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I-TASSER results for job id Rv1289

[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 4 1go8P ZN Rep, Mult 99,103,105
20.06 3 1o6oA III Rep, Mult 13,34,84,87,90,91
30.04 2 1s4bP ZN Rep, Mult 99,103,114
40.04 2 1v7uA FPP Rep, Mult 37,40,41,91,94,95,98,101,102,105
50.04 2 1ocoO HEA Rep, Mult 57,94,95
60.04 2 2yevB HAS Rep, Mult 49,50,53,102
70.04 2 3hy6A MG Rep, Mult 135,136,137
80.04 2 5csdB ACD Rep, Mult 33,50,53,56,60,91,95,114,118,122,125,126,129,135,142
90.02 1 2jfrA MG Rep, Mult 100,130
100.02 1 1upkA III Rep, Mult 10,13,14,18,58
110.02 1 3obvB SUC Rep, Mult 55,56,59,60,63
120.02 1 1xzwB UUU Rep, Mult 153,156
130.02 1 2bptA III Rep, Mult 13,33,34,87,90
140.02 1 1zoyC EPH Rep, Mult 146,149
150.02 1 4rkuL CLA Rep, Mult 53,57

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
10.0601y7910.4795.470.0720.7713.4.15.5NA
20.0601fa2A0.4965.310.0490.8193.2.1.2NA
30.0602eabA0.4905.120.0210.7813.2.1.63NA
40.0601cb8A0.4864.380.0420.7054.2.2.5NA
50.0601dl2A0.4925.280.0440.7953.2.1.1137
60.0602qnoA0.4835.080.0560.7673.2.1.4NA
70.0601ojnA0.4824.550.1070.7004.2.2.1NA
80.0602gtqA0.5124.480.0120.7383.4.11.2NA
90.0601wdpA0.5085.050.0330.8193.2.1.2NA
100.0603ismC0.4913.350.0300.6293.6.1.36,34,86
110.0601kktA0.4855.330.0420.7673.2.1.113NA
120.0603cyvA0.4904.990.0340.7524.1.1.37NA
130.0603ebgA0.5124.250.0960.7293.4.11.-NA
140.0601gaiA0.4974.710.0720.7523.2.1.3NA
150.0601ujkB0.4593.900.0740.6243.4.23.4610,14
160.0601rw9A0.4955.280.0740.7904.2.2.5NA
170.0602vn4A0.4974.800.0600.7523.2.1.3NA
180.0601j0mA0.5194.790.0890.7764.2.2.12NA
190.0601l2aE0.4895.010.0340.7623.2.1.4NA

