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I-TASSER results for job id Rv1873

[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 3 1uvhA FE Rep, Mult 33,36,37
20.06 3 4g86B BNT Rep, Mult 97,101,104,105,108
30.06 3 1dl2A NAG Rep, Mult 82,84,87,125
40.06 3 4rku1 CLA Rep, Mult 104,108,111
50.04 2 2ri8A GOL Rep, Mult 13,17,39,40
60.02 1 1h12A XYP Rep, Mult 12,13,68,74
70.02 1 4il6R HEM Rep, Mult 16,20
80.02 1 4d49E ARG Rep, Mult 86,120,121,124
90.02 1 1xvxA CO3 Rep, Mult 32,101
100.02 1 3pmmA IMD Rep, Mult 109,115,121,122
110.02 1 4u5vA RH2 Rep, Mult 79,80,121
120.02 1 2xquB CVM Rep, Mult 75,78
130.02 1 2j1pB GRG Rep, Mult 69,72
140.02 1 1iw7P MG Rep, Mult 41,45
150.02 1 2bgaA AZI Rep, Mult 33,44
160.02 1 3a6pA III Rep, Mult 58,73,78,112
170.02 1 2fp0A MG Rep, Mult 135,137,138

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
10.0601i8qA0.5464.440.0620.8624.2.2.1NA
20.0602gtqA0.5114.600.0990.8483.4.11.2NA
30.0601h12A0.5553.760.0700.7933.2.1.8NA
40.0603evhA0.5254.300.0680.7934.2.2.3NA
50.0602qnoA0.5364.190.0950.8143.2.1.44
60.0601g87B0.5234.620.0560.8553.2.1.4NA
70.0601l2aE0.5454.400.0640.8623.2.1.4NA
80.0601dl2A0.5584.190.0550.8553.2.1.113NA
90.0601ayxA0.5404.230.0560.8213.2.1.3NA
100.0601ia7A0.5584.390.0760.8903.2.1.4NA
110.0601ojnA0.5424.380.0720.8484.2.2.1136
120.0601ug9A0.5294.020.0500.8073.2.1.7094
130.0601is9A0.5563.590.0780.7863.2.1.426
140.0602vn7A0.5344.520.0690.8483.2.1.3NA
150.0601js4A0.5404.150.0500.8143.2.1.4NA
160.0603gzkA0.5504.410.0620.8763.2.1.4NA
170.0601nxcA0.5744.020.0400.8483.2.1.113NA
180.0601hcuB0.5564.600.0780.8763.2.1.113NA
190.0601w6jA0.5054.520.0630.8145.4.99.7NA

