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I-TASSER results for job id Rv3238c

[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
10.07 3 2z1qA FAD Rep, Mult 182,185,186,204,207
20.06 2 4quvA NDP Rep, Mult 72,137,140,144,164,165,166,171,176,178,179,214,218,221,222,226,229
30.05 2 1k6lH CDL Rep, Mult 199,206
40.05 2 3ajoA MG Rep, Mult 212,215
50.02 1 1rsrB UUU Rep, Mult 93,97,186,188,196,199
60.02 1 4a2nB SAH Rep, Mult 147,151,152,155,158,159,163,165,166,171,176,214,218
70.02 1 3mkhA FAD Rep, Mult 119,121,187,188,189,199
80.02 1 3rkoN LFA Rep, Mult 129,132,133,136,183,184
90.02 1 4a2nB CDL Rep, Mult 134,138,142,145
100.02 1 3l1lA ARG Rep, Mult 61,66,67,129,130,133,134,137,181
110.02 1 2h61E CA Rep, Mult 234,237
120.02 1 1d4m1 MYR Rep, Mult 223,224
130.02 1 1rsvA AZI Rep, Mult 94,97,186,203,206
140.02 1 1l0vO MQ7 Rep, Mult 19,20
150.02 1 2nw8A TRP Rep, Mult 226,229

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
10.0601xvgC0.4345.460.0680.6931.14.13.2596,199
20.0602bq1I0.4424.770.0690.6431.17.4.1NA
30.0601is2A0.4575.740.0640.7421.3.3.6183,186
40.0601biqB0.4745.470.0610.7501.17.4.1NA
50.0602iukB0.4156.740.0540.7871.13.11.12NA
60.0601prhA0.4395.520.0320.7091.14.99.1NA
70.0601mhyB0.4405.220.0400.6761.14.13.2559,96,194
80.0601bucA0.4345.360.0430.6721.3.99.2129
90.0601jk0A0.4364.620.0590.6231.17.4.1NA
100.0603b8cB0.4475.940.0450.7423.6.3.6200,205,207
110.0601aorB0.4625.920.0580.7871.2.7.5178
120.0601mhsA0.4665.740.0460.7543.6.3.6NA
130.0602fonB0.4525.800.0480.7421.3.3.651
140.0603djlA0.4615.850.0550.7661.3.99.-NA
150.0601br2A0.4066.120.0680.6973.6.1.32NA
160.0601mhyD0.4425.370.0750.6931.14.13.25NA
170.0601ygeA0.4745.820.0410.7871.13.11.12NA
180.0602ix6A0.4545.350.0590.6971.3.3.6NA
190.0602jifA0.4365.420.0440.6681.3.99.-129

