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I-TASSER results for job id Rv0628c

[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
10.06 2 2zt9G III Rep, Mult 138,146
20.03 1 4a5aA MG Rep, Mult 140,215
30.03 1 1s5lk CLA Rep, Mult 147,151
40.03 1 2ahiC NUC Rep, Mult 370,375
50.03 1 2al4C CX6 Rep, Mult 247,248,377,378,380
60.03 1 2qbyA MG Rep, Mult 45,129,219
70.03 1 2ohjA FE Rep, Mult 371,372
80.03 1 3lsfE PZI Rep, Mult 126,139,143,144,147
90.03 1 1qiyF III Rep, Mult 381,382
100.03 1 3tdjA 3TJ Rep, Mult 219,220,221,222,223
110.03 1 3h6tA CYZ Rep, Mult 126,136,139,143
120.03 1 3il1B B5D Rep, Mult 199,203,206
130.03 1 5c5cA UNX Rep, Mult 62,83,340,341,344
140.03 1 3lcmA FAD Rep, Mult 322,332
150.03 1 2xctS CPF Rep, Mult 329,330

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
10.0603bblA0.5264.010.1070.6615.1.1.1211,213
20.0603c3kB0.5303.930.0790.6615.1.1.1249
30.0601bgvA0.4395.300.0460.6191.4.1.2NA
40.0601aupA0.4275.060.0500.5851.4.1.2NA
50.0602fssA0.4085.330.0660.5771.2.1.2NA
60.0601hrdA0.4355.550.0740.6241.4.1.2NA
70.0602aw5B0.4575.750.0670.6761.1.1.40NA
80.0601b3bE0.4375.360.0780.6141.4.1.352
90.0601t34A0.6964.260.1150.8824.6.1.271,79
100.0602bmaA0.4415.190.0470.6111.4.1.4NA
110.0601gz3A0.4406.120.0420.6711.1.1.38NA
120.0601luaB0.4125.480.0700.5951.5.1.5142
130.0601b26A0.4355.530.0690.6191.4.1.3NA
140.0603c46B0.4266.890.0700.7082.7.7.6NA
150.0602rgyA0.5084.250.0920.6555.1.1.1NA
160.0601hwxA0.4385.740.0660.6341.4.1.3NA
170.0601lehA0.4125.520.0830.5881.4.1.9NA
180.0602o7qA0.4075.200.0950.5724.2.1.10,1.1.1.25NA
190.0601vjpA0.4075.660.0780.5725.5.1.4101,218,296

(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
00.280.8002.720.120.904uq6B GO:0001919 GO:0004872 GO:0004970 GO:0004971 GO:0005216 GO:0005234 GO:0005246 GO:0005783 GO:0005789 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0007268 GO:0008328 GO:0009986 GO:0010226 GO:0014069 GO:0015277 GO:0016020 GO:0016021 GO:0019901 GO:0030054 GO:0030165 GO:0030425 GO:0030426 GO:0030672 GO:0031623 GO:0032279 GO:0032281 GO:0032839 GO:0034220 GO:0035235 GO:0042734 GO:0042802 GO:0043025 GO:0043195 GO:0043197 GO:0043198 GO:0043204 GO:0043234 GO:0045184 GO:0045202 GO:0045211 GO:0050806 GO:0051262 GO:0051966 GO:0060992
10.250.8242.470.100.904gpaA GO:0004872 GO:0004970 GO:0004971 GO:0005216 GO:0005234 GO:0005886 GO:0006810 GO:0006811 GO:0007268 GO:0008328 GO:0014069 GO:0016020 GO:0016021 GO:0030054 GO:0030425 GO:0032281 GO:0032983 GO:0034220 GO:0035235 GO:0042995 GO:0043025 GO:0043195 GO:0045202 GO:0045211 GO:0050803 GO:0050804 GO:0051968 GO:0060992
20.230.8032.730.110.905idfB GO:0001919 GO:0004872 GO:0004970 GO:0004971 GO:0005216 GO:0005234 GO:0005886 GO:0006810 GO:0006811 GO:0008328 GO:0010226 GO:0014069 GO:0016020 GO:0016021 GO:0030054 GO:0030165 GO:0030425 GO:0032279 GO:0032281 GO:0034220 GO:0035235 GO:0043025 GO:0043083 GO:0043195 GO:0043197 GO:0043198 GO:0043204 GO:0043234 GO:0045202 GO:0045211 GO:0060992
