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I-TASSER results for job id Rv0180c

[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
10.08 5 2fynD HEM Rep, Mult 271,272,275,276,279,336,337,340,341,343,344,369,370,373
20.05 3 4oaaA TDG Rep, Mult 24,27,168,171,196,199,200,203,309,312,366,374,393
30.03 2 2qjyG HEM Rep, Mult 19,20,23,24,26,27,30,101,102,105,107,109,110,166,167,170
40.03 2 3gxqB NUC Rep, Mult 57,62
50.03 2 4gbyA XYP Rep, Mult 196,272,273,377,396
60.03 2 4tphA ALA Rep, Mult 24,192,196,199,276,315,373
70.02 1 3h6kB 33T Rep, Mult 43,44
80.02 1 1m57D PEH Rep, Mult 276,280
90.02 1 1siwA SF4 Rep, Mult 206,211,212,213,215,219
100.02 1 1n35A CH1 Rep, Mult 97,98,99,170
110.02 1 5aymA FE2 Rep, Mult 19,23,233,236,237
120.02 1 3prqX CLA Rep, Mult 281,288
130.02 1 2rb1X 261 Rep, Mult 376,380
140.02 1 2q68A CA Rep, Mult 383,384
150.02 1 3ogkD PO4 Rep, Mult 24,27,56,376
160.02 1 2yiuD HEM Rep, Mult 22,23,26,27,30,104,108,109,111,113,163,164,167
170.02 1 1i8nA ROP Rep, Mult 95,98
180.02 1 4zwbA MAL Rep, Mult 199,200,203,275,276,280,312,369,370,377
190.02 1 1n38A CH1 Rep, Mult 339,340,370,371,372,373
200.02 1 4gbzA BGC Rep, Mult 196,203,272,273,280,369,373,377,396

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
10.0603cuzA0.3417.370.0450.5662.3.3.9NA
20.0602c4mC0.3427.270.0550.5642.4.1.1NA
30.0601ti6A0.3347.280.0410.5571.97.1.2NA
40.0601h0hA0.3637.380.0320.6131.2.1.2NA
50.0603cf4A0.3487.160.0630.5801.2.99.256
60.0603iydC0.3447.270.0280.5712.7.7.6NA
70.0601ti2A0.3386.900.0450.5381.97.1.2NA
80.0603dt7A0.3417.220.0460.5604.1.1.32NA
90.0603hkzJ0.3437.370.0510.5822.7.7.6362
100.0601uwkA0.3637.030.0480.5824.2.1.49NA
110.0603l4uA0.3427.410.0540.5693.2.1.20,3.2.1.329,114
120.0601ahpA0.3147.590.0300.5422.4.1.1NA
130.0601ogyA0.3417.250.0620.5601.7.99.4NA
140.0602a06C0.3596.290.0610.5421.10.2.230,32
150.0602vumB0.3477.630.0490.6082.7.7.6NA
160.0602fknB0.3606.760.0620.5624.2.1.49NA
170.0603gtgB0.3477.810.0680.6132.7.7.6NA
180.0602g3mF0.3457.290.0750.5663.2.1.20NA
190.0601n1hA0.3677.120.0360.6062.7.7.48396

(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
00.130.6933.710.070.823o7qA GO:0005886 GO:0005887 GO:0005975 GO:0006004 GO:0006810 GO:0008643 GO:0015150 GO:0015293 GO:0015517 GO:0015518 GO:0015535 GO:0015751 GO:0015756 GO:0015757 GO:0016020 GO:0016021 GO:0055085
10.110.7084.290.080.884gbyA 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
20.110.6834.690.090.874m64A GO:0005215 GO:0005886 GO:0006810 GO:0006814 GO:0008643 GO:0015293 GO:0016020 GO:0016021 GO:0055085
30.100.6734.330.080.844m64B GO:0005215 GO:0005886 GO:0006810 GO:0006814 GO:0008643 GO:0015293 GO:0016020 GO:0016021 GO:0055085
40.100.6844.030.080.844zw9A 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
50.090.6924.080.080.854ybqB 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
60.090.6444.840.050.834j05A GO:0005215 GO:0016020 GO:0016021 GO:0022857 GO:0055085
70.080.6284.400.080.794m64D GO:0005215 GO:0005886 GO:0006810 GO:0006814 GO:0008643 GO:0015293 GO:0016020 GO:0016021 GO:0055085
80.070.6294.930.090.835eqgA 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
90.070.6314.580.110.814yb9D 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
100.070.6065.650.070.862cfpA GO:0005351 GO:0005886 GO:0005887 GO:0006810 GO:0008643 GO:0015293 GO:0015528 GO:0015767 GO:0015992 GO:0016020 GO:0016021 GO:0030395 GO:0055085
110.070.6244.730.120.814zp0A 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
120.070.6244.810.100.814ldsA GO:0005215 GO:0006810 GO:0016020 GO:0016021 GO:0022857 GO:0022891 GO:0055085
130.070.6285.070.080.844ja4A 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
140.070.6055.500.090.845ayoA GO:0005381 GO:0016020 GO:0016021 GO:0034755
150.070.5785.180.060.782gfpA GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0015893 GO:0016020 GO:0016021 GO:0055085
160.060.2717.290.040.444jevB GO:0003824 GO:0003992 GO:0005737 GO:0005829 GO:0006520 GO:0006525 GO:0006526 GO:0008483 GO:0008652 GO:0009016 GO:0009085 GO:0009089 GO:0016740 GO:0030170 GO:0042802
170.060.2677.220.040.441dceA GO:0004659 GO:0004663 GO:0005968 GO:0008270 GO:0008318 GO:0016740 GO:0017137 GO:0018342 GO:0018344
180.060.2266.400.030.343kexA GO:0000165 GO:0000166 GO:0003197 GO:0004672 GO:0004713 GO:0004888 GO:0005088 GO:0005524 GO:0005576 GO:0005615 GO:0005622 GO:0005886 GO:0005887 GO:0006468 GO:0007162 GO:0007165 GO:0007169 GO:0007422 GO:0007507 GO:0009968 GO:0014037 GO:0014065 GO:0014066 GO:0014068 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016323 GO:0016324 GO:0016328 GO:0016740 GO:0018108 GO:0019838 GO:0021545 GO:0030296 GO:0038128 GO:0038132 GO:0042060 GO:0042127 GO:0042802 GO:0042803 GO:0043235 GO:0043524 GO:0043547 GO:0046854 GO:0046934 GO:0046982 GO:0048015 GO:0051048 GO:0051402 GO:0061098 GO:0070886 GO:0097192 GO:2000145


Consensus prediction of GO terms
 
Molecular Function GO:0022892 GO:0015293
GO-Score 0.40 0.38
Biological Processes GO:0055085 GO:0008643 GO:0030001 GO:0015672 GO:0044238 GO:0071704
GO-Score 0.44 0.44 0.40 0.40 0.38 0.35
Cellular Component GO:0005887
GO-Score 0.30

(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.