GO:0015979 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0022900 GO:0022904 GO:0045158 GO:0046872 GO:0055114
140.060.2586.800.050.482rirE GO:0016491 GO:0030435 GO:0055114
150.060.2075.620.070.333fb3B GO:0004343 GO:0006044 GO:0006048 GO:0008080 GO:0016740 GO:0020015
160.060.2396.550.070.434prsB GO:0004970 GO:0016020 GO:0035235
170.060.2916.620.030.521mwuB GO:0008658 GO:0046677
180.060.1924.810.060.282jxnA GO:0003677 GO:0010421


Consensus prediction of GO terms
 
Molecular Function GO:0022857 GO:0090484
GO-Score 0.36 0.36
Biological Processes GO:0044763 GO:0015893
GO-Score 0.57 0.36
Cellular Component GO:0031226 GO:0016021
GO-Score 0.36 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.