30.220.7483.470.100.893qluB GO:0004872 GO:0004970 GO:0005216 GO:0005234 GO:0005783 GO:0005886 GO:0006621 GO:0006810 GO:0006811 GO:0007268 GO:0008066 GO:0008328 GO:0014069 GO:0015277 GO:0016020 GO:0016021 GO:0017124 GO:0030054 GO:0030165 GO:0030424 GO:0030425 GO:0031630 GO:0032983 GO:0034220 GO:0035235 GO:0035249 GO:0042391 GO:0042734 GO:0042802 GO:0043005 GO:0043025 GO:0043113 GO:0043195 GO:0043204 GO:0043525 GO:0045202 GO:0045211 GO:0051649 GO:0060079 GO:0071333
40.170.8002.720.120.903kg2A GO:0001919 GO:0004872 GO:0004970 GO:0004971 GO:0005216 GO:0005234 GO:0005246 GO:0005783 GO:0005789 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0007268 GO:0008328 GO:0009986 GO:0010226 GO:0014069 GO:0015277 GO:0016020 GO:0016021 GO:0019901 GO:0030054 GO:0030165 GO:0030425 GO:0030426 GO:0030672 GO:0031623 GO:0032279 GO:0032281 GO:0032839 GO:0034220 GO:0035235 GO:0042734 GO:0042802 GO:0043025 GO:0043195 GO:0043197 GO:0043198 GO:0043204 GO:0043234 GO:0045184 GO:0045202 GO:0045211 GO:0050806 GO:0051262 GO:0051966 GO:0060992
50.160.8002.700.120.894u1xC GO:0001919 GO:0004872 GO:0004970 GO:0004971 GO:0005216 GO:0005234 GO:0005246 GO:0005783 GO:0005789 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0007268 GO:0008328 GO:0009986 GO:0010226 GO:0014069 GO:0015277 GO:0016020 GO:0016021 GO:0019901 GO:0030054 GO:0030165 GO:0030425 GO:0030426 GO:0030672 GO:0031623 GO:0032279 GO:0032281 GO:0032839 GO:0034220 GO:0035235 GO:0042734 GO:0042802 GO:0043025 GO:0043195 GO:0043197 GO:0043198 GO:0043204 GO:0043234 GO:0045184 GO:0045202 GO:0045211 GO:0050806 GO:0051262 GO:0051966 GO:0060992
60.150.8072.760.110.915fwyB GO:0001919 GO:0004872 GO:0004970 GO:0004971 GO:0005216 GO:0005234 GO:0005886 GO:0006810 GO:0006811 GO:0008328 GO:0010226 GO:0014069 GO:0016020 GO:0016021 GO:0030054 GO:0030165 GO:0030425 GO:0032279 GO:0032281 GO:0034220 GO:0035235 GO:0043025 GO:0043083 GO:0043195 GO:0043197 GO:0043198 GO:0043204 GO:0043234 GO:0045202 GO:0045211 GO:0060992
70.150.7653.370.100.895ideC GO:0001919 GO:0004872 GO:0004970 GO:0004971 GO:0005216 GO:0005234 GO:0005246 GO:0005783 GO:0005789 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0007268 GO:0008328 GO:0009986 GO:0010226 GO:0014069 GO:0015277 GO:0016020 GO:0016021 GO:0019901 GO:0030054 GO:0030165 GO:0030425 GO:0030426 GO:0030672 GO:0031623 GO:0032279 GO:0032281 GO:0032839 GO:0034220 GO:0035235 GO:0042734 GO:0042802 GO:0043025 GO:0043195 GO:0043197 GO:0043198 GO:0043204 GO:0043234 GO:0045184 GO:0045202 GO:0045211 GO:0050806 GO:0051262 GO:0051966 GO:0060992
80.150.7562.850.110.854u1wA GO:0001919 GO:0004872 GO:0004970 GO:0004971 GO:0005216 GO:0005234 GO:0005246 GO:0005783 GO:0005789 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0007268 GO:0008328 GO:0009986 GO:0010226 GO:0014069 GO:0015277 GO:0016020 GO:0016021 GO:0019901 GO:0030054 GO:0030165 GO:0030425 GO:0030426 GO:0030672 GO:0031623 GO:0032279 GO:0032281 GO:0032839 GO:0034220 GO:0035235 GO:0042734 GO:0042802 GO:0043025 GO:0043195 GO:0043197 GO:0043198 GO:0043204 GO:0043234 GO:0045184 GO:0045202 GO:0045211 GO:0050806 GO:0051262 GO:0051966 GO:0060992
