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I-TASSER results for job id Rv0167

[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 2jk5C L2C Rep, Mult 142,149
20.06 3 3perA FE Rep, Mult 99,129,132
30.04 2 1xvgA BRJ Rep, Mult 133,134,137,210,213,214
40.04 2 3zuxA TCH Rep, Mult 97,99,212,244
50.04 2 5ezmA MPG Rep, Mult 212,215
60.04 2 2h6bA 3C4 Rep, Mult 247,250
70.04 2 5l8gV CA Rep, Mult 106,122,125
80.04 2 3m0fB GSH Rep, Mult 102,125,129
90.04 2 1mhy1 III Rep, Mult 101,102,105,106,108,109,112,113,126,129
100.02 1 3mmhB MG Rep, Mult 103,104
110.02 1 4xk8L CLA Rep, Mult 72,101
120.02 1 3zuyA PTY Rep, Mult 166,170,173,257,260,261,264
130.02 1 4il9A UNL Rep, Mult 213,217,220
140.02 1 3ddlB PX4 Rep, Mult 75,84
150.02 1 1uuxA IMD Rep, Mult 174,175
160.02 1 1nquA RDL Rep, Mult 209,210

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
10.0601syyA0.4184.730.0450.5851.17.4.1NA
20.0601vncA0.4136.120.0630.6911.11.1.1072,100
30.0601mhyD0.4575.420.0800.7131.14.13.25NA
40.0601kq3A0.4205.250.0900.6451.1.1.6NA
50.0602vuxB0.3935.370.0280.5891.17.4.1NA
60.0602uw1B0.4565.260.0670.6721.14.99.6NA
70.0603c46B0.3946.190.0500.6942.7.7.6133,136
80.0601fziA0.4565.380.0800.7131.14.13.25NA
90.0601biqB0.4094.990.0430.5851.17.4.1NA
100.0602j2fA0.4575.120.0480.6681.14.19.2,1.14.99.6NA
110.0601rsrB0.4114.860.0490.5811.17.4.1NA
120.0601h0nA0.4115.160.0530.6001.17.4.1NA
130.0601ca1A0.4225.460.0550.6413.1.4.3NA
140.0601mc0A0.2536.100.0340.4233.1.4.17108,255
150.0601khoA0.4115.260.0410.6193.1.4.3NA
160.0601sojL0.4126.000.0610.6833.1.4.1788,222
170.0601ta9B0.4205.310.0690.6381.1.1.6NA
180.0602ouyA0.4405.680.0430.6983.1.4.17NA
190.0601olpA0.4365.220.0500.6493.1.4.3NA

(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
00.070.5474.220.090.744cz8A GO:0006810 GO:0006812 GO:0015299 GO:0016020 GO:0016021 GO:0055085 GO:1902600
10.070.5534.270.110.754bwzA GO:0006810 GO:0006812 GO:0015299 GO:0016020 GO:0016021 GO:0046872 GO:0055085 GO:1902600
20.070.5444.440.070.744atvA GO:0005886 GO:0006810 GO:0006811 GO:0006814 GO:0006885 GO:0015081 GO:0015297 GO:0015491 GO:0015992 GO:0016020 GO:0016021 GO:0035725 GO:0055085 GO:0098655
30.070.5364.670.100.744n7wA GO:0016020 GO:0016021
40.070.4635.070.070.703dhiA GO:0004497 GO:0006725 GO:0016491 GO:0019439 GO:0042203 GO:0046872 GO:0055114
50.060.3855.400.050.583gw3A GO:0001889 GO:0004853 GO:0005654 GO:0005737 GO:0005829 GO:0006779 GO:0006782 GO:0006783 GO:0008198 GO:0010039 GO:0014070 GO:0014075 GO:0016829 GO:0016831 GO:0032355 GO:0042168 GO:0045471 GO:0046502 GO:0046689 GO:0051597 GO:0060992 GO:0071243
60.060.4204.990.060.621mhyB GO:0004497 GO:0006725 GO:0006730 GO:0015049 GO:0016491 GO:0016709 GO:0055114
70.060.5644.250.060.774czbB GO:0005886 GO:0006810 GO:0006811 GO:0006812 GO:0006814 GO:0015297 GO:0015299 GO:0016020 GO:0016021 GO:0042802 GO:0055085 GO:1902600
80.060.4485.540.070.712incA GO:0004497 GO:0006725 GO:0016491 GO:0046872 GO:0055114
90.060.4565.380.080.711fziA GO:0004497 GO:0006725 GO:0006730 GO:0015049 GO:0015050 GO:0015947 GO:0016491 GO:0046872 GO:0055114
100.060.4575.420.080.711mhyD GO:0004497 GO:0006725 GO:0006730 GO:0015049 GO:0016491 GO:0046872 GO:0055114
110.060.2916.380.060.512y27B GO:0000166 GO:0003824 GO:0005524 GO:0008152 GO:0010124 GO:0016874 GO:0046872 GO:0047475
120.060.3016.740.070.583ug4C GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0046373 GO:0046556
130.060.4445.410.110.702innA GO:0006725 GO:0016491 GO:0046872 GO:0055114
140.060.2685.320.070.402fckA GO:0008080 GO:0016740 GO:0016746
150.060.2745.860.030.444rpfA GO:0000166 GO:0004413 GO:0005524 GO:0005737 GO:0006566 GO:0008652 GO:0009088 GO:0016301 GO:0016310 GO:0016740
160.060.3685.970.040.603eddA GO:0003824 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0046872 GO:0047798
170.060.2524.470.040.362lznA GO:0000287 GO:0003677 GO:0003678 GO:0003896 GO:0003899 GO:0005524 GO:0006260 GO:0006269 GO:0008270 GO:0016740 GO:0016779 GO:0032508 GO:0046872 GO:1990077
180.060.5344.640.100.743zuxA GO:0016020 GO:0016021


Consensus prediction of GO terms
 
Molecular Function GO:0015299 GO:0046872 GO:0015491 GO:0015081 GO:0004497
GO-Score 0.13 0.13 0.07 0.07 0.07
Biological Processes GO:0044763 GO:0044765
GO-Score 0.37 0.37
Cellular Component GO:0031224
GO-Score 0.38

(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.