(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
00.070.5604.640.040.834uvkA GO:0000755 GO:0003682 GO:0005634 GO:0005829 GO:0006473 GO:0007064 GO:0009847 GO:0031505 GO:0031618 GO:0031934 GO:0034990 GO:1990707
10.070.4604.260.080.691s70B GO:0005737 GO:0007165 GO:0019208 GO:0019901 GO:0030018 GO:0030155 GO:0031672 GO:0035507 GO:0071889 GO:0072357
20.070.4425.290.100.713l0oA GO:0000166 GO:0003676 GO:0003723 GO:0004386 GO:0005524 GO:0006351 GO:0006353 GO:0006355 GO:0008186 GO:0016787
30.060.3725.210.050.625et1A GO:0003779 GO:0005737 GO:0005856 GO:0005902 GO:0005903 GO:0007605 GO:0007626 GO:0015629 GO:0017124 GO:0030046 GO:0030054 GO:0031941 GO:0032420 GO:0032421 GO:0032426 GO:0042995 GO:0043197 GO:0051015 GO:0051017 GO:0051491 GO:0051494 GO:0051639
40.060.3894.150.030.554rlvA GO:0002027 GO:0003283 GO:0005200 GO:0005622 GO:0005737 GO:0005829 GO:0005856 GO:0005886 GO:0006874 GO:0006888 GO:0007165 GO:0007399 GO:0008093 GO:0010628 GO:0010881 GO:0010882 GO:0014704 GO:0016020 GO:0016323 GO:0016324 GO:0019899 GO:0019901 GO:0030018 GO:0030054 GO:0030315 GO:0030507 GO:0030674 GO:0030913 GO:0031430 GO:0031647 GO:0031672 GO:0033292 GO:0033365 GO:0034394 GO:0034613 GO:0036309 GO:0036371 GO:0042383 GO:0043005 GO:0043034 GO:0043268 GO:0044325 GO:0045121 GO:0045202 GO:0045211 GO:0050821 GO:0051117 GO:0051279 GO:0051597 GO:0051924 GO:0051928 GO:0055117 GO:0060307 GO:0070296 GO:0070972 GO:0072659 GO:0072661 GO:0086004 GO:0086005 GO:0086014 GO:0086015 GO:0086046 GO:0086066 GO:0086070 GO:0086091 GO:0098907 GO:0098910 GO:1901018 GO:1901019 GO:1901021 GO:2001259
50.060.3635.090.070.582y4uA GO:0004860 GO:0005737 GO:0005783 GO:0005788 GO:0005790 GO:0005829 GO:0006417 GO:0006986 GO:0016020 GO:0019901 GO:0031205 GO:0036494 GO:0036498 GO:0043066 GO:0051087 GO:0051603 GO:0051607 GO:0051787 GO:0070062 GO:0070417 GO:1903561 GO:1903912 GO:1904030
60.060.3664.690.110.571n0rA
70.060.4225.140.040.673renA GO:0003824 GO:0004553 GO:0005975 GO:0016020 GO:0016021 GO:0016787
80.060.3325.730.050.583wwpA GO:0016829 GO:0046872
90.060.3315.720.050.592cuzA GO:0000049 GO:0000166 GO:0004812 GO:0004818 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006424 GO:0016874 GO:0016876 GO:0043039
100.060.3155.710.030.524p7kA GO:0000287 GO:0005737 GO:0005739 GO:0005829 GO:0005886 GO:0006584 GO:0007565 GO:0007612 GO:0007614 GO:0008168 GO:0008171 GO:0008210 GO:0009712 GO:0014070 GO:0016020 GO:0016021 GO:0016036 GO:0016206 GO:0016740 GO:0030424 GO:0030425 GO:0032259 GO:0032496 GO:0032502 GO:0035814 GO:0042135 GO:0042417 GO:0042420 GO:0042493 GO:0043197 GO:0044297 GO:0045211 GO:0045963 GO:0046498 GO:0046500 GO:0046872 GO:0048265 GO:0048609 GO:0048662 GO:0050668 GO:0051930 GO:0070062
110.060.2954.760.030.444otkA GO:0005618 GO:0005886 GO:0016491 GO:0040007 GO:0055114
120.060.3013.200.120.382zgdA
130.060.2913.800.040.391eq1A GO:0005576 GO:0006810 GO:0006869 GO:0008289
140.060.2906.080.040.552f6uA GO:0000287 GO:0002094 GO:0005737 GO:0006629 GO:0006650 GO:0008654 GO:0016740 GO:0016765 GO:0046474 GO:0046872 GO:0047294
150.060.2854.770.020.424k3vB GO:0006810 GO:0007155 GO:0030001 GO:0046872
160.060.2565.370.060.413h7mA GO:0000155 GO:0000160 GO:0000166 GO:0005524 GO:0005622 GO:0007165 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0023014
170.060.2164.000.040.302fc3A GO:0001682 GO:0003723 GO:0003735 GO:0004526 GO:0005622 GO:0005737 GO:0005840 GO:0006412 GO:0008033 GO:0019843 GO:0030529 GO:0042254 GO:0090501 GO:0090502
180.060.2124.530.010.311f6vA GO:0000166 GO:0003677 GO:0005524 GO:0006260 GO:0006313 GO:0015074 GO:0016787 GO:0016887 GO:0030430 GO:0032196 GO:0039693 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0019901 GO:0003682 GO:0005200 GO:0019208 GO:0051015 GO:0071889 GO:0044325 GO:0030507 GO:0008093 GO:0004386 GO:0017124 GO:0008186 GO:0005524 GO:0051117 GO:0003723
GO-Score 0.12 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07
Biological Processes GO:0031505 GO:0006473 GO:0000755 GO:0009847 GO:0007064 GO:0036309 GO:0034394 GO:0098907 GO:0006353 GO:0030155 GO:1901018 GO:0070972 GO:0030913 GO:0072661 GO:0050821 GO:0086091 GO:0051491 GO:0086005 GO:0051494 GO:0010881 GO:2001259 GO:0010628 GO:0003283 GO:0030046 GO:0007626 GO:1901021 GO:0006888 GO:0035507 GO:0033292 GO:0036371 GO:0060307 GO:0051597 GO:0098910 GO:0007605 GO:0086046 GO:0006355 GO:0051639
GO-Score 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07
Cellular Component GO:0044424
GO-Score 0.36

(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.