90.150.7622.950.100.873olzA GO:0004872 GO:0004970 GO:0005216 GO:0005234 GO:0005886 GO:0006810 GO:0006811 GO:0007165 GO:0007268 GO:0008066 GO:0016020 GO:0016021 GO:0030054 GO:0030424 GO:0030425 GO:0032839 GO:0034220 GO:0035235 GO:0042391 GO:0043195 GO:0043204 GO:0045202 GO:0045211 GO:0051967
100.140.7733.060.110.883sajC GO:0001919 GO:0001965 GO:0004872 GO:0004970 GO:0004971 GO:0005216 GO:0005234 GO:0005769 GO:0005783 GO:0005789 GO:0005829 GO:0005886 GO:0006810 GO:0006811 GO:0007616 GO:0008179 GO:0008328 GO:0009636 GO:0009986 GO:0010226 GO:0014069 GO:0014070 GO:0016020 GO:0016021 GO:0019228 GO:0019901 GO:0019904 GO:0021510 GO:0030054 GO:0030165 GO:0030425 GO:0031267 GO:0031489 GO:0031594 GO:0031623 GO:0031681 GO:0031698 GO:0032279 GO:0032281 GO:0032355 GO:0034220 GO:0035235 GO:0035249 GO:0042220 GO:0042493 GO:0042802 GO:0042803 GO:0042995 GO:0043005 GO:0043025 GO:0043197 GO:0043198 GO:0043234 GO:0043434 GO:0044309 GO:0045202 GO:0045211 GO:0045838 GO:0046685 GO:0048167 GO:0050804 GO:0050806 GO:0051018 GO:0051602 GO:0060076 GO:0060992 GO:0071230 GO:0071359 GO:0071363 GO:0071375 GO:0071407 GO:0071418
110.140.7653.160.100.884uqqA GO:0001662 GO:0004872 GO:0004970 GO:0005216 GO:0005234 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006874 GO:0006886 GO:0007268 GO:0008066 GO:0008328 GO:0014069 GO:0015277 GO:0016020 GO:0016021 GO:0019228 GO:0030054 GO:0030165 GO:0030424 GO:0030425 GO:0031624 GO:0031625 GO:0032839 GO:0032983 GO:0034220 GO:0035235 GO:0035249 GO:0042391 GO:0042734 GO:0042802 GO:0042803 GO:0043025 GO:0043113 GO:0043195 GO:0043204 GO:0043524 GO:0043525 GO:0045202 GO:0045211 GO:0046328 GO:0048169 GO:0048172 GO:0050804 GO:0050806 GO:0051402 GO:0051967 GO:0060079 GO:0060080
120.100.6894.220.080.884mqeA GO:0001649 GO:0004871 GO:0004930 GO:0004965 GO:0005576 GO:0005615 GO:0005737 GO:0005789 GO:0005886 GO:0005887 GO:0007165 GO:0007186 GO:0007193 GO:0007194 GO:0007214 GO:0008021 GO:0008134 GO:0008285 GO:0014048 GO:0014049 GO:0014053 GO:0016020 GO:0016021 GO:0030054 GO:0030425 GO:0030673 GO:0030817 GO:0031966 GO:0032811 GO:0033602 GO:0035094 GO:0038037 GO:0038039 GO:0042734 GO:0042995 GO:0043005 GO:0043025 GO:0043197 GO:0043198 GO:0043231 GO:0045121 GO:0045202 GO:0045211 GO:0045471 GO:0050805 GO:0060124
130.070.5944.680.110.805fxkA GO:0004872 GO:0004970 GO:0004972 GO:0005102 GO:0005216 GO:0005234 GO:0005886 GO:0006810 GO:0006811 GO:0007611 GO:0010942 GO:0014069 GO:0014070 GO:0014075 GO:0016020 GO:0016021 GO:0016594 GO:0016595 GO:0017146 GO:0019899 GO:0022843 GO:0030054 GO:0032590 GO:0034220 GO:0034765 GO:0035235 GO:0035254 GO:0042165 GO:0043025 GO:0043083 GO:0043195 GO:0043197 GO:0044307 GO:0045202 GO:0045211 GO:0046982 GO:0046983 GO:0048511 GO:0051262 GO:0051592 GO:0060076 GO:0060992 GO:0071287 GO:2000463