(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
00.150.5664.440.060.873k11A GO:0003824
10.070.5514.350.070.864q88A GO:0003824
20.070.5604.590.100.883qwtA GO:0003824
30.070.5254.330.060.812d8lA GO:0003824 GO:0005737 GO:0008152 GO:0016787 GO:0016798 GO:0102211
40.070.5874.260.090.863pmmA GO:0003824
50.070.5004.380.050.781wzzA GO:0000272 GO:0003824 GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798 GO:0030245
60.070.5023.930.090.751n4kA GO:0001666 GO:0005216 GO:0005220 GO:0005262 GO:0005635 GO:0005637 GO:0005730 GO:0005737 GO:0005783 GO:0005789 GO:0005955 GO:0006810 GO:0006811 GO:0006816 GO:0006915 GO:0009791 GO:0014069 GO:0015278 GO:0016020 GO:0016021 GO:0016529 GO:0019855 GO:0031088 GO:0031094 GO:0032469 GO:0035091 GO:0042045 GO:0043234 GO:0048016 GO:0050849 GO:0050882 GO:0051209 GO:0055085 GO:0070059 GO:0070588
70.070.5124.360.040.814wu0A GO:0003824
80.070.4924.190.080.743uj0A GO:0005216 GO:0005220 GO:0005262 GO:0005635 GO:0005737 GO:0005783 GO:0005789 GO:0005886 GO:0006810 GO:0006811 GO:0006816 GO:0006915 GO:0007165 GO:0007202 GO:0007204 GO:0007223 GO:0008022 GO:0014069 GO:0015278 GO:0016020 GO:0016021 GO:0016529 GO:0019903 GO:0030425 GO:0030667 GO:0032403 GO:0035091 GO:0038095 GO:0038096 GO:0043025 GO:0043231 GO:0043234 GO:0045121 GO:0048016 GO:0048471 GO:0050796 GO:0051209 GO:0051928 GO:0055085 GO:0070059 GO:0070588 GO:0071320 GO:0071456 GO:0097060 GO:1901215 GO:1903779
90.070.4514.290.060.734uwaA GO:0003151 GO:0005216 GO:0005219 GO:0005245 GO:0005262 GO:0005509 GO:0005516 GO:0006810 GO:0006811 GO:0006816 GO:0006874 GO:0006936 GO:0007275 GO:0014802 GO:0014808 GO:0015278 GO:0015643 GO:0016020 GO:0016021 GO:0016529 GO:0033017 GO:0042802 GO:0043588 GO:0043931 GO:0044325 GO:0048741 GO:0055085 GO:0070588 GO:0071313
100.070.5044.180.080.784ce7B GO:0003824 GO:0016787
110.070.4424.170.060.704i96A GO:0003151 GO:0005216 GO:0005219 GO:0005245 GO:0005262 GO:0005509 GO:0005516 GO:0006810 GO:0006811 GO:0006816 GO:0006874 GO:0006936 GO:0007275 GO:0014802 GO:0014808 GO:0015278 GO:0015643 GO:0016020 GO:0016021 GO:0016529 GO:0033017 GO:0042802 GO:0043588 GO:0043931 GO:0044325 GO:0048741 GO:0055085 GO:0070588 GO:0071313
120.060.4653.820.120.704jkqA GO:0001666 GO:0002027 GO:0003143 GO:0003220 GO:0003300 GO:0005216 GO:0005219 GO:0005262 GO:0005509 GO:0005513 GO:0005516 GO:0005790 GO:0005886 GO:0006810 GO:0006811 GO:0006816 GO:0006874 GO:0007275 GO:0010460 GO:0010881 GO:0010882 GO:0014701 GO:0014808 GO:0014850 GO:0015278 GO:0016020 GO:0016021 GO:0016529 GO:0019722 GO:0019899 GO:0019901 GO:0030017 GO:0030018 GO:0030509 GO:0031000 GO:0033017 GO:0034220 GO:0034236 GO:0034237 GO:0034704 GO:0035584 GO:0035994 GO:0042802 GO:0043234 GO:0043621 GO:0043924 GO:0044325 GO:0048763 GO:0051209 GO:0051284 GO:0051480 GO:0051775 GO:0055085 GO:0055117 GO:0060048 GO:0060070 GO:0060401 GO:0060402 GO:0070062 GO:0070296 GO:0070588 GO:0071313 GO:0071872 GO:0072599 GO:0086005 GO:0086029 GO:0086064 GO:0097050 GO:0097159 GO:0098735 GO:0098904 GO:0098907 GO:0098910 GO:0098911 GO:1901896 GO:1903779
130.060.4463.880.050.684l4iA GO:0001666 GO:0002027 GO:0003143 GO:0003220 GO:0003300 GO:0005216 GO:0005219 GO:0005262 GO:0005509 GO:0005513 GO:0005516 GO:0005790 GO:0006810 GO:0006811 GO:0006816 GO:0006874 GO:0007275 GO:0010460 GO:0010881 GO:0010882 GO:0014808 GO:0014850 GO:0015278 GO:0016020 GO:0016021 GO:0016529 GO:0019722 GO:0019899 GO:0019901 GO:0030017 GO:0030018 GO:0030509 GO:0031000 GO:0033017 GO:0034236 GO:0034237 GO:0034704 GO:0035584 GO:0035994 GO:0042802 GO:0043234 GO:0043621 GO:0043924 GO:0048763 GO:0051209 GO:0051284 GO:0051775 GO:0055085 GO:0055117 GO:0060048 GO:0060070 GO:0060401 GO:0060402 GO:0070062 GO:0070588 GO:0071313 GO:0071872 GO:0072599 GO:0086005 GO:0086029 GO:0097050 GO:0097159 GO:0098735 GO:0098904 GO:0098907 GO:0098910 GO:0098911 GO:1901896
140.060.4064.910.090.721ki1B GO:0005085 GO:0005089 GO:0005509 GO:0005829 GO:0005886 GO:0005905 GO:0006897 GO:0007264 GO:0012505 GO:0016020 GO:0019209 GO:0030027 GO:0030054 GO:0030139 GO:0032947 GO:0035023 GO:0035556 GO:0042327 GO:0042995 GO:0043005 GO:0043065 GO:0043524 GO:0043547 GO:0045202 GO:0046872 GO:0048013 GO:0048488 GO:0051056 GO:0051897 GO:0070064
150.060.5284.290.040.814xuvA GO:0003824 GO:0016787
160.060.4524.090.070.714i7iA GO:0003151 GO:0005216 GO:0005219 GO:0005245 GO:0005262 GO:0005509 GO:0005516 GO:0006810 GO:0006811 GO:0006816 GO:0006874 GO:0006936 GO:0007275 GO:0014802 GO:0014808 GO:0015278 GO:0015643 GO:0016020 GO:0016021 GO:0016529 GO:0033017 GO:0042802 GO:0043588 GO:0043931 GO:0044325 GO:0048741 GO:0055085 GO:0070588 GO:0071313
170.060.3305.570.060.661zh8A GO:0000166 GO:0008152 GO:0016491 GO:0055114
180.060.3625.190.080.652izpA GO:0005576 GO:0009405


Consensus prediction of GO terms
 
Molecular Function GO:0003824
GO-Score 0.35
Biological Processes GO:0008152
GO-Score 0.07
Cellular Component GO:0005737
GO-Score 0.07

(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.