(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
00.280.8222.950.130.984quvA GO:0000166 GO:0006696 GO:0016020 GO:0016021 GO:0016126 GO:0016491 GO:0016628 GO:0050613 GO:0050661 GO:0055114
10.210.5923.360.120.724a2nB GO:0004671 GO:0006481 GO:0016020 GO:0016021
20.070.4944.670.100.714djiA GO:0003333 GO:0005886 GO:0005887 GO:0006810 GO:0006865 GO:0015171 GO:0015179 GO:0015297 GO:0015807 GO:0016020 GO:0016021 GO:0051454 GO:1902475
30.070.4835.200.070.754he8F GO:0005886 GO:0008137 GO:0016020 GO:0016021 GO:0016491 GO:0042773 GO:0048038 GO:0055114
40.070.4905.600.050.805ek8A GO:0016702 GO:0046872 GO:0055114
50.070.4455.860.070.745fnoA GO:0005576 GO:0016491 GO:0016702 GO:0046872 GO:0050584 GO:0051213 GO:0055114
60.070.4455.530.070.734he8G GO:0005886 GO:0008137 GO:0016020 GO:0016021 GO:0016491 GO:0042773 GO:0048038 GO:0055114
70.070.4196.770.070.802iujA GO:0006633 GO:0016491 GO:0016702 GO:0031408 GO:0046872 GO:0051213 GO:0055114
80.070.4485.670.030.731no3A GO:0005737 GO:0006629 GO:0006631 GO:0006633 GO:0016491 GO:0016702 GO:0031408 GO:0046872 GO:0051213 GO:0055114
90.070.4775.400.040.772iukA GO:0005737 GO:0006629 GO:0006631 GO:0006633 GO:0016491 GO:0016702 GO:0031408 GO:0046872 GO:0051213 GO:0055114
100.070.4445.430.080.704he8I GO:0005886 GO:0006810 GO:0008137 GO:0016020 GO:0016021 GO:0016491 GO:0042773 GO:0048038 GO:0050136 GO:0055114
110.070.4435.650.020.733vf1A GO:0005506 GO:0016491 GO:0016702 GO:0046872 GO:0051213 GO:0055114
120.070.4425.640.040.704nreA GO:0005506 GO:0005509 GO:0005622 GO:0005634 GO:0005737 GO:0005829 GO:0005856 GO:0005886 GO:0006629 GO:0006915 GO:0008285 GO:0008289 GO:0010744 GO:0016020 GO:0016165 GO:0016491 GO:0016702 GO:0019369 GO:0019372 GO:0019898 GO:0030336 GO:0030850 GO:0030856 GO:0035360 GO:0036403 GO:0043651 GO:0045618 GO:0045786 GO:0045926 GO:0046872 GO:0050473 GO:0051122 GO:0051213 GO:0055114 GO:0070062 GO:0090197
130.070.4385.770.050.723rdeA GO:0001503 GO:0002820 GO:0004052 GO:0005506 GO:0005546 GO:0005737 GO:0005811 GO:0005829 GO:0005886 GO:0006629 GO:0006631 GO:0006646 GO:0008289 GO:0010811 GO:0016020 GO:0016491 GO:0016702 GO:0019369 GO:0019372 GO:0030282 GO:0030838 GO:0031234 GO:0034976 GO:0035358 GO:0035963 GO:0042060 GO:0043277 GO:0043651 GO:0046872 GO:0050473 GO:0051213 GO:0055114 GO:0070374 GO:0071277 GO:1901074 GO:2001303
140.060.4205.050.060.663lrbA GO:0003333 GO:0005886 GO:0006810 GO:0006865 GO:0015171 GO:0015297 GO:0016020 GO:0016021
150.060.4524.360.050.633ob6B GO:0003333 GO:0005886 GO:0005887 GO:0006810 GO:0006865 GO:0015171 GO:0015179 GO:0015181 GO:0015297 GO:0015807 GO:0016020 GO:0016021 GO:0051454 GO:1902475 GO:1903826
160.060.4625.100.050.683gi9C GO:0003333 GO:0005886 GO:0005887 GO:0015171 GO:0015179 GO:0015297 GO:0015807 GO:0016020 GO:0016021 GO:1902475
170.060.4275.710.050.712p0mA GO:0001503 GO:0002820 GO:0004052 GO:0005506 GO:0005546 GO:0005737 GO:0005811 GO:0005829 GO:0005886 GO:0006629 GO:0006631 GO:0006646 GO:0008289 GO:0010811 GO:0016020 GO:0016491 GO:0016702 GO:0019369 GO:0019372 GO:0030282 GO:0030838 GO:0031234 GO:0034976 GO:0035358 GO:0035963 GO:0042060 GO:0043277 GO:0043651 GO:0046872 GO:0050473 GO:0051122 GO:0051213 GO:0055114 GO:0070374 GO:0071277 GO:1901074 GO:2001303
180.060.4745.820.040.791ygeA GO:0005737 GO:0006629 GO:0006631 GO:0006633 GO:0016165 GO:0016491 GO:0016702 GO:0031408 GO:0046872 GO:0051213 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0000166 GO:0050662 GO:0016627 GO:0008757 GO:0003880
GO-Score 0.57 0.57 0.57 0.42 0.42
Biological Processes GO:0016126 GO:1902653 GO:0016129 GO:0044108 GO:0008204 GO:0097384 GO:0018410 GO:0006479 GO:0055114
GO-Score 0.57 0.57 0.57 0.57 0.57 0.57 0.42 0.42 0.38
Cellular Component GO:0016021
GO-Score 0.51

(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.