140.070.5954.460.120.784pe5C GO:0004872 GO:0004970 GO:0004972 GO:0005102 GO:0005216 GO:0005234 GO:0005886 GO:0006810 GO:0006811 GO:0007611 GO:0010942 GO:0014069 GO:0014070 GO:0014075 GO:0016020 GO:0016021 GO:0016594 GO:0016595 GO:0017146 GO:0019899 GO:0022843 GO:0030054 GO:0032590 GO:0034220 GO:0034765 GO:0035235 GO:0035254 GO:0042165 GO:0043025 GO:0043083 GO:0043195 GO:0043197 GO:0044307 GO:0045202 GO:0045211 GO:0046982 GO:0046983 GO:0048511 GO:0051262 GO:0051592 GO:0060076 GO:0060992 GO:0071287 GO:2000463
150.070.5805.000.070.814pe5D GO:0001508 GO:0001975 GO:0004872 GO:0004970 GO:0004972 GO:0005102 GO:0005149 GO:0005216 GO:0005234 GO:0005886 GO:0006810 GO:0006811 GO:0007611 GO:0007613 GO:0007616 GO:0008013 GO:0008144 GO:0008270 GO:0008306 GO:0009612 GO:0009636 GO:0009743 GO:0010042 GO:0010350 GO:0010942 GO:0014049 GO:0014069 GO:0014070 GO:0014075 GO:0016020 GO:0016021 GO:0017146 GO:0021766 GO:0021987 GO:0030018 GO:0030054 GO:0031749 GO:0032026 GO:0033555 GO:0034097 GO:0034220 GO:0035235 GO:0035255 GO:0042165 GO:0042220 GO:0042734 GO:0043005 GO:0043083 GO:0043113 GO:0043195 GO:0043197 GO:0043408 GO:0045202 GO:0045211 GO:0045471 GO:0046872 GO:0046982 GO:0048169 GO:0048511 GO:0050806 GO:0050839 GO:0051592 GO:0051597 GO:0051602 GO:0051707 GO:0060416 GO:0060992 GO:0071230 GO:0071287 GO:0071359 GO:0071363 GO:0071396 GO:0071407
160.070.5914.530.110.784tllA GO:0004872 GO:0004970 GO:0005216 GO:0005234 GO:0005886 GO:0006810 GO:0006811 GO:0016020 GO:0016021 GO:0030054 GO:0034220 GO:0035235 GO:0045202 GO:0045211
170.070.5814.760.100.795fxgA GO:0004872 GO:0004970 GO:0004972 GO:0005102 GO:0005216 GO:0005234 GO:0005886 GO:0006810 GO:0006811 GO:0007611 GO:0010942 GO:0014069 GO:0014070 GO:0014075 GO:0016020 GO:0016021 GO:0016594 GO:0016595 GO:0017146 GO:0019899 GO:0022843 GO:0030054 GO:0032590 GO:0034220 GO:0034765 GO:0035235 GO:0035254 GO:0042165 GO:0043025 GO:0043083 GO:0043195 GO:0043197 GO:0044307 GO:0045202 GO:0045211 GO:0046982 GO:0046983 GO:0048511 GO:0051262 GO:0051592 GO:0060076 GO:0060992 GO:0071287 GO:2000463
180.070.5924.480.110.785ipqA GO:0004872 GO:0004970 GO:0005216 GO:0005234 GO:0005886 GO:0006810 GO:0006811 GO:0016020 GO:0016021 GO:0030054 GO:0034220 GO:0035235 GO:0045202 GO:0045211


Consensus prediction of GO terms
 
Molecular Function GO:0005234 GO:0004971 GO:0030165 GO:0042802 GO:0015277 GO:0019901 GO:0005246
GO-Score 0.73 0.65 0.64 0.54 0.54 0.40 0.40
Biological Processes GO:0035235 GO:0034220 GO:0060992 GO:0010226 GO:0001919 GO:0071331 GO:0043065 GO:0031338 GO:2000300 GO:0072657 GO:1901216 GO:0051668 GO:0035437 GO:0060078 GO:0001678 GO:0043523 GO:0099565 GO:0009749 GO:0031629 GO:0045184 GO:0031623 GO:0050806 GO:0051966 GO:0051262
GO-Score 0.73 0.73 0.65 0.54 0.54 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.40 0.40 0.40 0.40 0.40
Cellular Component GO:0043195 GO:0014069 GO:0030054 GO:0045211 GO:0032281 GO:0043204 GO:0032279 GO:0043198 GO:0043197 GO:0042734 GO:0005576 GO:0032983 GO:0030426 GO:0030672 GO:0032839 GO:0009986 GO:0005789
GO-Score 0.73 0.73 0.73 0.73 0.65 0.64 0.54 0.54 0.54 0.54 0.46 0.42 0.40 0.40 0.40 0.40 0.40

(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.